Starting phenix.real_space_refine on Fri Dec 15 09:16:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h6h_34504/12_2023/8h6h_34504.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h6h_34504/12_2023/8h6h_34504.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h6h_34504/12_2023/8h6h_34504.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h6h_34504/12_2023/8h6h_34504.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h6h_34504/12_2023/8h6h_34504.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h6h_34504/12_2023/8h6h_34504.pdb" } resolution = 2.3 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= 0.033 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 S 64 5.16 5 Cl 4 4.86 5 C 10139 2.51 5 N 2642 2.21 5 O 2987 1.98 5 H 15181 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A ASP 313": "OD1" <-> "OD2" Residue "A ASP 323": "OD1" <-> "OD2" Residue "A TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A GLU 434": "OE1" <-> "OE2" Residue "A PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 624": "OD1" <-> "OD2" Residue "A GLU 639": "OE1" <-> "OE2" Residue "A GLU 700": "OE1" <-> "OE2" Residue "A TYR 856": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "B GLU 93": "OE1" <-> "OE2" Residue "B ASP 218": "OD1" <-> "OD2" Residue "B GLU 434": "OE1" <-> "OE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 502": "OE1" <-> "OE2" Residue "B TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 624": "OD1" <-> "OD2" Residue "B GLU 712": "OE1" <-> "OE2" Residue "B TYR 856": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 938": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 31017 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 15367 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 986, 15330 Classifications: {'peptide': 986} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 952} Conformer: "B" Number of residues, atoms: 986, 15330 Classifications: {'peptide': 986} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 952} bond proxies already assigned to first conformer: 15467 Chain: "B" Number of atoms: 15646 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 985, 15598 Classifications: {'peptide': 985} Link IDs: {'PCIS': 2, 'PTRANS': 31, 'TRANS': 951} Conformer: "B" Number of residues, atoms: 985, 15598 Classifications: {'peptide': 985} Link IDs: {'PCIS': 2, 'PTRANS': 31, 'TRANS': 951} bond proxies already assigned to first conformer: 15722 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N AHIS A 292 " occ=0.49 ... (32 atoms not shown) pdb=" HE1BHIS A 292 " occ=0.51 residue: pdb=" N APHE A 295 " occ=0.55 ... (38 atoms not shown) pdb=" HZ BPHE A 295 " occ=0.45 residue: pdb=" N AHIS B 292 " occ=0.53 ... (32 atoms not shown) pdb=" HE1BHIS B 292 " occ=0.47 residue: pdb=" N APHE B 295 " occ=0.38 ... (38 atoms not shown) pdb=" HZ BPHE B 295 " occ=0.62 residue: pdb=" N ASER B 939 " occ=0.59 ... (20 atoms not shown) pdb=" HG BSER B 939 " occ=0.41 Time building chain proxies: 24.75, per 1000 atoms: 0.80 Number of scatterers: 31017 At special positions: 0 Unit cell: (117.03, 138.61, 112.88, 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) Cl 4 17.00 S 64 16.00 O 2987 8.00 N 2642 7.00 C 10139 6.00 H 15181 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 27.62 Conformation dependent library (CDL) restraints added in 7.3 seconds 3964 Ramachandran restraints generated. 1982 Oldfield, 0 Emsley, 1982 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3704 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 24 sheets defined 37.0% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.59 Creating SS restraints... Processing helix chain 'A' and resid 13 through 23 Processing helix chain 'A' and resid 55 through 62 removed outlier: 3.551A pdb=" N VAL A 59 " --> pdb=" O PRO A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 71 Processing helix chain 'A' and resid 101 through 113 Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 155 through 160 Processing helix chain 'A' and resid 290 through 297 removed outlier: 3.610A pdb=" N ILE A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N APHE A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 327 through 330 Processing helix chain 'A' and resid 355 through 361 Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 418 through 433 removed outlier: 3.638A pdb=" N MET A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 454 removed outlier: 4.258A pdb=" N GLU A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY A 454 " --> pdb=" O HIS A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 472 Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 502 through 516 removed outlier: 4.362A pdb=" N LEU A 506 " --> pdb=" O GLU A 502 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE A 507 " --> pdb=" O ILE A 503 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA A 508 " --> pdb=" O GLN A 504 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N TYR A 511 " --> pdb=" O PHE A 507 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR A 512 " --> pdb=" O ALA A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 531 Processing helix chain 'A' and resid 555 through 557 No H-bonds generated for 'chain 'A' and resid 555 through 557' Processing helix chain 'A' and resid 558 through 572 removed outlier: 3.987A pdb=" N GLN A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 578 removed outlier: 3.937A pdb=" N VAL A 576 " --> pdb=" O ASP A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 606 Processing helix chain 'A' and resid 634 through 650 Processing helix chain 'A' and resid 665 through 685 Processing helix chain 'A' and resid 687 through 709 Processing helix chain 'A' and resid 749 through 759 removed outlier: 3.884A pdb=" N PHE A 753 " --> pdb=" O PHE A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 778 Processing helix chain 'A' and resid 808 through 812 removed outlier: 3.780A pdb=" N GLY A 812 " --> pdb=" O ARG A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 833 removed outlier: 3.892A pdb=" N LYS A 832 " --> pdb=" O LYS A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 852 removed outlier: 3.580A pdb=" N LEU A 852 " --> pdb=" O PHE A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 860 removed outlier: 5.898A pdb=" N TYR A 856 " --> pdb=" O VAL A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 866 Processing helix chain 'A' and resid 890 through 903 Processing helix chain 'B' and resid 13 through 23 Processing helix chain 'B' and resid 55 through 62 Processing helix chain 'B' and resid 63 through 71 Processing helix chain 'B' and resid 101 through 113 Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 290 through 297 removed outlier: 3.610A pdb=" N ILE B 294 " --> pdb=" O ALA B 290 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N APHE B 295 " --> pdb=" O VAL B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 304 Processing helix chain 'B' and resid 326 through 330 Processing helix chain 'B' and resid 355 through 361 Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 418 through 433 removed outlier: 3.500A pdb=" N MET B 422 " --> pdb=" O SER B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 454 removed outlier: 4.256A pdb=" N GLU B 440 " --> pdb=" O SER B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 472 Processing helix chain 'B' and resid 472 through 484 Processing helix chain 'B' and resid 501 through 504 Processing helix chain 'B' and resid 505 through 515 removed outlier: 5.134A pdb=" N TYR B 511 " --> pdb=" O PHE B 507 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR B 512 " --> pdb=" O ALA B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 531 Processing helix chain 'B' and resid 555 through 557 No H-bonds generated for 'chain 'B' and resid 555 through 557' Processing helix chain 'B' and resid 558 through 572 removed outlier: 3.991A pdb=" N GLN B 562 " --> pdb=" O LEU B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 578 removed outlier: 4.000A pdb=" N VAL B 576 " --> pdb=" O ASP B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 606 Processing helix chain 'B' and resid 634 through 650 Processing helix chain 'B' and resid 665 through 685 Processing helix chain 'B' and resid 687 through 709 Processing helix chain 'B' and resid 749 through 759 removed outlier: 3.895A pdb=" N PHE B 753 " --> pdb=" O PHE B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 778 Processing helix chain 'B' and resid 791 through 795 removed outlier: 3.803A pdb=" N LYS B 794 " --> pdb=" O ASP B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 833 removed outlier: 3.847A pdb=" N LYS B 832 " --> pdb=" O LYS B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 852 removed outlier: 3.576A pdb=" N LEU B 852 " --> pdb=" O PHE B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 860 removed outlier: 5.907A pdb=" N TYR B 856 " --> pdb=" O VAL B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 866 Processing helix chain 'B' and resid 890 through 903 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 6.369A pdb=" N GLN B 306 " --> pdb=" O PRO B 322 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA B 308 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE B 320 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU B 310 " --> pdb=" O ILE B 318 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE B 318 " --> pdb=" O MET B 338 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ARG B 334 " --> pdb=" O PRO B 322 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR B 324 " --> pdb=" O ASP B 332 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N ASP B 332 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU B 242 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG B 231 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU B 222 " --> pdb=" O LYS B 237 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 3 through 6 removed outlier: 6.369A pdb=" N GLN B 306 " --> pdb=" O PRO B 322 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA B 308 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE B 320 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU B 310 " --> pdb=" O ILE B 318 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE B 318 " --> pdb=" O MET B 338 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ARG B 334 " --> pdb=" O PRO B 322 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR B 324 " --> pdb=" O ASP B 332 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N ASP B 332 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU B 345 " --> pdb=" O ASN B 342 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 31 through 36 removed outlier: 4.056A pdb=" N PHE A 31 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ASP A 33 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ALA A 48 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL A 35 " --> pdb=" O GLY A 46 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLY A 46 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N GLU A 83 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N LEU A 50 " --> pdb=" O GLU A 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 122 removed outlier: 3.573A pdb=" N GLU A 222 " --> pdb=" O LYS A 237 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU A 242 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU A 345 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 121 through 122 removed outlier: 3.573A pdb=" N GLU A 222 " --> pdb=" O LYS A 237 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU A 242 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 9.281A pdb=" N ASP A 332 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N TYR A 324 " --> pdb=" O ASP A 332 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ARG A 334 " --> pdb=" O PRO A 322 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE A 318 " --> pdb=" O MET A 338 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU A 310 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE A 320 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA A 308 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLN A 306 " --> pdb=" O PRO A 322 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 144 through 147 removed outlier: 6.703A pdb=" N PHE A 173 " --> pdb=" O VAL A 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 208 through 212 removed outlier: 6.465A pdb=" N LEU A 203 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N TYR A 212 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N PHE A 201 " --> pdb=" O TYR A 212 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN A 200 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 457 through 459 removed outlier: 6.674A pdb=" N SER A 935 " --> pdb=" O HIS A 977 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N VAL A 979 " --> pdb=" O SER A 935 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LYS A 937 " --> pdb=" O VAL A 979 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N LEU A 981 " --> pdb=" O LYS A 937 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N SER A 939 " --> pdb=" O LEU A 981 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N PHE A 983 " --> pdb=" O SER A 939 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N THR A 941 " --> pdb=" O PHE A 983 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 498 through 499 removed outlier: 6.360A pdb=" N ASN A 540 " --> pdb=" O PRO A 550 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 580 through 582 Processing sheet with id=AB2, first strand: chain 'A' and resid 663 through 664 Processing sheet with id=AB3, first strand: chain 'A' and resid 779 through 780 Processing sheet with id=AB4, first strand: chain 'A' and resid 814 through 815 Processing sheet with id=AB5, first strand: chain 'A' and resid 907 through 908 Processing sheet with id=AB6, first strand: chain 'B' and resid 31 through 36 removed outlier: 4.038A pdb=" N PHE B 31 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASP B 33 " --> pdb=" O ALA B 48 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ALA B 48 " --> pdb=" O ASP B 33 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL B 35 " --> pdb=" O GLY B 46 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLY B 46 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL B 44 " --> pdb=" O VAL B 79 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N PHE B 81 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLY B 46 " --> pdb=" O PHE B 81 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N GLU B 83 " --> pdb=" O GLY B 46 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N ALA B 48 " --> pdb=" O GLU B 83 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 144 through 147 removed outlier: 6.690A pdb=" N PHE B 173 " --> pdb=" O VAL B 181 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 209 through 212 removed outlier: 6.463A pdb=" N LEU B 203 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N TYR B 212 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N PHE B 201 " --> pdb=" O TYR B 212 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 457 through 459 removed outlier: 6.685A pdb=" N SER B 935 " --> pdb=" O HIS B 977 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N VAL B 979 " --> pdb=" O SER B 935 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LYS B 937 " --> pdb=" O VAL B 979 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU B 981 " --> pdb=" O LYS B 937 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASER B 939 " --> pdb=" O LEU B 981 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N PHE B 983 " --> pdb=" O ASER B 939 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N THR B 941 " --> pdb=" O PHE B 983 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 498 through 499 removed outlier: 6.361A pdb=" N ASN B 540 " --> pdb=" O PRO B 550 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 580 through 582 Processing sheet with id=AC3, first strand: chain 'B' and resid 663 through 664 Processing sheet with id=AC4, first strand: chain 'B' and resid 779 through 780 Processing sheet with id=AC5, first strand: chain 'B' and resid 814 through 815 Processing sheet with id=AC6, first strand: chain 'B' and resid 907 through 908 775 hydrogen bonds defined for protein. 2138 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: 13.48 Time building geometry restraints manager: 28.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15162 1.03 - 1.23: 25 1.23 - 1.42: 6939 1.42 - 1.61: 9145 1.61 - 1.81: 106 Bond restraints: 31377 Sorted by residual: bond pdb=" C ILE B 318 " pdb=" O ILE B 318 " ideal model delta sigma weight residual 1.245 1.234 0.011 1.41e-02 5.03e+03 5.76e-01 bond pdb=" CB LYS B 154 " pdb=" CG LYS B 154 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 5.10e-01 bond pdb=" CA ASP B 76 " pdb=" CB ASP B 76 " ideal model delta sigma weight residual 1.537 1.527 0.010 1.38e-02 5.25e+03 4.88e-01 bond pdb=" CA VAL B 74 " pdb=" C VAL B 74 " ideal model delta sigma weight residual 1.520 1.526 -0.006 8.80e-03 1.29e+04 4.85e-01 bond pdb=" CA ASP A 621 " pdb=" C ASP A 621 " ideal model delta sigma weight residual 1.527 1.521 0.007 9.80e-03 1.04e+04 4.74e-01 ... (remaining 31372 not shown) Histogram of bond angle deviations from ideal: 74.28 - 86.23: 3 86.23 - 98.17: 0 98.17 - 110.11: 28629 110.11 - 122.06: 22520 122.06 - 134.00: 5289 Bond angle restraints: 56441 Sorted by residual: angle pdb=" N ALA B 931 " pdb=" CA ALA B 931 " pdb=" HA ALA B 931 " ideal model delta sigma weight residual 110.00 74.79 35.21 3.00e+00 1.11e-01 1.38e+02 angle pdb=" CB ALA B 931 " pdb=" CA ALA B 931 " pdb=" HA ALA B 931 " ideal model delta sigma weight residual 109.00 74.28 34.72 3.00e+00 1.11e-01 1.34e+02 angle pdb=" C ALA B 931 " pdb=" CA ALA B 931 " pdb=" HA ALA B 931 " ideal model delta sigma weight residual 109.00 74.43 34.57 3.00e+00 1.11e-01 1.33e+02 angle pdb=" C VAL B 74 " pdb=" CA VAL B 74 " pdb=" CB VAL B 74 " ideal model delta sigma weight residual 114.35 109.87 4.48 1.06e+00 8.90e-01 1.78e+01 angle pdb=" N VAL B 181 " pdb=" CA VAL B 181 " pdb=" C VAL B 181 " ideal model delta sigma weight residual 111.45 107.54 3.91 9.30e-01 1.16e+00 1.77e+01 ... (remaining 56436 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 13138 17.97 - 35.93: 1011 35.93 - 53.90: 263 53.90 - 71.86: 86 71.86 - 89.83: 34 Dihedral angle restraints: 14532 sinusoidal: 7554 harmonic: 6978 Sorted by residual: dihedral pdb=" CA PHE B 73 " pdb=" C PHE B 73 " pdb=" N VAL B 74 " pdb=" CA VAL B 74 " ideal model delta harmonic sigma weight residual -180.00 -160.43 -19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA ASP A 131 " pdb=" CB ASP A 131 " pdb=" CG ASP A 131 " pdb=" OD1 ASP A 131 " ideal model delta sinusoidal sigma weight residual -30.00 -89.94 59.94 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CA ASP A 427 " pdb=" CB ASP A 427 " pdb=" CG ASP A 427 " pdb=" OD1 ASP A 427 " ideal model delta sinusoidal sigma weight residual -30.00 -89.62 59.62 1 2.00e+01 2.50e-03 1.19e+01 ... (remaining 14529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2120 0.060 - 0.120: 252 0.120 - 0.180: 19 0.180 - 0.240: 0 0.240 - 0.300: 1 Chirality restraints: 2392 Sorted by residual: chirality pdb=" CA ALA B 931 " pdb=" N ALA B 931 " pdb=" C ALA B 931 " pdb=" CB ALA B 931 " both_signs ideal model delta sigma weight residual False 2.48 2.19 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA ILE A 268 " pdb=" N ILE A 268 " pdb=" C ILE A 268 " pdb=" CB ILE A 268 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA ILE A 244 " pdb=" N ILE A 244 " pdb=" C ILE A 244 " pdb=" CB ILE A 244 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 2389 not shown) Planarity restraints: 4750 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 854 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO B 855 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 855 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 855 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 74 " -0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO B 75 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 75 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 75 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 854 " -0.019 5.00e-02 4.00e+02 2.81e-02 1.26e+00 pdb=" N PRO A 855 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 855 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 855 " -0.016 5.00e-02 4.00e+02 ... (remaining 4747 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.20: 2008 2.20 - 2.80: 63614 2.80 - 3.40: 84719 3.40 - 4.00: 120800 4.00 - 4.60: 181999 Nonbonded interactions: 453140 Sorted by model distance: nonbonded pdb=" O SER B 485 " pdb="HH11 ARG B 486 " model vdw 1.606 1.850 nonbonded pdb=" HA ALA B 931 " pdb=" HB3 ALA B 931 " model vdw 1.614 1.952 nonbonded pdb=" H ALA B 931 " pdb=" HA ALA B 931 " model vdw 1.619 1.816 nonbonded pdb=" O LYS A 134 " pdb="HH22 ARG A 167 " model vdw 1.630 1.850 nonbonded pdb=" O LYS B 134 " pdb="HH22 ARG B 167 " model vdw 1.632 1.850 ... (remaining 453135 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 291 or resid 293 through 294 or resid 296 throug \ h 311 or (resid 312 and (name N or name CA or name C or name O or name CB or nam \ e CG or name OD1 or name ND2 or name H or name HA )) or resid 313 through 315 or \ (resid 316 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name OE1 or name OE2 or name H or name HA )) or resid 317 through 484 \ or (resid 485 and (name N or name CA or name C or name O or name CB or name OG \ or name H or name HA )) or resid 486 through 938 or resid 940 through 986 or res \ id 1001 through 1002)) selection = (chain 'B' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name H or name HA )) or (resid 3 and (name N or name C \ A or name C or name O or name CB or name OG1 or name CG2 or name H or name HA )) \ or resid 4 through 5 or (resid 6 and (name N or name CA or name C or name O or \ name CB or name OG1 or name CG2 or name H or name HA )) or resid 7 through 8 or \ (resid 9 and (name N or name CA or name C or name O or name CB or name CG or nam \ e OD1 or name ND2 or name H or name HA )) or resid 10 through 13 or (resid 14 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD or nam \ e HA )) or (resid 15 and (name N or name CA or name C or name O or name CB or na \ me CG1 or name CG2 or name H or name HA )) or (resid 16 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD or name OE1 or name OE2 or n \ ame H or name HA )) or (resid 17 and (name N or name CA or name C or name O or n \ ame CB or name CG or name CD1 or name CD2 or name H or name HA )) or resid 18 th \ rough 20 or (resid 21 and (name N or name CA or name C or name O or name CB or n \ ame CG or name CD or name CE or name NZ or name H or name HA )) or (resid 22 and \ (name N or name CA or name C or name O or name CB or name CG or name CD1 or nam \ e CD2 or name CE1 or name CE2 or name CZ or name H or name HA )) or resid 23 thr \ ough 24 or (resid 25 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD or name CE or name NZ or name H or name HA )) or resid 26 throu \ gh 36 or (resid 37 and (name N or name CA or name C or name O or name CB or name \ OG1 or name CG2 or name H or name HA )) or (resid 38 and (name N or name CA or \ name C or name O or name CB or name CG or name OD1 or name OD2 or name H or name \ HA )) or (resid 39 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 40 through 46 or (resid 47 and (name N or name CA or \ name C or name O or name CB or name CG1 or name CG2 or name CD1 or name H or nam \ e HA )) or resid 48 through 49 or (resid 50 and (name N or name CA or name C or \ name O or name CB or name CG or name CD1 or name CD2 or name H or name HA )) or \ resid 51 through 59 or (resid 60 and (name N or name CA or name C or name O or n \ ame CB or name CG or name CD1 or name CD2 or name H or name HA )) or (resid 61 a \ nd (name N or name CA or name C or name O or name CB or name CG or name SD or na \ me CE or name H or name HA )) or (resid 62 and (name N or name CA or name C or n \ ame O or name CB or name CG or name CD or name OE1 or name OE2 or name H or name \ HA )) or (resid 63 and (name N or name CA or name C or name O or name CB or nam \ e CG or name OD1 or name ND2 or name H or name HA )) or (resid 64 and (name N or \ name CA or name C or name O or name CB or name SG or name H or name HA )) or re \ sid 65 or (resid 66 and (name N or name CA or name C or name O or name CB or nam \ e CG1 or name CG2 or name H or name HA )) or resid 67 through 71 or (resid 72 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD or nam \ e OE1 or name NE2 or name H or name HA )) or resid 73 or (resid 74 and (name N o \ r name CA or name C or name O or name CB or name CG1 or name CG2 or name H or na \ me HA )) or (resid 75 and (name N or name CA or name C or name O or name CB or n \ ame CG or name CD or name HA )) or resid 76 or (resid 77 and (name N or name CA \ or name C or name O or name CB or name CG or name CD or name NE or name CZ or na \ me NH1 or name NH2 or name H or name HA )) or resid 78 through 79 or (resid 80 a \ nd (name N or name CA or name C or name O or name CB or name SG or name H or nam \ e HA )) or resid 81 through 86 or (resid 87 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name CE or name NZ or name H or name \ HA )) or resid 88 through 89 or (resid 90 and (name N or name CA or name C or na \ me O or name CB or name CG1 or name CG2 or name CD1 or name H or name HA )) or r \ esid 91 through 92 or (resid 93 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD or name OE1 or name OE2 or name H or name HA )) or r \ esid 94 through 98 or (resid 99 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD or name OE1 or name OE2 or name H or name HA )) or r \ esid 100 through 101 or (resid 102 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name OE1 or name OE2 or name H or name HA )) o \ r resid 103 through 108 or (resid 109 and (name N or name CA or name C or name O \ or name CB or name CG or name CD or name CE or name NZ or name H or name HA )) \ or resid 110 through 116 or (resid 117 and (name N or name CA or name C or name \ O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name \ H or name HA )) or resid 118 through 135 or (resid 136 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 137 through 139 or \ (resid 140 and (name N or name CA or name C or name O or name CB or name CG or \ name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA )) or resid 14 \ 1 through 171 or (resid 172 and (name N or name CA or name C or name O or name C \ B or name OG or name H or name HA )) or (resid 173 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name H or name HA )) or resid 174 through 175 or (resid 176 an \ d (name N or name CA or name C or name O or name CB or name CG or name ND1 or na \ me CD2 or name CE1 or name NE2 or name H or name HA )) or resid 177 through 181 \ or (resid 182 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD1 or name CD2 or name H or name HA )) or resid 183 through 191 or (resi \ d 192 and (name N or name CA or name C or name O or name CB or name CG or name C \ D or name OE1 or name OE2 or name H or name HA )) or (resid 193 and (name N or n \ ame CA or name C or name O or name CB or name CG or name OD1 or name ND2 or name \ H or name HA )) or resid 194 through 198 or (resid 199 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD or name NE or name CZ or nam \ e NH1 or name NH2 or name H or name HA )) or resid 200 through 216 or (resid 217 \ through 218 and (name N or name CA or name C or name O or name CB or name CG or \ name OD1 or name OD2 or name H or name HA )) or resid 219 through 223 or (resid \ 224 and (name N or name CA or name C or name O or name CB or name OG1 or name C \ G2 or name H or name HA )) or (resid 225 and (name N or name CA or name C or nam \ e O or name CB or name SG or name H or name HA )) or resid 226 through 271 or (r \ esid 272 and (name N or name CA or name C or name O or name CB or name OG or nam \ e H or name HA )) or resid 273 through 291 or resid 293 through 294 or resid 296 \ through 796 or (resid 797 and (name N or name CA or name C or name O or name CB \ or name CG or name OD1 or name ND2 or name H or name HA )) or resid 798 through \ 938 or resid 940 through 986 or resid 1001 through 1002)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.38 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: 4.880 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: 0.450 Extract box with map and model: 23.780 Check model and map are aligned: 0.420 Set scattering table: 0.270 Process input model: 121.670 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.130 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:11.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 163.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 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: