Starting phenix.real_space_refine (version: 1.21rc1) on Mon May 8 21:52:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rja_4901/05_2023/6rja_4901.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rja_4901/05_2023/6rja_4901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rja_4901/05_2023/6rja_4901.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rja_4901/05_2023/6rja_4901.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rja_4901/05_2023/6rja_4901.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rja_4901/05_2023/6rja_4901.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.011 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: 5 Type Number sf(0) Gaussians P 194 5.49 5 S 50 5.16 5 C 12214 2.51 5 N 3522 2.21 5 O 4392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 5": "OD1" <-> "OD2" Residue "A TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 111": "NH1" <-> "NH2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "B ASP 5": "OD1" <-> "OD2" Residue "B TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B ARG 120": "NH1" <-> "NH2" Residue "C ASP 9": "OD1" <-> "OD2" Residue "C PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 46": "NH1" <-> "NH2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C ARG 166": "NH1" <-> "NH2" Residue "C ARG 179": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 235": "NH1" <-> "NH2" Residue "C ARG 240": "NH1" <-> "NH2" Residue "C TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 267": "NH1" <-> "NH2" Residue "C ASP 283": "OD1" <-> "OD2" Residue "C GLU 311": "OE1" <-> "OE2" Residue "C ASP 330": "OD1" <-> "OD2" Residue "C ASP 333": "OD1" <-> "OD2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 363": "OD1" <-> "OD2" Residue "C TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 390": "OE1" <-> "OE2" Residue "C PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 413": "NH1" <-> "NH2" Residue "C ARG 487": "NH1" <-> "NH2" Residue "C GLU 499": "OE1" <-> "OE2" Residue "C TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 502": "OD1" <-> "OD2" Residue "C ARG 703": "NH1" <-> "NH2" Residue "C ASP 708": "OD1" <-> "OD2" Residue "C ARG 831": "NH1" <-> "NH2" Residue "C ASP 859": "OD1" <-> "OD2" Residue "C ARG 876": "NH1" <-> "NH2" Residue "C GLU 883": "OE1" <-> "OE2" Residue "C GLU 887": "OE1" <-> "OE2" Residue "C GLU 916": "OE1" <-> "OE2" Residue "C ARG 921": "NH1" <-> "NH2" Residue "C ASP 939": "OD1" <-> "OD2" Residue "C ARG 966": "NH1" <-> "NH2" Residue "C GLU 1002": "OE1" <-> "OE2" Residue "C ASP 1014": "OD1" <-> "OD2" Residue "C PHE 1021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1097": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1120": "OD1" <-> "OD2" Residue "F ASP 9": "OD1" <-> "OD2" Residue "F PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 46": "NH1" <-> "NH2" Residue "F ARG 57": "NH1" <-> "NH2" Residue "F ARG 68": "NH1" <-> "NH2" Residue "F PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "F ARG 166": "NH1" <-> "NH2" Residue "F ARG 179": "NH1" <-> "NH2" Residue "F ARG 190": "NH1" <-> "NH2" Residue "F ARG 235": "NH1" <-> "NH2" Residue "F ARG 240": "NH1" <-> "NH2" Residue "F TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 267": "NH1" <-> "NH2" Residue "F ASP 283": "OD1" <-> "OD2" Residue "F GLU 311": "OE1" <-> "OE2" Residue "F ASP 330": "OD1" <-> "OD2" Residue "F ASP 333": "OD1" <-> "OD2" Residue "F TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 363": "OD1" <-> "OD2" Residue "F TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 390": "OE1" <-> "OE2" Residue "F PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 413": "NH1" <-> "NH2" Residue "F ARG 487": "NH1" <-> "NH2" Residue "F GLU 499": "OE1" <-> "OE2" Residue "F TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 502": "OD1" <-> "OD2" Residue "F ARG 703": "NH1" <-> "NH2" Residue "F ASP 708": "OD1" <-> "OD2" Residue "F ARG 831": "NH1" <-> "NH2" Residue "F ASP 859": "OD1" <-> "OD2" Residue "F ARG 876": "NH1" <-> "NH2" Residue "F GLU 883": "OE1" <-> "OE2" Residue "F GLU 887": "OE1" <-> "OE2" Residue "F GLU 916": "OE1" <-> "OE2" Residue "F ARG 921": "NH1" <-> "NH2" Residue "F ASP 939": "OD1" <-> "OD2" Residue "F ARG 966": "NH1" <-> "NH2" Residue "F GLU 1002": "OE1" <-> "OE2" Residue "F ASP 1014": "OD1" <-> "OD2" Residue "F PHE 1021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1097": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 1120": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 20372 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1506 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain: "B" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1506 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain: "C" Number of atoms: 6638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 6638 Classifications: {'peptide': 815} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 795} Chain breaks: 7 Chain: "D" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1656 Classifications: {'RNA': 78} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 37, 'rna3p_pyr': 32} Link IDs: {'rna2p': 9, 'rna3p': 68} Chain breaks: 2 Chain: "E" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 386 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "F" Number of atoms: 6638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 6638 Classifications: {'peptide': 815} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 795} Chain breaks: 7 Chain: "G" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1656 Classifications: {'RNA': 78} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 37, 'rna3p_pyr': 32} Link IDs: {'rna2p': 9, 'rna3p': 68} Chain breaks: 2 Chain: "H" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 386 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Time building chain proxies: 11.05, per 1000 atoms: 0.54 Number of scatterers: 20372 At special positions: 0 Unit cell: (120.015, 207.137, 107.569, 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 50 16.00 P 194 15.00 O 4392 8.00 N 3522 7.00 C 12214 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.77 Conformation dependent library (CDL) restraints added in 2.3 seconds 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3736 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 20 sheets defined 45.6% alpha, 13.8% beta 64 base pairs and 115 stacking pairs defined. Time for finding SS restraints: 6.02 Creating SS restraints... Processing helix chain 'A' and resid 4 through 19 Processing helix chain 'A' and resid 21 through 25 Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.774A pdb=" N LYS A 50 " --> pdb=" O ASP A 47 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET A 51 " --> pdb=" O ILE A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 47 through 51' Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.541A pdb=" N VAL A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 80 removed outlier: 3.782A pdb=" N ALA A 70 " --> pdb=" O ASP A 66 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR A 80 " --> pdb=" O GLN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 89 Processing helix chain 'A' and resid 90 through 110 removed outlier: 3.544A pdb=" N TYR A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 178 Processing helix chain 'B' and resid 4 through 19 Processing helix chain 'B' and resid 21 through 25 Processing helix chain 'B' and resid 34 through 43 Processing helix chain 'B' and resid 47 through 51 removed outlier: 3.775A pdb=" N LYS B 50 " --> pdb=" O ASP B 47 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET B 51 " --> pdb=" O ILE B 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 47 through 51' Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.540A pdb=" N VAL B 56 " --> pdb=" O GLY B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 80 removed outlier: 3.781A pdb=" N ALA B 70 " --> pdb=" O ASP B 66 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR B 80 " --> pdb=" O GLN B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 89 Processing helix chain 'B' and resid 90 through 110 removed outlier: 3.545A pdb=" N TYR B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 178 Processing helix chain 'C' and resid 40 through 73 removed outlier: 3.543A pdb=" N LEU C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 95 Processing helix chain 'C' and resid 103 through 115 removed outlier: 3.634A pdb=" N HIS C 115 " --> pdb=" O ASN C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 147 Processing helix chain 'C' and resid 150 through 163 Processing helix chain 'C' and resid 185 through 204 removed outlier: 3.813A pdb=" N TYR C 189 " --> pdb=" O PRO C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 221 Processing helix chain 'C' and resid 250 through 254 removed outlier: 4.007A pdb=" N ILE C 254 " --> pdb=" O ILE C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 285 removed outlier: 3.623A pdb=" N GLN C 276 " --> pdb=" O SER C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 311 Processing helix chain 'C' and resid 315 through 327 removed outlier: 3.940A pdb=" N LEU C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 356 Processing helix chain 'C' and resid 369 through 382 Processing helix chain 'C' and resid 384 through 395 Processing helix chain 'C' and resid 402 through 416 removed outlier: 3.812A pdb=" N VAL C 406 " --> pdb=" O SER C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 436 Processing helix chain 'C' and resid 445 through 454 Processing helix chain 'C' and resid 470 through 476 Processing helix chain 'C' and resid 479 through 500 Processing helix chain 'C' and resid 692 through 705 Processing helix chain 'C' and resid 737 through 748 Processing helix chain 'C' and resid 854 through 868 removed outlier: 3.798A pdb=" N TYR C 858 " --> pdb=" O THR C 854 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP C 859 " --> pdb=" O GLN C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 869 through 871 No H-bonds generated for 'chain 'C' and resid 869 through 871' Processing helix chain 'C' and resid 872 through 878 removed outlier: 3.772A pdb=" N ARG C 876 " --> pdb=" O PHE C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 891 Proline residue: C 888 - end of helix removed outlier: 3.717A pdb=" N GLU C 891 " --> pdb=" O GLU C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 918 Processing helix chain 'C' and resid 986 through 988 No H-bonds generated for 'chain 'C' and resid 986 through 988' Processing helix chain 'C' and resid 1000 through 1011 removed outlier: 3.502A pdb=" N TYR C1004 " --> pdb=" O SER C1000 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 73 removed outlier: 3.544A pdb=" N LEU F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 95 Processing helix chain 'F' and resid 103 through 115 removed outlier: 3.634A pdb=" N HIS F 115 " --> pdb=" O ASN F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 147 Processing helix chain 'F' and resid 150 through 163 Processing helix chain 'F' and resid 185 through 204 removed outlier: 3.814A pdb=" N TYR F 189 " --> pdb=" O PRO F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 221 Processing helix chain 'F' and resid 250 through 254 removed outlier: 4.006A pdb=" N ILE F 254 " --> pdb=" O ILE F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 285 removed outlier: 3.624A pdb=" N GLN F 276 " --> pdb=" O SER F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 311 Processing helix chain 'F' and resid 315 through 327 removed outlier: 3.940A pdb=" N LEU F 327 " --> pdb=" O ILE F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 356 Processing helix chain 'F' and resid 369 through 382 Processing helix chain 'F' and resid 384 through 395 Processing helix chain 'F' and resid 402 through 416 removed outlier: 3.812A pdb=" N VAL F 406 " --> pdb=" O SER F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 428 through 436 Processing helix chain 'F' and resid 445 through 454 Processing helix chain 'F' and resid 470 through 476 Processing helix chain 'F' and resid 479 through 500 Processing helix chain 'F' and resid 692 through 705 Processing helix chain 'F' and resid 737 through 748 Processing helix chain 'F' and resid 854 through 868 removed outlier: 3.798A pdb=" N TYR F 858 " --> pdb=" O THR F 854 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP F 859 " --> pdb=" O GLN F 855 " (cutoff:3.500A) Processing helix chain 'F' and resid 869 through 871 No H-bonds generated for 'chain 'F' and resid 869 through 871' Processing helix chain 'F' and resid 872 through 878 removed outlier: 3.771A pdb=" N ARG F 876 " --> pdb=" O PHE F 872 " (cutoff:3.500A) Processing helix chain 'F' and resid 878 through 891 Proline residue: F 888 - end of helix removed outlier: 3.717A pdb=" N GLU F 891 " --> pdb=" O GLU F 887 " (cutoff:3.500A) Processing helix chain 'F' and resid 910 through 918 Processing helix chain 'F' and resid 986 through 988 No H-bonds generated for 'chain 'F' and resid 986 through 988' Processing helix chain 'F' and resid 1000 through 1011 removed outlier: 3.503A pdb=" N TYR F1004 " --> pdb=" O SER F1000 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 122 removed outlier: 6.634A pdb=" N ILE A 115 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL A 136 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY A 117 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU A 134 " --> pdb=" O GLY A 117 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLY A 119 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N MET A 121 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ALA A 130 " --> pdb=" O MET A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 142 through 144 removed outlier: 6.648A pdb=" N SER A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 114 through 122 removed outlier: 6.634A pdb=" N ILE B 115 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL B 136 " --> pdb=" O ILE B 115 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY B 117 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU B 134 " --> pdb=" O GLY B 117 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLY B 119 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N MET B 121 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ALA B 130 " --> pdb=" O MET B 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 142 through 144 removed outlier: 6.648A pdb=" N SER B 147 " --> pdb=" O LEU B 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 710 through 712 removed outlier: 3.764A pdb=" N ILE C 10 " --> pdb=" O GLU C 509 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 168 through 172 Processing sheet with id=AA7, first strand: chain 'C' and resid 268 through 269 removed outlier: 3.746A pdb=" N ALA C 268 " --> pdb=" O HIS C 425 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 935 through 941 removed outlier: 3.509A pdb=" N LEU C 935 " --> pdb=" O ILE C 849 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL C 845 " --> pdb=" O ASP C 939 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LYS C 941 " --> pdb=" O THR C 843 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N THR C 843 " --> pdb=" O LYS C 941 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ALA C 829 " --> pdb=" O LEU C 846 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 958 " --> pdb=" O TYR C 828 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 977 through 980 removed outlier: 3.833A pdb=" N LYS C 977 " --> pdb=" O ASN C 972 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN C 972 " --> pdb=" O LYS C 977 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU C 983 " --> pdb=" O TRP C 965 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 977 through 980 removed outlier: 3.833A pdb=" N LYS C 977 " --> pdb=" O ASN C 972 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN C 972 " --> pdb=" O LYS C 977 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA C 967 " --> pdb=" O THR C1022 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR C1022 " --> pdb=" O ALA C 967 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL C 969 " --> pdb=" O LYS C1020 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 989 through 990 Processing sheet with id=AB3, first strand: chain 'C' and resid 1085 through 1088 removed outlier: 4.273A pdb=" N CYS C1085 " --> pdb=" O LEU C1058 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLU C1057 " --> pdb=" O LEU C1045 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU C1028 " --> pdb=" O VAL C1099 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS C1098 " --> pdb=" O ILE C1110 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 710 through 712 removed outlier: 3.765A pdb=" N ILE F 10 " --> pdb=" O GLU F 509 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 168 through 172 Processing sheet with id=AB6, first strand: chain 'F' and resid 268 through 269 removed outlier: 3.746A pdb=" N ALA F 268 " --> pdb=" O HIS F 425 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 935 through 941 removed outlier: 3.509A pdb=" N LEU F 935 " --> pdb=" O ILE F 849 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL F 845 " --> pdb=" O ASP F 939 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LYS F 941 " --> pdb=" O THR F 843 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N THR F 843 " --> pdb=" O LYS F 941 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ALA F 829 " --> pdb=" O LEU F 846 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL F 958 " --> pdb=" O TYR F 828 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 977 through 980 removed outlier: 3.833A pdb=" N LYS F 977 " --> pdb=" O ASN F 972 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN F 972 " --> pdb=" O LYS F 977 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU F 983 " --> pdb=" O TRP F 965 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 977 through 980 removed outlier: 3.833A pdb=" N LYS F 977 " --> pdb=" O ASN F 972 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN F 972 " --> pdb=" O LYS F 977 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA F 967 " --> pdb=" O THR F1022 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR F1022 " --> pdb=" O ALA F 967 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL F 969 " --> pdb=" O LYS F1020 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 989 through 990 Processing sheet with id=AC2, first strand: chain 'F' and resid 1085 through 1088 removed outlier: 4.273A pdb=" N CYS F1085 " --> pdb=" O LEU F1058 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLU F1057 " --> pdb=" O LEU F1045 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU F1028 " --> pdb=" O VAL F1099 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS F1098 " --> pdb=" O ILE F1110 " (cutoff:3.500A) 726 hydrogen bonds defined for protein. 2118 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 150 hydrogen bonds 292 hydrogen bond angles 0 basepair planarities 64 basepair parallelities 115 stacking parallelities Total time for adding SS restraints: 8.10 Time building geometry restraints manager: 9.07 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: 4442 1.33 - 1.45: 5508 1.45 - 1.57: 10714 1.57 - 1.69: 380 1.69 - 1.81: 92 Bond restraints: 21136 Sorted by residual: bond pdb=" N ILE C 436 " pdb=" CA ILE C 436 " ideal model delta sigma weight residual 1.464 1.485 -0.021 1.23e-02 6.61e+03 2.89e+00 bond pdb=" N ILE F 436 " pdb=" CA ILE F 436 " ideal model delta sigma weight residual 1.464 1.485 -0.021 1.23e-02 6.61e+03 2.87e+00 bond pdb=" C GLU C 887 " pdb=" N PRO C 888 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.36e-02 5.41e+03 2.28e+00 bond pdb=" C GLU F 887 " pdb=" N PRO F 888 " ideal model delta sigma weight residual 1.335 1.356 -0.020 1.36e-02 5.41e+03 2.20e+00 bond pdb=" CA GLU F 887 " pdb=" C GLU F 887 " ideal model delta sigma weight residual 1.524 1.542 -0.018 1.26e-02 6.30e+03 2.14e+00 ... (remaining 21131 not shown) Histogram of bond angle deviations from ideal: 99.82 - 106.69: 1421 106.69 - 113.57: 11600 113.57 - 120.44: 8546 120.44 - 127.31: 7271 127.31 - 134.19: 464 Bond angle restraints: 29302 Sorted by residual: angle pdb=" C ASN C 21 " pdb=" N LYS C 22 " pdb=" CA LYS C 22 " ideal model delta sigma weight residual 121.54 131.04 -9.50 1.91e+00 2.74e-01 2.47e+01 angle pdb=" C ASN F 21 " pdb=" N LYS F 22 " pdb=" CA LYS F 22 " ideal model delta sigma weight residual 121.54 130.99 -9.45 1.91e+00 2.74e-01 2.45e+01 angle pdb=" CA THR A 123 " pdb=" CB THR A 123 " pdb=" CG2 THR A 123 " ideal model delta sigma weight residual 110.50 116.77 -6.27 1.70e+00 3.46e-01 1.36e+01 angle pdb=" CA TYR B 26 " pdb=" CB TYR B 26 " pdb=" CG TYR B 26 " ideal model delta sigma weight residual 113.90 120.53 -6.63 1.80e+00 3.09e-01 1.36e+01 angle pdb=" CA THR B 123 " pdb=" CB THR B 123 " pdb=" CG2 THR B 123 " ideal model delta sigma weight residual 110.50 116.76 -6.26 1.70e+00 3.46e-01 1.36e+01 ... (remaining 29297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 10776 17.76 - 35.51: 1245 35.51 - 53.27: 255 53.27 - 71.03: 50 71.03 - 88.78: 14 Dihedral angle restraints: 12340 sinusoidal: 6514 harmonic: 5826 Sorted by residual: dihedral pdb=" CA GLN C1052 " pdb=" C GLN C1052 " pdb=" N LYS C1053 " pdb=" CA LYS C1053 " ideal model delta harmonic sigma weight residual -180.00 -153.30 -26.70 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA GLN F1052 " pdb=" C GLN F1052 " pdb=" N LYS F1053 " pdb=" CA LYS F1053 " ideal model delta harmonic sigma weight residual -180.00 -153.31 -26.69 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA GLU C 384 " pdb=" C GLU C 384 " pdb=" N ARG C 385 " pdb=" CA ARG C 385 " ideal model delta harmonic sigma weight residual -180.00 -155.90 -24.10 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 12337 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2397 0.050 - 0.100: 743 0.100 - 0.149: 151 0.149 - 0.199: 22 0.199 - 0.249: 5 Chirality restraints: 3318 Sorted by residual: chirality pdb=" C1' U D 7 " pdb=" O4' U D 7 " pdb=" C2' U D 7 " pdb=" N1 U D 7 " both_signs ideal model delta sigma weight residual False 2.47 2.22 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C1' U G 7 " pdb=" O4' U G 7 " pdb=" C2' U G 7 " pdb=" N1 U G 7 " both_signs ideal model delta sigma weight residual False 2.47 2.22 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" C1' A G 68 " pdb=" O4' A G 68 " pdb=" C2' A G 68 " pdb=" N9 A G 68 " both_signs ideal model delta sigma weight residual False 2.46 2.25 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 3315 not shown) Planarity restraints: 3048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U G 7 " 0.033 2.00e-02 2.50e+03 1.84e-02 7.62e+00 pdb=" N1 U G 7 " -0.043 2.00e-02 2.50e+03 pdb=" C2 U G 7 " 0.001 2.00e-02 2.50e+03 pdb=" O2 U G 7 " -0.001 2.00e-02 2.50e+03 pdb=" N3 U G 7 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U G 7 " 0.002 2.00e-02 2.50e+03 pdb=" O4 U G 7 " 0.010 2.00e-02 2.50e+03 pdb=" C5 U G 7 " 0.000 2.00e-02 2.50e+03 pdb=" C6 U G 7 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U D 7 " -0.032 2.00e-02 2.50e+03 1.83e-02 7.54e+00 pdb=" N1 U D 7 " 0.043 2.00e-02 2.50e+03 pdb=" C2 U D 7 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U D 7 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U D 7 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U D 7 " -0.001 2.00e-02 2.50e+03 pdb=" O4 U D 7 " -0.010 2.00e-02 2.50e+03 pdb=" C5 U D 7 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U D 7 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 150 " -0.040 5.00e-02 4.00e+02 6.09e-02 5.93e+00 pdb=" N PRO C 151 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 151 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 151 " -0.034 5.00e-02 4.00e+02 ... (remaining 3045 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 6071 2.83 - 3.35: 15898 3.35 - 3.87: 33821 3.87 - 4.38: 40115 4.38 - 4.90: 64548 Nonbonded interactions: 160453 Sorted by model distance: nonbonded pdb=" O SER F 101 " pdb=" OG SER F 101 " model vdw 2.314 2.440 nonbonded pdb=" O SER C 101 " pdb=" OG SER C 101 " model vdw 2.314 2.440 nonbonded pdb=" OH TYR F 225 " pdb=" OG1 THR F 383 " model vdw 2.320 2.440 nonbonded pdb=" OH TYR C 225 " pdb=" OG1 THR C 383 " model vdw 2.320 2.440 nonbonded pdb=" O ALA F 376 " pdb=" OG1 THR F 380 " model vdw 2.351 2.440 ... (remaining 160448 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.750 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: 13.240 Check model and map are aligned: 0.290 Set scattering table: 0.150 Process input model: 57.270 Find NCS groups from input model: 0.980 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:13.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 : 0.005 0.053 21136 Z= 0.340 Angle : 0.857 9.496 29302 Z= 0.471 Chirality : 0.050 0.249 3318 Planarity : 0.006 0.061 3048 Dihedral : 14.791 88.785 8604 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.15), residues: 1960 helix: -1.92 (0.14), residues: 814 sheet: -0.73 (0.33), residues: 234 loop : -3.18 (0.15), residues: 912 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 289 time to evaluate : 2.043 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 291 average time/residue: 1.3226 time to fit residues: 435.3710 Evaluate side-chains 192 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 191 time to evaluate : 1.893 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2874 time to fit residues: 3.0197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 0.7980 chunk 162 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 55 optimal weight: 0.0030 chunk 109 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 167 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 101 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 194 optimal weight: 0.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 101 GLN A 127 ASN A 177 ASN B 37 ASN B 78 ASN B 101 GLN B 127 ASN B 151 GLN B 161 GLN B 177 ASN C 31 ASN C 49 ASN C 231 ASN C 279 ASN ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN C 303 GLN ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 416 ASN ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1039 GLN C1081 ASN C1112 ASN F 31 ASN F 49 ASN F 231 ASN F 279 ASN ** F 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 ASN F 302 ASN F 303 GLN ** F 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 416 ASN ** F 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 813 GLN F1039 GLN F1081 ASN F1112 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 21136 Z= 0.193 Angle : 0.538 7.050 29302 Z= 0.292 Chirality : 0.037 0.142 3318 Planarity : 0.004 0.040 3048 Dihedral : 11.267 68.308 4422 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer Outliers : 2.83 % 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: -1.90 (0.17), residues: 1960 helix: 0.04 (0.18), residues: 824 sheet: -0.85 (0.31), residues: 258 loop : -2.74 (0.16), residues: 878 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 203 time to evaluate : 2.156 Fit side-chains outliers start: 50 outliers final: 16 residues processed: 231 average time/residue: 1.2737 time to fit residues: 337.0741 Evaluate side-chains 201 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 185 time to evaluate : 1.628 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 4 average time/residue: 0.3758 time to fit residues: 4.2405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 108 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 161 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 210 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 193 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 156 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: