Starting phenix.real_space_refine on Thu Aug 8 03:16:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5b_13831/08_2024/7q5b_13831.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5b_13831/08_2024/7q5b_13831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5b_13831/08_2024/7q5b_13831.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5b_13831/08_2024/7q5b_13831.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5b_13831/08_2024/7q5b_13831.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5b_13831/08_2024/7q5b_13831.cif" } resolution = 3.98 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 Anisotropic ADP refinement not supported. Converting 264 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 166 5.49 5 S 75 5.16 5 C 13330 2.51 5 N 3864 2.21 5 O 4311 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 77": "NH1" <-> "NH2" Residue "A ARG 90": "NH1" <-> "NH2" Residue "A ARG 141": "NH1" <-> "NH2" Residue "A ASP 164": "OD1" <-> "OD2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 184": "OD1" <-> "OD2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A ARG 241": "NH1" <-> "NH2" Residue "A ASP 257": "OD1" <-> "OD2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 299": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A GLU 351": "OE1" <-> "OE2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 423": "NH1" <-> "NH2" Residue "A PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 436": "NH1" <-> "NH2" Residue "B TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 77": "NH1" <-> "NH2" Residue "B ARG 90": "NH1" <-> "NH2" Residue "B ARG 141": "NH1" <-> "NH2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "B ASP 164": "OD1" <-> "OD2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 185": "NH1" <-> "NH2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B ASP 225": "OD1" <-> "OD2" Residue "B ARG 241": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 299": "NH1" <-> "NH2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "B PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 374": "OD1" <-> "OD2" Residue "B TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 401": "NH1" <-> "NH2" Residue "B ARG 451": "NH1" <-> "NH2" Residue "B ARG 499": "NH1" <-> "NH2" Residue "B ARG 500": "NH1" <-> "NH2" Residue "C ASP 22": "OD1" <-> "OD2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 90": "NH1" <-> "NH2" Residue "C TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 185": "NH1" <-> "NH2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 200": "OD1" <-> "OD2" Residue "C PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 241": "NH1" <-> "NH2" Residue "C ARG 269": "NH1" <-> "NH2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 299": "NH1" <-> "NH2" Residue "C TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C ARG 364": "NH1" <-> "NH2" Residue "C ARG 365": "NH1" <-> "NH2" Residue "C ASP 374": "OD1" <-> "OD2" Residue "C PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 412": "OE1" <-> "OE2" Residue "C PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 451": "NH1" <-> "NH2" Residue "C GLU 457": "OE1" <-> "OE2" Residue "C ARG 499": "NH1" <-> "NH2" Residue "C ARG 500": "NH1" <-> "NH2" Residue "C PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D ARG 185": "NH1" <-> "NH2" Residue "D PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 241": "NH1" <-> "NH2" Residue "D TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 322": "OD1" <-> "OD2" Residue "X TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 108": "OE1" <-> "OE2" Residue "Y PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 74": "OE1" <-> "OE2" Residue "Z GLU 77": "OE1" <-> "OE2" Residue "Z GLU 98": "OE1" <-> "OE2" Residue "Z TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 121": "NH1" <-> "NH2" Residue "Z ARG 135": "NH1" <-> "NH2" Residue "Z ASP 145": "OD1" <-> "OD2" Residue "Z PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 218": "NH1" <-> "NH2" Residue "Z ARG 276": "NH1" <-> "NH2" Residue "Z ASP 282": "OD1" <-> "OD2" Residue "Z ARG 286": "NH1" <-> "NH2" Residue "Z ARG 298": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 21746 Number of models: 1 Model: "" Number of chains: 13 Chain: "R" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1140 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain: "S" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 634 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "r" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 705 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "s" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 185 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 3438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3438 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 397} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3936 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 457} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 3912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3912 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 22, 'TRANS': 459} Chain breaks: 2 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "D" Number of atoms: 2681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2681 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 16, 'TRANS': 317} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "X" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 591 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 4, 'TRANS': 65} Chain: "Y" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1416 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 171} Chain: "Z" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2328 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 1 Chain: "t" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 390 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Chain: "u" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 390 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Time building chain proxies: 12.15, per 1000 atoms: 0.56 Number of scatterers: 21746 At special positions: 0 Unit cell: (151.58, 166.42, 151.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 75 16.00 P 166 15.00 O 4311 8.00 N 3864 7.00 C 13330 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 134 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.86 Conformation dependent library (CDL) restraints added in 3.0 seconds 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4368 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 13 sheets defined 43.1% alpha, 7.5% beta 75 base pairs and 127 stacking pairs defined. Time for finding SS restraints: 8.41 Creating SS restraints... Processing helix chain 'A' and resid 29 through 38 removed outlier: 3.881A pdb=" N LEU A 35 " --> pdb=" O HIS A 31 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N THR A 36 " --> pdb=" O MET A 32 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 60 removed outlier: 3.637A pdb=" N TYR A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 84 through 92 Processing helix chain 'A' and resid 103 through 112 Processing helix chain 'A' and resid 119 through 129 Processing helix chain 'A' and resid 131 through 138 Processing helix chain 'A' and resid 204 through 214 Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 232 through 243 removed outlier: 3.614A pdb=" N LEU A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 257 removed outlier: 4.057A pdb=" N THR A 256 " --> pdb=" O HIS A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 275 Processing helix chain 'A' and resid 281 through 296 removed outlier: 4.350A pdb=" N TYR A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Proline residue: A 287 - end of helix Processing helix chain 'A' and resid 304 through 309 Processing helix chain 'A' and resid 334 through 362 removed outlier: 3.753A pdb=" N HIS A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'B' and resid 29 through 38 removed outlier: 3.771A pdb=" N LEU B 35 " --> pdb=" O HIS B 31 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N THR B 36 " --> pdb=" O MET B 32 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLN B 37 " --> pdb=" O LYS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 60 removed outlier: 4.026A pdb=" N TYR B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 83 No H-bonds generated for 'chain 'B' and resid 81 through 83' Processing helix chain 'B' and resid 84 through 94 Processing helix chain 'B' and resid 95 through 98 removed outlier: 3.739A pdb=" N PHE B 98 " --> pdb=" O HIS B 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 95 through 98' Processing helix chain 'B' and resid 103 through 112 Processing helix chain 'B' and resid 119 through 131 Processing helix chain 'B' and resid 133 through 138 removed outlier: 3.757A pdb=" N LYS B 138 " --> pdb=" O CYS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 145 removed outlier: 3.578A pdb=" N LEU B 144 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 215 Processing helix chain 'B' and resid 232 through 242 Processing helix chain 'B' and resid 253 through 256 removed outlier: 3.545A pdb=" N THR B 256 " --> pdb=" O HIS B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 253 through 256' Processing helix chain 'B' and resid 257 through 275 removed outlier: 3.732A pdb=" N ARG B 269 " --> pdb=" O GLN B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 296 removed outlier: 3.800A pdb=" N GLN B 288 " --> pdb=" O VAL B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 311 removed outlier: 3.912A pdb=" N ASP B 309 " --> pdb=" O PRO B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 328 removed outlier: 3.539A pdb=" N ARG B 328 " --> pdb=" O VAL B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 362 removed outlier: 4.042A pdb=" N HIS B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN B 360 " --> pdb=" O GLU B 356 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN B 361 " --> pdb=" O MET B 357 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN B 362 " --> pdb=" O GLU B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 454 removed outlier: 3.819A pdb=" N LYS B 453 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 449 through 454' Processing helix chain 'B' and resid 487 through 491 Processing helix chain 'B' and resid 499 through 504 removed outlier: 3.840A pdb=" N LEU B 503 " --> pdb=" O ARG B 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 34 Processing helix chain 'C' and resid 47 through 60 removed outlier: 3.510A pdb=" N TYR C 51 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN C 52 " --> pdb=" O PHE C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 103 through 112 removed outlier: 3.673A pdb=" N SER C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 132 Processing helix chain 'C' and resid 204 through 213 Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'C' and resid 258 through 275 removed outlier: 3.806A pdb=" N ARG C 269 " --> pdb=" O GLN C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 296 Processing helix chain 'C' and resid 304 through 309 removed outlier: 3.825A pdb=" N ASP C 309 " --> pdb=" O PRO C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 340 Processing helix chain 'C' and resid 341 through 352 removed outlier: 3.770A pdb=" N GLN C 345 " --> pdb=" O ALA C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 428 No H-bonds generated for 'chain 'C' and resid 426 through 428' Processing helix chain 'C' and resid 447 through 454 removed outlier: 3.686A pdb=" N LYS C 453 " --> pdb=" O THR C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 511 Processing helix chain 'D' and resid 28 through 34 removed outlier: 4.173A pdb=" N MET D 32 " --> pdb=" O VAL D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 60 removed outlier: 3.557A pdb=" N TYR D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 94 Processing helix chain 'D' and resid 95 through 98 removed outlier: 3.809A pdb=" N PHE D 98 " --> pdb=" O HIS D 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 95 through 98' Processing helix chain 'D' and resid 103 through 112 Processing helix chain 'D' and resid 119 through 131 Processing helix chain 'D' and resid 204 through 214 Processing helix chain 'D' and resid 233 through 242 Processing helix chain 'D' and resid 258 through 275 removed outlier: 4.090A pdb=" N LEU D 267 " --> pdb=" O THR D 263 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN D 268 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG D 269 " --> pdb=" O GLN D 265 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 295 Processing helix chain 'D' and resid 304 through 310 removed outlier: 3.846A pdb=" N ASP D 309 " --> pdb=" O PRO D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 363 removed outlier: 3.577A pdb=" N HIS D 338 " --> pdb=" O GLU D 334 " (cutoff:3.500A) Processing helix chain 'X' and resid 422 through 435 Processing helix chain 'X' and resid 438 through 446 Processing helix chain 'X' and resid 450 through 465 removed outlier: 3.856A pdb=" N LYS X 463 " --> pdb=" O VAL X 459 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS X 464 " --> pdb=" O ASN X 460 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG X 465 " --> pdb=" O GLU X 461 " (cutoff:3.500A) Processing helix chain 'X' and resid 465 through 476 removed outlier: 3.600A pdb=" N GLU X 470 " --> pdb=" O PRO X 466 " (cutoff:3.500A) Processing helix chain 'X' and resid 481 through 489 removed outlier: 4.158A pdb=" N GLU X 487 " --> pdb=" O GLU X 483 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE X 488 " --> pdb=" O TYR X 484 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS X 489 " --> pdb=" O CYS X 485 " (cutoff:3.500A) Processing helix chain 'Y' and resid 82 through 88 Processing helix chain 'Y' and resid 128 through 147 removed outlier: 3.862A pdb=" N GLY Y 147 " --> pdb=" O ILE Y 143 " (cutoff:3.500A) Processing helix chain 'Y' and resid 172 through 179 Processing helix chain 'Y' and resid 220 through 237 Proline residue: Y 232 - end of helix Processing helix chain 'Z' and resid 72 through 95 removed outlier: 3.916A pdb=" N ARG Z 76 " --> pdb=" O ALA Z 72 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU Z 77 " --> pdb=" O LEU Z 73 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA Z 78 " --> pdb=" O GLU Z 74 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR Z 79 " --> pdb=" O SER Z 75 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA Z 93 " --> pdb=" O ALA Z 89 " (cutoff:3.500A) Processing helix chain 'Z' and resid 97 through 114 Processing helix chain 'Z' and resid 121 through 137 removed outlier: 3.714A pdb=" N VAL Z 125 " --> pdb=" O ARG Z 121 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU Z 137 " --> pdb=" O ALA Z 133 " (cutoff:3.500A) Processing helix chain 'Z' and resid 142 through 147 Processing helix chain 'Z' and resid 153 through 169 removed outlier: 3.738A pdb=" N ILE Z 157 " --> pdb=" O SER Z 153 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS Z 166 " --> pdb=" O LEU Z 162 " (cutoff:3.500A) Processing helix chain 'Z' and resid 178 through 186 removed outlier: 3.547A pdb=" N ILE Z 182 " --> pdb=" O PRO Z 178 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN Z 183 " --> pdb=" O SER Z 179 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS Z 184 " --> pdb=" O LEU Z 180 " (cutoff:3.500A) Processing helix chain 'Z' and resid 196 through 211 removed outlier: 3.508A pdb=" N LYS Z 200 " --> pdb=" O ILE Z 196 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG Z 208 " --> pdb=" O LYS Z 204 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS Z 211 " --> pdb=" O GLN Z 207 " (cutoff:3.500A) Processing helix chain 'Z' and resid 219 through 235 Processing helix chain 'Z' and resid 241 through 247 removed outlier: 3.852A pdb=" N ILE Z 244 " --> pdb=" O HIS Z 241 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL Z 245 " --> pdb=" O THR Z 242 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA Z 246 " --> pdb=" O GLU Z 243 " (cutoff:3.500A) Processing helix chain 'Z' and resid 251 through 266 Processing helix chain 'Z' and resid 287 through 294 Processing helix chain 'Z' and resid 448 through 455 removed outlier: 4.043A pdb=" N VAL Z 455 " --> pdb=" O TYR Z 451 " (cutoff:3.500A) Processing helix chain 'Z' and resid 476 through 478 No H-bonds generated for 'chain 'Z' and resid 476 through 478' Processing helix chain 'Z' and resid 479 through 491 removed outlier: 3.854A pdb=" N ILE Z 486 " --> pdb=" O LEU Z 482 " (cutoff:3.500A) Processing helix chain 'Z' and resid 492 through 497 removed outlier: 4.062A pdb=" N LEU Z 496 " --> pdb=" O ALA Z 492 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU Z 497 " --> pdb=" O ASP Z 493 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 492 through 497' Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 195 removed outlier: 4.169A pdb=" N ASP A 164 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A 183 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE A 161 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 402 through 407 removed outlier: 6.365A pdb=" N LYS A 405 " --> pdb=" O GLU A 412 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLU A 412 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN A 407 " --> pdb=" O ALA A 410 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE A 425 " --> pdb=" O TYR A 411 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 66 through 68 Processing sheet with id=AA5, first strand: chain 'B' and resid 162 through 165 removed outlier: 3.534A pdb=" N SER B 162 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP B 164 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL B 181 " --> pdb=" O ASP B 164 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 180 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 424 through 426 removed outlier: 3.578A pdb=" N TYR B 411 " --> pdb=" O ILE B 425 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA B 410 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYS B 405 " --> pdb=" O ALA B 410 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLU B 412 " --> pdb=" O VAL B 403 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 458 through 464 removed outlier: 6.595A pdb=" N HIS B 474 " --> pdb=" O THR B 459 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LEU B 461 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LEU B 472 " --> pdb=" O LEU B 461 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 192 through 193 Processing sheet with id=AA9, first strand: chain 'C' and resid 424 through 425 removed outlier: 3.629A pdb=" N ILE C 425 " --> pdb=" O TYR C 411 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA C 410 " --> pdb=" O ILE C 406 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS C 404 " --> pdb=" O GLU C 412 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU C 377 " --> pdb=" O LYS C 431 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 458 through 464 removed outlier: 6.920A pdb=" N LEU C 472 " --> pdb=" O ILE C 462 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 66 through 68 removed outlier: 3.706A pdb=" N TYR D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU D 68 " --> pdb=" O MET D 71 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 190 through 195 removed outlier: 4.096A pdb=" N VAL D 181 " --> pdb=" O ASP D 164 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP D 164 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE D 161 " --> pdb=" O THR D 221 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Y' and resid 92 through 93 removed outlier: 3.727A pdb=" N GLY Y 125 " --> pdb=" O ILE Y 70 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE Y 70 " --> pdb=" O GLY Y 125 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N LEU Y 67 " --> pdb=" O SER Y 163 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N SER Y 163 " --> pdb=" O LEU Y 67 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR Y 73 " --> pdb=" O ILE Y 157 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ILE Y 157 " --> pdb=" O THR Y 73 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY Y 162 " --> pdb=" O LEU Y 214 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR Y 215 " --> pdb=" O VAL Y 203 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLU Y 186 " --> pdb=" O PHE Y 190 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N GLY Y 192 " --> pdb=" O SER Y 184 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N SER Y 184 " --> pdb=" O GLY Y 192 " (cutoff:3.500A) 640 hydrogen bonds defined for protein. 1845 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 176 hydrogen bonds 352 hydrogen bond angles 0 basepair planarities 75 basepair parallelities 127 stacking parallelities Total time for adding SS restraints: 7.90 Time building geometry restraints manager: 10.67 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: 5073 1.33 - 1.45: 5262 1.45 - 1.57: 11760 1.57 - 1.69: 330 1.69 - 1.81: 126 Bond restraints: 22551 Sorted by residual: bond pdb=" N GLN C 75 " pdb=" CA GLN C 75 " ideal model delta sigma weight residual 1.457 1.519 -0.062 1.29e-02 6.01e+03 2.30e+01 bond pdb=" N TYR C 74 " pdb=" CA TYR C 74 " ideal model delta sigma weight residual 1.457 1.515 -0.058 1.29e-02 6.01e+03 2.01e+01 bond pdb=" C GLN C 75 " pdb=" O GLN C 75 " ideal model delta sigma weight residual 1.235 1.291 -0.056 1.26e-02 6.30e+03 1.95e+01 bond pdb=" CA TYR C 74 " pdb=" C TYR C 74 " ideal model delta sigma weight residual 1.523 1.557 -0.034 1.34e-02 5.57e+03 6.32e+00 bond pdb=" C GLN C 75 " pdb=" N ASP C 76 " ideal model delta sigma weight residual 1.333 1.369 -0.036 1.56e-02 4.11e+03 5.42e+00 ... (remaining 22546 not shown) Histogram of bond angle deviations from ideal: 98.61 - 106.45: 1587 106.45 - 114.29: 13024 114.29 - 122.13: 12230 122.13 - 129.97: 4171 129.97 - 137.82: 204 Bond angle restraints: 31216 Sorted by residual: angle pdb=" C GLN C 75 " pdb=" N ASP C 76 " pdb=" CA ASP C 76 " ideal model delta sigma weight residual 122.79 104.00 18.79 1.63e+00 3.76e-01 1.33e+02 angle pdb=" C TYR C 74 " pdb=" N GLN C 75 " pdb=" CA GLN C 75 " ideal model delta sigma weight residual 121.54 137.82 -16.28 1.91e+00 2.74e-01 7.26e+01 angle pdb=" N PRO D 150 " pdb=" CA PRO D 150 " pdb=" CB PRO D 150 " ideal model delta sigma weight residual 103.25 111.59 -8.34 1.05e+00 9.07e-01 6.31e+01 angle pdb=" N PRO D 254 " pdb=" CA PRO D 254 " pdb=" CB PRO D 254 " ideal model delta sigma weight residual 103.25 111.15 -7.90 1.05e+00 9.07e-01 5.66e+01 angle pdb=" N PRO D 152 " pdb=" CA PRO D 152 " pdb=" CB PRO D 152 " ideal model delta sigma weight residual 103.25 111.07 -7.82 1.05e+00 9.07e-01 5.55e+01 ... (remaining 31211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 12459 35.90 - 71.79: 812 71.79 - 107.69: 23 107.69 - 143.59: 9 143.59 - 179.48: 11 Dihedral angle restraints: 13314 sinusoidal: 6606 harmonic: 6708 Sorted by residual: dihedral pdb=" CA THR A 231 " pdb=" C THR A 231 " pdb=" N ALA A 232 " pdb=" CA ALA A 232 " ideal model delta harmonic sigma weight residual 180.00 141.22 38.78 0 5.00e+00 4.00e-02 6.02e+01 dihedral pdb=" CA LYS B 421 " pdb=" C LYS B 421 " pdb=" N HIS B 422 " pdb=" CA HIS B 422 " ideal model delta harmonic sigma weight residual 180.00 145.85 34.15 0 5.00e+00 4.00e-02 4.67e+01 dihedral pdb=" CA VAL D 292 " pdb=" C VAL D 292 " pdb=" N TYR D 293 " pdb=" CA TYR D 293 " ideal model delta harmonic sigma weight residual 180.00 148.33 31.67 0 5.00e+00 4.00e-02 4.01e+01 ... (remaining 13311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 3223 0.091 - 0.182: 265 0.182 - 0.272: 24 0.272 - 0.363: 2 0.363 - 0.454: 2 Chirality restraints: 3516 Sorted by residual: chirality pdb=" CB ILE A 395 " pdb=" CA ILE A 395 " pdb=" CG1 ILE A 395 " pdb=" CG2 ILE A 395 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.15e+00 chirality pdb=" CB ILE B 153 " pdb=" CA ILE B 153 " pdb=" CG1 ILE B 153 " pdb=" CG2 ILE B 153 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CB THR D 41 " pdb=" CA THR D 41 " pdb=" OG1 THR D 41 " pdb=" CG2 THR D 41 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 3513 not shown) Planarity restraints: 3379 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 75 " 0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C GLN C 75 " -0.060 2.00e-02 2.50e+03 pdb=" O GLN C 75 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP C 76 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 494 " 0.050 5.00e-02 4.00e+02 7.65e-02 9.35e+00 pdb=" N PRO C 495 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO C 495 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 495 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 366 " 0.046 5.00e-02 4.00e+02 7.00e-02 7.84e+00 pdb=" N PRO C 367 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO C 367 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 367 " 0.039 5.00e-02 4.00e+02 ... (remaining 3376 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3419 2.76 - 3.30: 20381 3.30 - 3.83: 38624 3.83 - 4.37: 43357 4.37 - 4.90: 68937 Nonbonded interactions: 174718 Sorted by model distance: nonbonded pdb=" O CYS Z 134 " pdb=" OG1 THR Z 139 " model vdw 2.231 3.040 nonbonded pdb=" OG1 THR B 202 " pdb=" O ARG B 229 " model vdw 2.234 3.040 nonbonded pdb=" O ILE B 222 " pdb=" OG1 THR B 247 " model vdw 2.238 3.040 nonbonded pdb=" O LEU A 342 " pdb=" OG1 THR A 346 " model vdw 2.266 3.040 nonbonded pdb=" NH1 ARG B 185 " pdb=" OP1 DT u 5 " model vdw 2.274 3.120 ... (remaining 174713 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 18 through 20 and (name N or name CA or name C or name O \ or name CB )) or resid 21 through 142 or (resid 143 and (name N or name CA or na \ me C or name O or name CB )) or resid 154 through 353 or (resid 356 through 361 \ and (name N or name CA or name C or name O or name CB )) or resid 362 through 38 \ 4 or (resid 389 and (name N or name CA or name C or name O or name CB )) or resi \ d 390 through 395 or (resid 396 and (name N or name CA or name C or name O or na \ me CB )) or resid 397 through 437)) selection = (chain 'B' and ((resid 18 through 20 and (name N or name CA or name C or name O \ or name CB )) or resid 21 through 142 or (resid 143 and (name N or name CA or na \ me C or name O or name CB )) or resid 154 through 197 or resid 201 through 353 o \ r (resid 356 through 361 and (name N or name CA or name C or name O or name CB ) \ ) or resid 362 through 395 or (resid 396 and (name N or name CA or name C or nam \ e O or name CB )) or resid 397 through 437)) selection = (chain 'C' and (resid 18 through 197 or resid 201 through 384 or (resid 389 and \ (name N or name CA or name C or name O or name CB )) or resid 390 through 436 or \ (resid 437 and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = chain 't' selection = chain 'u' } 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.020 Extract box with map and model: 1.080 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 64.390 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6056 moved from start: 0.0000 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: