Starting phenix.real_space_refine on Sun Jul 21 01:32:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d63_27215/07_2024/8d63_27215.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d63_27215/07_2024/8d63_27215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d63_27215/07_2024/8d63_27215.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d63_27215/07_2024/8d63_27215.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d63_27215/07_2024/8d63_27215.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d63_27215/07_2024/8d63_27215.cif" } resolution = 3.14 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= 0.012 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 5 5.49 5 S 30 5.16 5 C 8375 2.51 5 N 2085 2.21 5 O 2290 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 30": "OE1" <-> "OE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D GLU 159": "OE1" <-> "OE2" Residue "D GLU 292": "OE1" <-> "OE2" Residue "E GLU 30": "OE1" <-> "OE2" Residue "E GLU 159": "OE1" <-> "OE2" Residue "E GLU 292": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 12785 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "B" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "C" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "D" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "E" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'LBN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'LBN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'LBN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'LBN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'LBN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.12, per 1000 atoms: 0.56 Number of scatterers: 12785 At special positions: 0 Unit cell: (92.4, 91.3, 122.1, 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 30 16.00 P 5 15.00 O 2290 8.00 N 2085 7.00 C 8375 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: 4.31 Conformation dependent library (CDL) restraints added in 2.3 seconds 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2910 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 15 sheets defined 34.9% alpha, 35.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 61 through 69 removed outlier: 3.943A pdb=" N ARG A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN A 69 " --> pdb=" O ARG A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.697A pdb=" N SER A 179 " --> pdb=" O ASP A 176 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER A 180 " --> pdb=" O HIS A 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 176 through 180' Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 208 through 220 removed outlier: 3.730A pdb=" N LEU A 212 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 252 removed outlier: 3.723A pdb=" N ILE A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 286 Processing helix chain 'A' and resid 296 through 300 removed outlier: 3.563A pdb=" N CYS A 300 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'B' and resid 61 through 69 removed outlier: 3.943A pdb=" N ARG B 65 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN B 69 " --> pdb=" O ARG B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 removed outlier: 3.697A pdb=" N SER B 179 " --> pdb=" O ASP B 176 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER B 180 " --> pdb=" O HIS B 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 176 through 180' Processing helix chain 'B' and resid 201 through 208 Processing helix chain 'B' and resid 208 through 220 removed outlier: 3.730A pdb=" N LEU B 212 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 252 removed outlier: 3.723A pdb=" N ILE B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 286 Processing helix chain 'B' and resid 296 through 300 removed outlier: 3.563A pdb=" N CYS B 300 " --> pdb=" O ILE B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 317 Processing helix chain 'C' and resid 61 through 69 removed outlier: 3.943A pdb=" N ARG C 65 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN C 69 " --> pdb=" O ARG C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 180 removed outlier: 3.697A pdb=" N SER C 179 " --> pdb=" O ASP C 176 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER C 180 " --> pdb=" O HIS C 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 176 through 180' Processing helix chain 'C' and resid 201 through 208 Processing helix chain 'C' and resid 208 through 220 removed outlier: 3.730A pdb=" N LEU C 212 " --> pdb=" O PHE C 208 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TRP C 220 " --> pdb=" O ILE C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 252 removed outlier: 3.723A pdb=" N ILE C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 286 Processing helix chain 'C' and resid 296 through 300 removed outlier: 3.563A pdb=" N CYS C 300 " --> pdb=" O ILE C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 317 Processing helix chain 'D' and resid 61 through 69 removed outlier: 3.942A pdb=" N ARG D 65 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN D 69 " --> pdb=" O ARG D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 180 removed outlier: 3.697A pdb=" N SER D 179 " --> pdb=" O ASP D 176 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SER D 180 " --> pdb=" O HIS D 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 176 through 180' Processing helix chain 'D' and resid 201 through 208 Processing helix chain 'D' and resid 208 through 220 removed outlier: 3.730A pdb=" N LEU D 212 " --> pdb=" O PHE D 208 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP D 220 " --> pdb=" O ILE D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 252 removed outlier: 3.723A pdb=" N ILE D 252 " --> pdb=" O TYR D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 286 Processing helix chain 'D' and resid 296 through 300 removed outlier: 3.563A pdb=" N CYS D 300 " --> pdb=" O ILE D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 317 Processing helix chain 'E' and resid 61 through 69 removed outlier: 3.943A pdb=" N ARG E 65 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN E 69 " --> pdb=" O ARG E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 180 removed outlier: 3.697A pdb=" N SER E 179 " --> pdb=" O ASP E 176 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER E 180 " --> pdb=" O HIS E 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 176 through 180' Processing helix chain 'E' and resid 201 through 208 Processing helix chain 'E' and resid 208 through 220 removed outlier: 3.730A pdb=" N LEU E 212 " --> pdb=" O PHE E 208 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TRP E 220 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 252 removed outlier: 3.723A pdb=" N ILE E 252 " --> pdb=" O TYR E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 286 Processing helix chain 'E' and resid 296 through 300 removed outlier: 3.563A pdb=" N CYS E 300 " --> pdb=" O ILE E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 317 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58 removed outlier: 6.381A pdb=" N THR A 32 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY A 25 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LYS A 34 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE A 23 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP A 36 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N THR A 44 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP A 13 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 9.648A pdb=" N VAL A 12 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N ASP A 144 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL A 14 " --> pdb=" O ASP A 144 " (cutoff:3.500A) removed outlier: 8.894A pdb=" N GLN A 146 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL A 16 " --> pdb=" O GLN A 146 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N TYR A 148 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE A 18 " --> pdb=" O TYR A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.731A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.731A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 56 through 58 removed outlier: 6.381A pdb=" N THR B 32 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY B 25 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LYS B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE B 23 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP B 36 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N THR B 44 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ASP B 13 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 9.648A pdb=" N VAL B 12 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N ASP B 144 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL B 14 " --> pdb=" O ASP B 144 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N GLN B 146 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL B 16 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N TYR B 148 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE B 18 " --> pdb=" O TYR B 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.731A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.731A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 58 removed outlier: 6.381A pdb=" N THR C 32 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY C 25 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LYS C 34 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE C 23 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP C 36 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N THR C 44 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ASP C 13 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 9.648A pdb=" N VAL C 12 " --> pdb=" O PHE C 142 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N ASP C 144 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL C 14 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N GLN C 146 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL C 16 " --> pdb=" O GLN C 146 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N TYR C 148 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE C 18 " --> pdb=" O TYR C 148 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.731A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.731A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 56 through 58 removed outlier: 6.381A pdb=" N THR D 32 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY D 25 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LYS D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE D 23 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASP D 36 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N THR D 44 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP D 13 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 9.648A pdb=" N VAL D 12 " --> pdb=" O PHE D 142 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N ASP D 144 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL D 14 " --> pdb=" O ASP D 144 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N GLN D 146 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL D 16 " --> pdb=" O GLN D 146 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N TYR D 148 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE D 18 " --> pdb=" O TYR D 148 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.731A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.731A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 56 through 58 removed outlier: 6.381A pdb=" N THR E 32 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY E 25 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LYS E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE E 23 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP E 36 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N THR E 44 " --> pdb=" O ASP E 13 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP E 13 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 9.648A pdb=" N VAL E 12 " --> pdb=" O PHE E 142 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N ASP E 144 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL E 14 " --> pdb=" O ASP E 144 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N GLN E 146 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL E 16 " --> pdb=" O GLN E 146 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N TYR E 148 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE E 18 " --> pdb=" O TYR E 148 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.731A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.731A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1845 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: 3.59 Time building geometry restraints manager: 4.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2015 1.31 - 1.43: 3755 1.43 - 1.56: 7223 1.56 - 1.68: 77 1.68 - 1.81: 50 Bond restraints: 13120 Sorted by residual: bond pdb=" C34 LBN C 401 " pdb=" O7 LBN C 401 " ideal model delta sigma weight residual 1.331 1.427 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C34 LBN B 401 " pdb=" O7 LBN B 401 " ideal model delta sigma weight residual 1.331 1.426 -0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C34 LBN E 401 " pdb=" O7 LBN E 401 " ideal model delta sigma weight residual 1.331 1.426 -0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C34 LBN D 401 " pdb=" O7 LBN D 401 " ideal model delta sigma weight residual 1.331 1.426 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C34 LBN A 401 " pdb=" O7 LBN A 401 " ideal model delta sigma weight residual 1.331 1.426 -0.095 2.00e-02 2.50e+03 2.25e+01 ... (remaining 13115 not shown) Histogram of bond angle deviations from ideal: 98.83 - 105.87: 288 105.87 - 112.90: 6903 112.90 - 119.94: 4400 119.94 - 126.97: 6064 126.97 - 134.00: 175 Bond angle restraints: 17830 Sorted by residual: angle pdb=" N ASN C 60 " pdb=" CA ASN C 60 " pdb=" C ASN C 60 " ideal model delta sigma weight residual 111.07 119.92 -8.85 1.07e+00 8.73e-01 6.84e+01 angle pdb=" N ASN E 60 " pdb=" CA ASN E 60 " pdb=" C ASN E 60 " ideal model delta sigma weight residual 111.07 119.92 -8.85 1.07e+00 8.73e-01 6.84e+01 angle pdb=" N ASN A 60 " pdb=" CA ASN A 60 " pdb=" C ASN A 60 " ideal model delta sigma weight residual 111.07 119.91 -8.84 1.07e+00 8.73e-01 6.83e+01 angle pdb=" N ASN B 60 " pdb=" CA ASN B 60 " pdb=" C ASN B 60 " ideal model delta sigma weight residual 111.07 119.90 -8.83 1.07e+00 8.73e-01 6.80e+01 angle pdb=" N ASN D 60 " pdb=" CA ASN D 60 " pdb=" C ASN D 60 " ideal model delta sigma weight residual 111.07 119.87 -8.80 1.07e+00 8.73e-01 6.77e+01 ... (remaining 17825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.58: 7170 21.58 - 43.15: 435 43.15 - 64.73: 100 64.73 - 86.31: 25 86.31 - 107.88: 20 Dihedral angle restraints: 7750 sinusoidal: 3245 harmonic: 4505 Sorted by residual: dihedral pdb=" CA LEU B 118 " pdb=" C LEU B 118 " pdb=" N PHE B 119 " pdb=" CA PHE B 119 " ideal model delta harmonic sigma weight residual -180.00 -156.48 -23.52 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA LEU D 118 " pdb=" C LEU D 118 " pdb=" N PHE D 119 " pdb=" CA PHE D 119 " ideal model delta harmonic sigma weight residual -180.00 -156.48 -23.52 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA LEU A 118 " pdb=" C LEU A 118 " pdb=" N PHE A 119 " pdb=" CA PHE A 119 " ideal model delta harmonic sigma weight residual -180.00 -156.50 -23.50 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 7747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1518 0.064 - 0.129: 353 0.129 - 0.193: 53 0.193 - 0.257: 21 0.257 - 0.322: 10 Chirality restraints: 1955 Sorted by residual: chirality pdb=" CA GLU C 59 " pdb=" N GLU C 59 " pdb=" C GLU C 59 " pdb=" CB GLU C 59 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA GLU D 59 " pdb=" N GLU D 59 " pdb=" C GLU D 59 " pdb=" CB GLU D 59 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CA GLU A 59 " pdb=" N GLU A 59 " pdb=" C GLU A 59 " pdb=" CB GLU A 59 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 1952 not shown) Planarity restraints: 2250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 50 " 0.033 5.00e-02 4.00e+02 5.08e-02 4.12e+00 pdb=" N PRO D 51 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 51 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 51 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 50 " 0.033 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO A 51 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 51 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 51 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 50 " 0.033 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO B 51 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 51 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 51 " 0.028 5.00e-02 4.00e+02 ... (remaining 2247 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3431 2.81 - 3.33: 10726 3.33 - 3.86: 19914 3.86 - 4.38: 23566 4.38 - 4.90: 42808 Nonbonded interactions: 100445 Sorted by model distance: nonbonded pdb=" O TYR B 248 " pdb=" CD1 ILE B 252 " model vdw 2.290 3.460 nonbonded pdb=" O TYR D 248 " pdb=" CD1 ILE D 252 " model vdw 2.290 3.460 nonbonded pdb=" O TYR E 248 " pdb=" CD1 ILE E 252 " model vdw 2.291 3.460 nonbonded pdb=" O TYR C 248 " pdb=" CD1 ILE C 252 " model vdw 2.291 3.460 nonbonded pdb=" O TYR A 248 " pdb=" CD1 ILE A 252 " model vdw 2.291 3.460 ... (remaining 100440 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.370 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: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 34.760 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 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 : 0.009 0.096 13120 Z= 0.581 Angle : 0.987 15.995 17830 Z= 0.540 Chirality : 0.062 0.322 1955 Planarity : 0.005 0.051 2250 Dihedral : 16.369 107.881 4840 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.98 % Favored : 94.69 % Rotamer: Outliers : 0.36 % Allowed : 1.45 % Favored : 98.18 % 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: -1.01 (0.21), residues: 1525 helix: -0.01 (0.21), residues: 530 sheet: 0.04 (0.25), residues: 490 loop : -1.99 (0.23), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 161 HIS 0.007 0.002 HIS C 177 PHE 0.024 0.003 PHE C 247 TYR 0.011 0.002 TYR A 204 ARG 0.005 0.001 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 160 time to evaluate : 1.433 Fit side-chains REVERT: A 163 ARG cc_start: 0.8147 (mmt-90) cc_final: 0.7737 (mmt-90) REVERT: A 245 TYR cc_start: 0.8383 (t80) cc_final: 0.8072 (t80) REVERT: C 61 THR cc_start: 0.8940 (m) cc_final: 0.8676 (p) REVERT: C 206 TRP cc_start: 0.7842 (m100) cc_final: 0.7614 (m100) REVERT: D 150 GLU cc_start: 0.7606 (pt0) cc_final: 0.7236 (pt0) REVERT: E 61 THR cc_start: 0.9014 (m) cc_final: 0.8737 (p) REVERT: E 150 GLU cc_start: 0.7678 (pt0) cc_final: 0.7462 (pt0) REVERT: E 174 ARG cc_start: 0.8206 (ttm-80) cc_final: 0.7964 (ttm170) REVERT: E 177 HIS cc_start: 0.6673 (p90) cc_final: 0.6049 (p90) outliers start: 5 outliers final: 0 residues processed: 161 average time/residue: 0.3054 time to fit residues: 68.1557 Evaluate side-chains 114 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 62 GLN A 151 ASN A 251 ASN B 60 ASN B 62 GLN B 251 ASN C 60 ASN C 62 GLN D 60 ASN D 62 GLN E 60 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13120 Z= 0.225 Angle : 0.515 5.642 17830 Z= 0.267 Chirality : 0.046 0.136 1955 Planarity : 0.004 0.035 2250 Dihedral : 14.195 112.513 1910 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.36 % Allowed : 4.65 % Favored : 94.98 % 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: -0.12 (0.22), residues: 1525 helix: 1.14 (0.22), residues: 540 sheet: 0.17 (0.25), residues: 500 loop : -1.70 (0.24), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 206 HIS 0.003 0.001 HIS E 177 PHE 0.022 0.002 PHE A 247 TYR 0.012 0.001 TYR E 245 ARG 0.002 0.000 ARG A 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 120 time to evaluate : 1.340 Fit side-chains REVERT: A 150 GLU cc_start: 0.7689 (pt0) cc_final: 0.7330 (pt0) REVERT: A 163 ARG cc_start: 0.8113 (mmt-90) cc_final: 0.7711 (mmt-90) REVERT: C 206 TRP cc_start: 0.7743 (m100) cc_final: 0.7535 (m100) REVERT: D 150 GLU cc_start: 0.7625 (pt0) cc_final: 0.7309 (pt0) REVERT: E 174 ARG cc_start: 0.8172 (ttm-80) cc_final: 0.7922 (ttm170) outliers start: 5 outliers final: 3 residues processed: 124 average time/residue: 0.3057 time to fit residues: 52.9291 Evaluate side-chains 112 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain E residue 60 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 92 optimal weight: 6.9990 chunk 37 optimal weight: 0.0870 chunk 136 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 109 optimal weight: 3.9990 overall best weight: 2.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 251 ASN E 251 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13120 Z= 0.333 Angle : 0.540 5.704 17830 Z= 0.278 Chirality : 0.047 0.145 1955 Planarity : 0.004 0.035 2250 Dihedral : 13.353 109.160 1910 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.58 % Allowed : 7.42 % Favored : 92.00 % 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: 0.17 (0.22), residues: 1525 helix: 1.56 (0.22), residues: 540 sheet: 0.16 (0.24), residues: 500 loop : -1.57 (0.25), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 206 HIS 0.004 0.001 HIS E 177 PHE 0.020 0.002 PHE E 247 TYR 0.011 0.001 TYR E 270 ARG 0.002 0.000 ARG A 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 114 time to evaluate : 1.490 Fit side-chains REVERT: D 150 GLU cc_start: 0.7675 (pt0) cc_final: 0.7396 (pt0) REVERT: E 174 ARG cc_start: 0.8172 (ttm-80) cc_final: 0.7952 (ttm170) outliers start: 8 outliers final: 7 residues processed: 120 average time/residue: 0.3266 time to fit residues: 54.5952 Evaluate side-chains 111 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 279 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.0570 chunk 102 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 ASN E 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13120 Z= 0.204 Angle : 0.466 5.134 17830 Z= 0.240 Chirality : 0.045 0.138 1955 Planarity : 0.003 0.030 2250 Dihedral : 12.135 107.720 1910 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.44 % Allowed : 7.56 % Favored : 92.00 % 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: 0.57 (0.22), residues: 1525 helix: 2.03 (0.23), residues: 530 sheet: 0.47 (0.24), residues: 490 loop : -1.55 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 43 HIS 0.002 0.001 HIS E 177 PHE 0.020 0.001 PHE D 247 TYR 0.011 0.001 TYR E 245 ARG 0.001 0.000 ARG E 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 123 time to evaluate : 1.472 Fit side-chains REVERT: A 150 GLU cc_start: 0.7821 (pt0) cc_final: 0.7482 (pt0) REVERT: D 150 GLU cc_start: 0.7721 (pt0) cc_final: 0.7456 (pt0) REVERT: E 174 ARG cc_start: 0.8174 (ttm-80) cc_final: 0.7894 (ttm170) outliers start: 6 outliers final: 5 residues processed: 128 average time/residue: 0.2956 time to fit residues: 53.1317 Evaluate side-chains 117 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain E residue 250 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.9582 > 50: distance: 64 - 68: 10.898 distance: 68 - 69: 31.949 distance: 69 - 70: 37.964 distance: 70 - 71: 39.465 distance: 70 - 72: 36.170 distance: 72 - 73: 36.217 distance: 73 - 74: 46.358 distance: 73 - 76: 35.928 distance: 74 - 75: 42.384 distance: 74 - 80: 41.250 distance: 76 - 77: 21.602 distance: 77 - 78: 24.742 distance: 77 - 79: 16.989 distance: 80 - 81: 21.184 distance: 81 - 82: 34.915 distance: 81 - 84: 30.755 distance: 82 - 83: 22.891 distance: 82 - 94: 33.489 distance: 84 - 85: 33.568 distance: 85 - 86: 11.689 distance: 85 - 87: 12.336 distance: 86 - 88: 18.375 distance: 87 - 89: 19.348 distance: 87 - 90: 18.331 distance: 88 - 89: 6.283 distance: 89 - 91: 14.094 distance: 90 - 92: 31.193 distance: 91 - 93: 15.362 distance: 92 - 93: 25.470 distance: 94 - 95: 17.888 distance: 95 - 96: 30.547 distance: 95 - 98: 9.882 distance: 96 - 97: 38.892 distance: 96 - 101: 20.406 distance: 98 - 99: 28.883 distance: 98 - 100: 21.134 distance: 101 - 102: 18.145 distance: 101 - 107: 13.068 distance: 102 - 103: 33.356 distance: 102 - 105: 41.466 distance: 103 - 104: 22.207 distance: 103 - 108: 23.013 distance: 105 - 106: 16.127 distance: 106 - 107: 19.838 distance: 108 - 109: 19.866 distance: 109 - 110: 26.145 distance: 109 - 112: 21.455 distance: 110 - 111: 31.527 distance: 110 - 113: 10.814 distance: 113 - 114: 18.709 distance: 114 - 115: 9.123 distance: 114 - 117: 19.058 distance: 115 - 116: 14.755 distance: 117 - 118: 19.670 distance: 118 - 119: 17.879 distance: 118 - 120: 4.717 distance: 121 - 122: 9.047 distance: 121 - 204: 6.253 distance: 122 - 123: 8.792 distance: 122 - 125: 9.742 distance: 123 - 124: 8.498 distance: 123 - 130: 5.367 distance: 124 - 201: 6.842 distance: 125 - 126: 3.682 distance: 126 - 127: 4.003 distance: 127 - 129: 3.441 distance: 130 - 131: 8.208 distance: 131 - 132: 9.271 distance: 132 - 133: 10.720 distance: 132 - 141: 12.320 distance: 134 - 135: 5.630 distance: 135 - 136: 6.082 distance: 135 - 137: 5.324 distance: 136 - 138: 3.928 distance: 137 - 139: 3.231 distance: 138 - 140: 5.987 distance: 139 - 140: 5.339 distance: 141 - 142: 11.051 distance: 142 - 143: 3.313 distance: 142 - 145: 5.787 distance: 143 - 144: 7.499 distance: 143 - 149: 4.450 distance: 145 - 146: 12.498 distance: 145 - 147: 8.819 distance: 146 - 148: 4.638