Starting phenix.real_space_refine (version: 1.21rc1) on Sat May 13 00:20:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5d_10694/05_2023/6y5d_10694_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5d_10694/05_2023/6y5d_10694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5d_10694/05_2023/6y5d_10694.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5d_10694/05_2023/6y5d_10694.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5d_10694/05_2023/6y5d_10694_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5d_10694/05_2023/6y5d_10694_updated.pdb" } resolution = 4.1 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= 0.006 sd= 0.040 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 Zn 2 6.06 5 P 612 5.49 5 S 54 5.16 5 C 17252 2.51 5 N 5588 2.21 5 O 6864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 91": "OD1" <-> "OD2" Residue "D TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "E TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 325": "OE1" <-> "OE2" Residue "K PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 478": "OE1" <-> "OE2" Residue "K GLU 487": "OE1" <-> "OE2" Residue "K GLU 515": "OE1" <-> "OE2" Residue "K PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 325": "OE1" <-> "OE2" Residue "L PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 478": "OE1" <-> "OE2" Residue "L GLU 487": "OE1" <-> "OE2" Residue "L GLU 515": "OE1" <-> "OE2" Residue "L PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 91": "OD1" <-> "OD2" Residue "P TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 91": "OD1" <-> "OD2" Residue "T TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 30372 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 789 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 789 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 831 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3119 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Chain: "J" Number of atoms: 3154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3154 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Chain: "K" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2980 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain: "L" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2980 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain: "M" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 789 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "N" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "O" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 806 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "P" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 698 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "Q" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 772 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "R" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 618 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "S" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 787 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "T" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "U" Number of atoms: 3119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3119 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Chain: "V" Number of atoms: 3154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3154 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-2': 1, 'PTD:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-2': 1, 'PTD:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-2': 1, 'PTD:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PTD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PTD:plan-2': 2, 'PTD:plan-1': 2} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-2': 1, 'PTD:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "O" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-2': 1, 'PTD:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "S" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PTD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PTD:plan-2': 2, 'PTD:plan-1': 2} Unresolved non-hydrogen planarities: 4 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14165 SG CYS K 396 76.480 20.279 43.285 0.00566.57 S ATOM 14171 SG CYS K 397 78.707 19.449 46.231 0.00570.62 S ATOM 14230 SG CYS K 404 80.023 21.567 43.400 0.00566.15 S ATOM 17145 SG CYS L 396 99.066 112.815 22.367 0.00600.00 S ATOM 17151 SG CYS L 397 96.012 114.889 23.197 0.00600.00 S ATOM 17210 SG CYS L 404 95.615 111.456 21.678 0.00600.00 S Time building chain proxies: 15.89, per 1000 atoms: 0.52 Number of scatterers: 30372 At special positions: 0 Unit cell: (163.4, 157.38, 141.9, 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) Zn 2 29.99 S 54 16.00 P 612 15.00 O 6864 8.00 N 5588 7.00 C 17252 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=18, symmetry=0 Number of additional bonds: simple=18, symmetry=0 Coordination: Other bonds: Time building additional restraints: 15.62 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 601 " pdb="ZN ZN K 601 " - pdb=" NE2 HIS K 390 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 397 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 404 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 396 " pdb=" ZN L 601 " pdb="ZN ZN L 601 " - pdb=" NE2 HIS L 390 " pdb="ZN ZN L 601 " - pdb=" SG CYS L 397 " pdb="ZN ZN L 601 " - pdb=" SG CYS L 404 " pdb="ZN ZN L 601 " - pdb=" SG CYS L 396 " Number of angles added : 6 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4176 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 99 helices and 5 sheets defined 57.9% alpha, 4.1% beta 306 base pairs and 562 stacking pairs defined. Time for finding SS restraints: 13.82 Creating SS restraints... Processing helix chain 'A' and resid 46 through 57 Processing helix chain 'A' and resid 65 through 78 removed outlier: 3.746A pdb=" N ASP A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 114 Processing helix chain 'A' and resid 122 through 131 Processing helix chain 'B' and resid 26 through 29 Processing helix chain 'B' and resid 32 through 41 Processing helix chain 'B' and resid 51 through 76 removed outlier: 4.043A pdb=" N VAL B 61 " --> pdb=" O GLY B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 94 removed outlier: 4.177A pdb=" N GLN B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 29 through 35 Processing helix chain 'C' and resid 46 through 73 removed outlier: 4.423A pdb=" N VAL C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 114 through 116 No H-bonds generated for 'chain 'C' and resid 114 through 116' Processing helix chain 'D' and resid 39 through 49 removed outlier: 3.501A pdb=" N LYS D 47 " --> pdb=" O TYR D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 84 Processing helix chain 'D' and resid 92 through 102 Processing helix chain 'D' and resid 106 through 124 Processing helix chain 'E' and resid 46 through 57 Processing helix chain 'E' and resid 65 through 79 removed outlier: 3.934A pdb=" N ASP E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE E 79 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 114 Processing helix chain 'E' and resid 122 through 132 Processing helix chain 'F' and resid 27 through 29 No H-bonds generated for 'chain 'F' and resid 27 through 29' Processing helix chain 'F' and resid 32 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.686A pdb=" N TYR F 52 " --> pdb=" O GLY F 49 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU F 53 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS F 60 " --> pdb=" O GLY F 57 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE F 67 " --> pdb=" O GLU F 64 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG F 68 " --> pdb=" O ASN F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 94 Processing helix chain 'G' and resid 18 through 22 Processing helix chain 'G' and resid 29 through 36 removed outlier: 3.987A pdb=" N ARG G 36 " --> pdb=" O HIS G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 73 Processing helix chain 'G' and resid 81 through 90 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 114 through 116 No H-bonds generated for 'chain 'G' and resid 114 through 116' Processing helix chain 'H' and resid 39 through 49 Processing helix chain 'H' and resid 57 through 84 Processing helix chain 'H' and resid 92 through 102 Processing helix chain 'H' and resid 107 through 124 removed outlier: 3.612A pdb=" N SER H 124 " --> pdb=" O THR H 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 162 through 176 removed outlier: 4.020A pdb=" N ARG K 176 " --> pdb=" O LEU K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 199 removed outlier: 3.611A pdb=" N ALA K 183 " --> pdb=" O SER K 180 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP K 191 " --> pdb=" O GLY K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 261 through 265 removed outlier: 3.990A pdb=" N GLN K 264 " --> pdb=" O PRO K 261 " (cutoff:3.500A) Processing helix chain 'K' and resid 273 through 290 removed outlier: 3.895A pdb=" N ASP K 290 " --> pdb=" O GLU K 286 " (cutoff:3.500A) Processing helix chain 'K' and resid 332 through 334 No H-bonds generated for 'chain 'K' and resid 332 through 334' Processing helix chain 'K' and resid 346 through 354 Processing helix chain 'K' and resid 380 through 389 Processing helix chain 'K' and resid 400 through 402 No H-bonds generated for 'chain 'K' and resid 400 through 402' Processing helix chain 'K' and resid 406 through 423 Processing helix chain 'K' and resid 435 through 448 Processing helix chain 'K' and resid 452 through 455 Processing helix chain 'K' and resid 457 through 477 removed outlier: 5.037A pdb=" N GLY K 461 " --> pdb=" O LYS K 458 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE K 464 " --> pdb=" O GLY K 461 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR K 477 " --> pdb=" O CYS K 474 " (cutoff:3.500A) Processing helix chain 'K' and resid 498 through 514 Processing helix chain 'K' and resid 517 through 519 No H-bonds generated for 'chain 'K' and resid 517 through 519' Processing helix chain 'L' and resid 162 through 176 removed outlier: 3.881A pdb=" N ARG L 176 " --> pdb=" O LEU L 172 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 199 removed outlier: 3.660A pdb=" N ALA L 183 " --> pdb=" O SER L 180 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP L 191 " --> pdb=" O GLY L 188 " (cutoff:3.500A) Processing helix chain 'L' and resid 261 through 265 removed outlier: 4.036A pdb=" N GLN L 264 " --> pdb=" O PRO L 261 " (cutoff:3.500A) Processing helix chain 'L' and resid 273 through 290 removed outlier: 3.680A pdb=" N GLU L 286 " --> pdb=" O LYS L 282 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASN L 289 " --> pdb=" O LYS L 285 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP L 290 " --> pdb=" O GLU L 286 " (cutoff:3.500A) Processing helix chain 'L' and resid 332 through 334 No H-bonds generated for 'chain 'L' and resid 332 through 334' Processing helix chain 'L' and resid 346 through 354 Processing helix chain 'L' and resid 380 through 388 Processing helix chain 'L' and resid 400 through 402 No H-bonds generated for 'chain 'L' and resid 400 through 402' Processing helix chain 'L' and resid 406 through 423 Processing helix chain 'L' and resid 435 through 448 Processing helix chain 'L' and resid 452 through 455 Processing helix chain 'L' and resid 457 through 476 removed outlier: 4.981A pdb=" N GLY L 461 " --> pdb=" O LYS L 458 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE L 464 " --> pdb=" O GLY L 461 " (cutoff:3.500A) Processing helix chain 'L' and resid 498 through 514 Processing helix chain 'L' and resid 517 through 519 No H-bonds generated for 'chain 'L' and resid 517 through 519' Processing helix chain 'M' and resid 46 through 57 Processing helix chain 'M' and resid 65 through 78 removed outlier: 3.731A pdb=" N ASP M 78 " --> pdb=" O GLU M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 114 Processing helix chain 'M' and resid 122 through 131 Processing helix chain 'N' and resid 26 through 29 No H-bonds generated for 'chain 'N' and resid 26 through 29' Processing helix chain 'N' and resid 32 through 41 Processing helix chain 'N' and resid 51 through 76 removed outlier: 4.118A pdb=" N VAL N 61 " --> pdb=" O GLY N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 94 removed outlier: 4.014A pdb=" N GLN N 94 " --> pdb=" O ALA N 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 18 through 21 No H-bonds generated for 'chain 'O' and resid 18 through 21' Processing helix chain 'O' and resid 29 through 36 Processing helix chain 'O' and resid 48 through 73 Processing helix chain 'O' and resid 81 through 89 Processing helix chain 'O' and resid 92 through 97 Processing helix chain 'O' and resid 114 through 116 No H-bonds generated for 'chain 'O' and resid 114 through 116' Processing helix chain 'P' and resid 39 through 49 Processing helix chain 'P' and resid 57 through 84 Processing helix chain 'P' and resid 92 through 102 Processing helix chain 'P' and resid 106 through 124 Processing helix chain 'Q' and resid 46 through 57 Processing helix chain 'Q' and resid 65 through 78 removed outlier: 3.866A pdb=" N ASP Q 78 " --> pdb=" O GLU Q 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 114 Processing helix chain 'Q' and resid 122 through 131 Processing helix chain 'R' and resid 26 through 29 Processing helix chain 'R' and resid 32 through 41 Processing helix chain 'R' and resid 51 through 76 removed outlier: 4.133A pdb=" N VAL R 61 " --> pdb=" O GLY R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 94 removed outlier: 3.994A pdb=" N GLN R 94 " --> pdb=" O ALA R 90 " (cutoff:3.500A) Processing helix chain 'S' and resid 18 through 22 Processing helix chain 'S' and resid 29 through 36 Processing helix chain 'S' and resid 48 through 73 Processing helix chain 'S' and resid 81 through 89 Processing helix chain 'S' and resid 92 through 97 Processing helix chain 'T' and resid 39 through 49 Processing helix chain 'T' and resid 57 through 84 Processing helix chain 'T' and resid 92 through 102 Processing helix chain 'T' and resid 106 through 124 Processing sheet with id= A, first strand: chain 'K' and resid 225 through 233 removed outlier: 6.523A pdb=" N SER K 317 " --> pdb=" O PHE K 226 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL K 228 " --> pdb=" O SER K 317 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ASP K 319 " --> pdb=" O VAL K 228 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N PHE K 230 " --> pdb=" O ASP K 319 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N THR K 321 " --> pdb=" O PHE K 230 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LEU K 232 " --> pdb=" O THR K 321 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ALA K 323 " --> pdb=" O LEU K 232 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 237 through 241 Processing sheet with id= C, first strand: chain 'K' and resid 364 through 366 removed outlier: 3.619A pdb=" N GLY K 369 " --> pdb=" O GLU K 366 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'L' and resid 206 through 208 removed outlier: 6.403A pdb=" N SER L 317 " --> pdb=" O PHE L 226 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL L 228 " --> pdb=" O SER L 317 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASP L 319 " --> pdb=" O VAL L 228 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N PHE L 230 " --> pdb=" O ASP L 319 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N THR L 321 " --> pdb=" O PHE L 230 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LEU L 232 " --> pdb=" O THR L 321 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA L 323 " --> pdb=" O LEU L 232 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'L' and resid 237 through 241 921 hydrogen bonds defined for protein. 2478 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 782 hydrogen bonds 1564 hydrogen bond angles 0 basepair planarities 306 basepair parallelities 562 stacking parallelities Total time for adding SS restraints: 17.99 Time building geometry restraints manager: 16.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5979 1.33 - 1.46: 12378 1.46 - 1.59: 12863 1.59 - 1.72: 857 1.72 - 1.86: 87 Bond restraints: 32164 Sorted by residual: bond pdb=" NE ARG L 423 " pdb=" CZ ARG L 423 " ideal model delta sigma weight residual 1.326 1.388 -0.062 1.10e-02 8.26e+03 3.22e+01 bond pdb=" CG ARG G 30 " pdb=" CD ARG G 30 " ideal model delta sigma weight residual 1.520 1.384 0.136 3.00e-02 1.11e+03 2.06e+01 bond pdb=" CG ARG G 33 " pdb=" CD ARG G 33 " ideal model delta sigma weight residual 1.520 1.387 0.133 3.00e-02 1.11e+03 1.98e+01 bond pdb=" NE ARG K 423 " pdb=" CZ ARG K 423 " ideal model delta sigma weight residual 1.326 1.375 -0.049 1.10e-02 8.26e+03 1.97e+01 bond pdb=" CD ARG B 96 " pdb=" NE ARG B 96 " ideal model delta sigma weight residual 1.458 1.396 0.062 1.40e-02 5.10e+03 1.94e+01 ... (remaining 32159 not shown) Histogram of bond angle deviations from ideal: 97.87 - 105.10: 2869 105.10 - 112.34: 17250 112.34 - 119.58: 10248 119.58 - 126.81: 14085 126.81 - 134.05: 1534 Bond angle restraints: 45986 Sorted by residual: angle pdb=" N THR L 395 " pdb=" CA THR L 395 " pdb=" C THR L 395 " ideal model delta sigma weight residual 113.61 101.66 11.95 1.50e+00 4.44e-01 6.35e+01 angle pdb=" N GLY C 38 " pdb=" CA GLY C 38 " pdb=" C GLY C 38 " ideal model delta sigma weight residual 115.30 104.35 10.95 1.39e+00 5.18e-01 6.20e+01 angle pdb=" C HIS D 50 " pdb=" N PRO D 51 " pdb=" CA PRO D 51 " ideal model delta sigma weight residual 119.47 128.45 -8.98 1.16e+00 7.43e-01 5.99e+01 angle pdb=" C LYS L 355 " pdb=" N PRO L 356 " pdb=" CA PRO L 356 " ideal model delta sigma weight residual 119.84 129.45 -9.61 1.25e+00 6.40e-01 5.91e+01 angle pdb=" C HIS T 50 " pdb=" N PRO T 51 " pdb=" CA PRO T 51 " ideal model delta sigma weight residual 119.47 128.29 -8.82 1.16e+00 7.43e-01 5.78e+01 ... (remaining 45981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 14567 35.76 - 71.53: 2675 71.53 - 107.29: 47 107.29 - 143.05: 0 143.05 - 178.82: 6 Dihedral angle restraints: 17295 sinusoidal: 10837 harmonic: 6458 Sorted by residual: dihedral pdb=" C4' DC I 81 " pdb=" C3' DC I 81 " pdb=" O3' DC I 81 " pdb=" P DC I 82 " ideal model delta sinusoidal sigma weight residual 220.00 41.18 178.82 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC U 81 " pdb=" C3' DC U 81 " pdb=" O3' DC U 81 " pdb=" P DC U 82 " ideal model delta sinusoidal sigma weight residual 220.00 41.36 178.64 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT V 60 " pdb=" C3' DT V 60 " pdb=" O3' DT V 60 " pdb=" P DT V 61 " ideal model delta sinusoidal sigma weight residual 220.00 44.45 175.55 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 17292 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 4271 0.093 - 0.187: 807 0.187 - 0.280: 73 0.280 - 0.374: 20 0.374 - 0.467: 3 Chirality restraints: 5174 Sorted by residual: chirality pdb=" C3' DA J 4 " pdb=" C4' DA J 4 " pdb=" O3' DA J 4 " pdb=" C2' DA J 4 " both_signs ideal model delta sigma weight residual False -2.66 -2.19 -0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" CA LYS B 32 " pdb=" N LYS B 32 " pdb=" C LYS B 32 " pdb=" CB LYS B 32 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.38e+00 chirality pdb=" C3' DA V 4 " pdb=" C4' DA V 4 " pdb=" O3' DA V 4 " pdb=" C2' DA V 4 " both_signs ideal model delta sigma weight residual False -2.66 -2.26 -0.40 2.00e-01 2.50e+01 3.92e+00 ... (remaining 5171 not shown) Planarity restraints: 3704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE K 265 " 0.073 2.00e-02 2.50e+03 4.45e-02 3.46e+01 pdb=" CG PHE K 265 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE K 265 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 PHE K 265 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 PHE K 265 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE K 265 " 0.015 2.00e-02 2.50e+03 pdb=" CZ PHE K 265 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE P 71 " 0.069 2.00e-02 2.50e+03 4.40e-02 3.39e+01 pdb=" CG PHE P 71 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE P 71 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 PHE P 71 " -0.047 2.00e-02 2.50e+03 pdb=" CE1 PHE P 71 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE P 71 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE P 71 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 103 " -0.028 2.00e-02 2.50e+03 5.59e-02 3.12e+01 pdb=" C GLY B 103 " 0.097 2.00e-02 2.50e+03 pdb=" O GLY B 103 " -0.035 2.00e-02 2.50e+03 pdb=" OXT GLY B 103 " -0.034 2.00e-02 2.50e+03 ... (remaining 3701 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6207 2.78 - 3.31: 26558 3.31 - 3.84: 58752 3.84 - 4.37: 74815 4.37 - 4.90: 101329 Nonbonded interactions: 267661 Sorted by model distance: nonbonded pdb=" O TYR C 40 " pdb=" OG SER D 79 " model vdw 2.251 2.440 nonbonded pdb=" O GLY B 102 " pdb=" OG SER H 65 " model vdw 2.287 2.440 nonbonded pdb=" O ASN K 260 " pdb=" OG SER K 263 " model vdw 2.303 2.440 nonbonded pdb=" NH2 ARG Q 43 " pdb=" OP1 DG V 72 " model vdw 2.390 2.520 nonbonded pdb=" O PHE L 491 " pdb=" NZ LYS L 501 " model vdw 2.394 2.520 ... (remaining 267656 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 41 through 134) selection = (chain 'E' and resid 41 through 134) selection = (chain 'M' and resid 41 through 134) selection = chain 'Q' } ncs_group { reference = (chain 'B' and resid 25 through 101) selection = (chain 'F' and resid 25 through 101) selection = (chain 'N' and resid 25 through 101) selection = chain 'R' } ncs_group { reference = (chain 'C' and (resid 14 through 113 or resid 201)) selection = (chain 'G' and (resid 14 through 113 or resid 701)) selection = (chain 'O' and (resid 14 through 113 or resid 201)) selection = (chain 'S' and (resid 14 through 113 or resid 702)) } ncs_group { reference = (chain 'D' and resid 36 through 125) selection = (chain 'H' and resid 36 through 125) selection = chain 'P' selection = (chain 'T' and resid 36 through 125) } ncs_group { reference = chain 'I' selection = chain 'U' } ncs_group { reference = chain 'J' selection = chain 'V' } ncs_group { reference = chain 'K' selection = chain 'L' } 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=0.00 max=1.00 mean=0.84 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 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: 9.450 Check model and map are aligned: 0.500 Set scattering table: 0.320 Process input model: 102.710 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 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 : 0.013 0.136 32164 Z= 0.795 Angle : 1.229 11.949 45986 Z= 0.833 Chirality : 0.074 0.467 5174 Planarity : 0.011 0.068 3704 Dihedral : 25.870 178.819 13119 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.97 % Favored : 97.94 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.16), residues: 2182 helix: 0.70 (0.13), residues: 1384 sheet: -0.06 (0.44), residues: 92 loop : 0.10 (0.23), residues: 706 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 445 time to evaluate : 2.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 447 average time/residue: 0.3757 time to fit residues: 271.9250 Evaluate side-chains 218 residues out of total 1902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 217 time to evaluate : 2.122 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5176 time to fit residues: 3.2233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 231 optimal weight: 6.9990 chunk 207 optimal weight: 8.9990 chunk 115 optimal weight: 30.0000 chunk 70 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 214 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 159 optimal weight: 20.0000 chunk 248 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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: