Starting phenix.real_space_refine on Mon Apr 6 02:11:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y7p_72665/04_2026/9y7p_72665.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y7p_72665/04_2026/9y7p_72665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y7p_72665/04_2026/9y7p_72665.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y7p_72665/04_2026/9y7p_72665.map" model { file = "/net/cci-nas-00/data/ceres_data/9y7p_72665/04_2026/9y7p_72665.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y7p_72665/04_2026/9y7p_72665.cif" } resolution = 2.5 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 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= 0.001 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: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 9610 2.51 5 N 2315 2.21 5 O 2650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14665 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2812 Classifications: {'peptide': 347} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "B" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2812 Classifications: {'peptide': 347} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "C" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2812 Classifications: {'peptide': 347} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "D" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2812 Classifications: {'peptide': 347} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "E" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2812 Classifications: {'peptide': 347} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 107 Unusual residues: {'NAG': 1, 'PX4': 6} Inner-chain residues flagged as termini: ['pdbres="GLY A 508 "'] Classifications: {'peptide': 1, 'undetermined': 7} Modifications used: {'COO': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PX4:plan-1': 6} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 121 Unusual residues: {'NAG': 2, 'PX4': 6} Inner-chain residues flagged as termini: ['pdbres="GLY B 507 "'] Classifications: {'peptide': 1, 'undetermined': 8} Modifications used: {'COO': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PX4:plan-1': 6} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 121 Unusual residues: {'NAG': 2, 'PX4': 6} Inner-chain residues flagged as termini: ['pdbres="GLY C 507 "'] Classifications: {'peptide': 1, 'undetermined': 8} Modifications used: {'COO': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PX4:plan-1': 6} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 121 Unusual residues: {'NAG': 2, 'PX4': 6} Inner-chain residues flagged as termini: ['pdbres="GLY D 507 "'] Classifications: {'peptide': 1, 'undetermined': 8} Modifications used: {'COO': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PX4:plan-1': 6} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 116 Unusual residues: {'NAG': 2, 'PX4': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PX4:plan-1': 6} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 3.64, per 1000 atoms: 0.25 Number of scatterers: 14665 At special positions: 0 Unit cell: (92.4, 89.04, 130.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 2650 8.00 N 2315 7.00 C 9610 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 243 " distance=2.04 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 243 " distance=2.04 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 186 " distance=2.03 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 243 " distance=2.04 Simple disulfide: pdb=" SG CYS D 172 " - pdb=" SG CYS D 186 " distance=2.03 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 243 " distance=2.04 Simple disulfide: pdb=" SG CYS E 172 " - pdb=" SG CYS E 186 " distance=2.03 Simple disulfide: pdb=" SG CYS E 232 " - pdb=" SG CYS E 243 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 72 " " NAG A 503 " - " ASN A 103 " " NAG B 501 " - " ASN B 72 " " NAG B 502 " - " ASN B 103 " " NAG C 501 " - " ASN C 72 " " NAG C 502 " - " ASN C 103 " " NAG D 501 " - " ASN D 72 " " NAG D 502 " - " ASN D 103 " " NAG E 503 " - " ASN E 72 " " NAG E 504 " - " ASN E 103 " Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 559.7 milliseconds 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3330 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 20 sheets defined 42.2% alpha, 40.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 43 through 52 removed outlier: 3.703A pdb=" N PHE A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A 48 " --> pdb=" O PRO A 44 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 57 removed outlier: 3.511A pdb=" N SER A 56 " --> pdb=" O GLY A 53 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY A 57 " --> pdb=" O ARG A 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 53 through 57' Processing helix chain 'A' and resid 105 through 108 Processing helix chain 'A' and resid 120 through 127 removed outlier: 3.784A pdb=" N LEU A 124 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP A 125 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 127 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 261 Processing helix chain 'A' and resid 261 through 275 removed outlier: 4.049A pdb=" N SER A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 282 through 305 Processing helix chain 'A' and resid 315 through 344 Processing helix chain 'A' and resid 410 through 443 removed outlier: 3.909A pdb=" N ALA A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) Proline residue: A 427 - end of helix Processing helix chain 'A' and resid 444 through 449 Processing helix chain 'B' and resid 43 through 52 removed outlier: 3.702A pdb=" N PHE B 47 " --> pdb=" O SER B 43 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 57 removed outlier: 3.510A pdb=" N SER B 56 " --> pdb=" O GLY B 53 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY B 57 " --> pdb=" O ARG B 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 53 through 57' Processing helix chain 'B' and resid 105 through 108 Processing helix chain 'B' and resid 120 through 127 removed outlier: 3.783A pdb=" N LEU B 124 " --> pdb=" O PRO B 121 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP B 125 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE B 127 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 261 Processing helix chain 'B' and resid 261 through 275 removed outlier: 4.049A pdb=" N SER B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 278 No H-bonds generated for 'chain 'B' and resid 276 through 278' Processing helix chain 'B' and resid 282 through 305 Processing helix chain 'B' and resid 315 through 344 Processing helix chain 'B' and resid 410 through 443 removed outlier: 3.909A pdb=" N ALA B 424 " --> pdb=" O THR B 420 " (cutoff:3.500A) Proline residue: B 427 - end of helix Processing helix chain 'B' and resid 444 through 449 Processing helix chain 'C' and resid 43 through 52 removed outlier: 3.703A pdb=" N PHE C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU C 48 " --> pdb=" O PRO C 44 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 57 removed outlier: 3.510A pdb=" N SER C 56 " --> pdb=" O GLY C 53 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY C 57 " --> pdb=" O ARG C 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 53 through 57' Processing helix chain 'C' and resid 105 through 108 Processing helix chain 'C' and resid 120 through 127 removed outlier: 3.783A pdb=" N LEU C 124 " --> pdb=" O PRO C 121 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP C 125 " --> pdb=" O SER C 122 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE C 127 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 261 Processing helix chain 'C' and resid 261 through 275 removed outlier: 4.049A pdb=" N SER C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 278 No H-bonds generated for 'chain 'C' and resid 276 through 278' Processing helix chain 'C' and resid 282 through 305 Processing helix chain 'C' and resid 315 through 344 Processing helix chain 'C' and resid 410 through 443 removed outlier: 3.909A pdb=" N ALA C 424 " --> pdb=" O THR C 420 " (cutoff:3.500A) Proline residue: C 427 - end of helix Processing helix chain 'C' and resid 444 through 449 Processing helix chain 'D' and resid 43 through 52 removed outlier: 3.703A pdb=" N PHE D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU D 48 " --> pdb=" O PRO D 44 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP D 49 " --> pdb=" O SER D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 57 removed outlier: 3.511A pdb=" N SER D 56 " --> pdb=" O GLY D 53 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY D 57 " --> pdb=" O ARG D 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 57' Processing helix chain 'D' and resid 105 through 108 Processing helix chain 'D' and resid 120 through 127 removed outlier: 3.783A pdb=" N LEU D 124 " --> pdb=" O PRO D 121 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP D 125 " --> pdb=" O SER D 122 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE D 127 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 261 Processing helix chain 'D' and resid 261 through 275 removed outlier: 4.049A pdb=" N SER D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 278 No H-bonds generated for 'chain 'D' and resid 276 through 278' Processing helix chain 'D' and resid 282 through 305 Processing helix chain 'D' and resid 315 through 344 Processing helix chain 'D' and resid 410 through 443 removed outlier: 3.908A pdb=" N ALA D 424 " --> pdb=" O THR D 420 " (cutoff:3.500A) Proline residue: D 427 - end of helix Processing helix chain 'D' and resid 444 through 449 Processing helix chain 'E' and resid 43 through 52 removed outlier: 3.702A pdb=" N PHE E 47 " --> pdb=" O SER E 43 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU E 48 " --> pdb=" O PRO E 44 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP E 49 " --> pdb=" O SER E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 57 removed outlier: 3.510A pdb=" N SER E 56 " --> pdb=" O GLY E 53 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY E 57 " --> pdb=" O ARG E 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 57' Processing helix chain 'E' and resid 105 through 108 Processing helix chain 'E' and resid 120 through 127 removed outlier: 3.783A pdb=" N LEU E 124 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP E 125 " --> pdb=" O SER E 122 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE E 127 " --> pdb=" O LEU E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 261 Processing helix chain 'E' and resid 261 through 275 removed outlier: 4.049A pdb=" N SER E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 278 No H-bonds generated for 'chain 'E' and resid 276 through 278' Processing helix chain 'E' and resid 282 through 305 Processing helix chain 'E' and resid 315 through 344 Processing helix chain 'E' and resid 410 through 443 removed outlier: 3.908A pdb=" N ALA E 424 " --> pdb=" O THR E 420 " (cutoff:3.500A) Proline residue: E 427 - end of helix Processing helix chain 'E' and resid 444 through 449 Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 118 removed outlier: 4.273A pdb=" N LYS A 159 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ASP A 91 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER A 84 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ARG A 93 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE A 82 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASN A 95 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASN A 103 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN A 72 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 137 through 142 removed outlier: 6.567A pdb=" N THR A 169 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ALA A 140 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR A 167 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N PHE A 142 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ARG A 165 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ASP A 91 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER A 84 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ARG A 93 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE A 82 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASN A 95 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASN A 103 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN A 72 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 134 removed outlier: 5.266A pdb=" N THR A 242 " --> pdb=" O SER A 192 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU A 245 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY A 230 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU A 228 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 221 through 223 Processing sheet with id=AA5, first strand: chain 'B' and resid 116 through 118 removed outlier: 4.273A pdb=" N LYS B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP B 91 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER B 84 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ARG B 93 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N PHE B 82 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASN B 95 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASN B 103 " --> pdb=" O ASN B 72 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN B 72 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 137 through 142 removed outlier: 6.566A pdb=" N THR B 169 " --> pdb=" O LYS B 138 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ALA B 140 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR B 167 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N PHE B 142 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ARG B 165 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP B 91 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER B 84 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ARG B 93 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N PHE B 82 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASN B 95 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASN B 103 " --> pdb=" O ASN B 72 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN B 72 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 132 through 134 removed outlier: 5.266A pdb=" N THR B 242 " --> pdb=" O SER B 192 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU B 245 " --> pdb=" O GLY B 230 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY B 230 " --> pdb=" O GLU B 245 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU B 228 " --> pdb=" O LYS B 247 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 221 through 223 Processing sheet with id=AA9, first strand: chain 'C' and resid 116 through 118 removed outlier: 4.274A pdb=" N LYS C 159 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP C 91 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER C 84 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ARG C 93 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N PHE C 82 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASN C 95 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASN C 103 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASN C 72 " --> pdb=" O ASN C 103 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 137 through 142 removed outlier: 6.567A pdb=" N THR C 169 " --> pdb=" O LYS C 138 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ALA C 140 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR C 167 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N PHE C 142 " --> pdb=" O ARG C 165 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ARG C 165 " --> pdb=" O PHE C 142 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP C 91 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER C 84 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ARG C 93 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N PHE C 82 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASN C 95 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASN C 103 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASN C 72 " --> pdb=" O ASN C 103 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 132 through 134 removed outlier: 5.266A pdb=" N THR C 242 " --> pdb=" O SER C 192 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU C 245 " --> pdb=" O GLY C 230 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY C 230 " --> pdb=" O GLU C 245 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU C 228 " --> pdb=" O LYS C 247 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 221 through 223 Processing sheet with id=AB4, first strand: chain 'D' and resid 116 through 118 removed outlier: 4.274A pdb=" N LYS D 159 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ASP D 91 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER D 84 " --> pdb=" O ASP D 91 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ARG D 93 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE D 82 " --> pdb=" O ARG D 93 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASN D 95 " --> pdb=" O ASN D 80 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASN D 103 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN D 72 " --> pdb=" O ASN D 103 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 137 through 142 removed outlier: 6.567A pdb=" N THR D 169 " --> pdb=" O LYS D 138 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ALA D 140 " --> pdb=" O THR D 167 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR D 167 " --> pdb=" O ALA D 140 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N PHE D 142 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ARG D 165 " --> pdb=" O PHE D 142 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ASP D 91 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER D 84 " --> pdb=" O ASP D 91 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ARG D 93 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE D 82 " --> pdb=" O ARG D 93 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASN D 95 " --> pdb=" O ASN D 80 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASN D 103 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN D 72 " --> pdb=" O ASN D 103 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 132 through 134 removed outlier: 5.267A pdb=" N THR D 242 " --> pdb=" O SER D 192 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU D 245 " --> pdb=" O GLY D 230 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY D 230 " --> pdb=" O GLU D 245 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU D 228 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 221 through 223 Processing sheet with id=AB8, first strand: chain 'E' and resid 116 through 118 removed outlier: 4.274A pdb=" N LYS E 159 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP E 91 " --> pdb=" O SER E 84 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER E 84 " --> pdb=" O ASP E 91 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ARG E 93 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N PHE E 82 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASN E 95 " --> pdb=" O ASN E 80 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASN E 103 " --> pdb=" O ASN E 72 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN E 72 " --> pdb=" O ASN E 103 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 137 through 142 removed outlier: 6.568A pdb=" N THR E 169 " --> pdb=" O LYS E 138 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ALA E 140 " --> pdb=" O THR E 167 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR E 167 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N PHE E 142 " --> pdb=" O ARG E 165 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ARG E 165 " --> pdb=" O PHE E 142 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP E 91 " --> pdb=" O SER E 84 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER E 84 " --> pdb=" O ASP E 91 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ARG E 93 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N PHE E 82 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASN E 95 " --> pdb=" O ASN E 80 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASN E 103 " --> pdb=" O ASN E 72 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN E 72 " --> pdb=" O ASN E 103 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 132 through 134 removed outlier: 5.266A pdb=" N THR E 242 " --> pdb=" O SER E 192 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU E 245 " --> pdb=" O GLY E 230 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY E 230 " --> pdb=" O GLU E 245 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU E 228 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 221 through 223 820 hydrogen bonds defined for protein. 2400 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: 2.62 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2270 1.32 - 1.45: 4152 1.45 - 1.57: 8413 1.57 - 1.70: 0 1.70 - 1.82: 150 Bond restraints: 14985 Sorted by residual: bond pdb=" N ASP C 182 " pdb=" CA ASP C 182 " ideal model delta sigma weight residual 1.454 1.485 -0.032 1.23e-02 6.61e+03 6.75e+00 bond pdb=" N TYR E 441 " pdb=" CA TYR E 441 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.32e-02 5.74e+03 6.75e+00 bond pdb=" N TYR C 441 " pdb=" CA TYR C 441 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.32e-02 5.74e+03 6.70e+00 bond pdb=" N TYR A 441 " pdb=" CA TYR A 441 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.32e-02 5.74e+03 6.64e+00 bond pdb=" N TYR D 441 " pdb=" CA TYR D 441 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.32e-02 5.74e+03 6.64e+00 ... (remaining 14980 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 18490 1.13 - 2.26: 1265 2.26 - 3.39: 327 3.39 - 4.51: 62 4.51 - 5.64: 31 Bond angle restraints: 20175 Sorted by residual: angle pdb=" CA TRP E 438 " pdb=" C TRP E 438 " pdb=" O TRP E 438 " ideal model delta sigma weight residual 120.55 117.47 3.08 1.06e+00 8.90e-01 8.46e+00 angle pdb=" CA TRP B 438 " pdb=" C TRP B 438 " pdb=" O TRP B 438 " ideal model delta sigma weight residual 120.55 117.48 3.07 1.06e+00 8.90e-01 8.39e+00 angle pdb=" CA TRP D 438 " pdb=" C TRP D 438 " pdb=" O TRP D 438 " ideal model delta sigma weight residual 120.55 117.48 3.07 1.06e+00 8.90e-01 8.38e+00 angle pdb=" CA TRP C 438 " pdb=" C TRP C 438 " pdb=" O TRP C 438 " ideal model delta sigma weight residual 120.55 117.49 3.06 1.06e+00 8.90e-01 8.31e+00 angle pdb=" CA TRP A 438 " pdb=" C TRP A 438 " pdb=" O TRP A 438 " ideal model delta sigma weight residual 120.55 117.50 3.05 1.06e+00 8.90e-01 8.28e+00 ... (remaining 20170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.15: 7885 13.15 - 26.30: 825 26.30 - 39.45: 295 39.45 - 52.60: 80 52.60 - 65.75: 50 Dihedral angle restraints: 9135 sinusoidal: 4005 harmonic: 5130 Sorted by residual: dihedral pdb=" CA TYR C 231 " pdb=" C TYR C 231 " pdb=" N CYS C 232 " pdb=" CA CYS C 232 " ideal model delta harmonic sigma weight residual 180.00 156.90 23.10 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA TYR E 231 " pdb=" C TYR E 231 " pdb=" N CYS E 232 " pdb=" CA CYS E 232 " ideal model delta harmonic sigma weight residual 180.00 156.90 23.10 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA TYR D 231 " pdb=" C TYR D 231 " pdb=" N CYS D 232 " pdb=" CA CYS D 232 " ideal model delta harmonic sigma weight residual 180.00 156.91 23.09 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 9132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1202 0.027 - 0.053: 581 0.053 - 0.080: 234 0.080 - 0.107: 162 0.107 - 0.134: 71 Chirality restraints: 2250 Sorted by residual: chirality pdb=" CA TYR D 437 " pdb=" N TYR D 437 " pdb=" C TYR D 437 " pdb=" CB TYR D 437 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CA ILE B 278 " pdb=" N ILE B 278 " pdb=" C ILE B 278 " pdb=" CB ILE B 278 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA ILE C 278 " pdb=" N ILE C 278 " pdb=" C ILE C 278 " pdb=" CB ILE C 278 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 2247 not shown) Planarity restraints: 2495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 422 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.67e+00 pdb=" C SER C 422 " 0.051 2.00e-02 2.50e+03 pdb=" O SER C 422 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG C 423 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 422 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.66e+00 pdb=" C SER E 422 " -0.051 2.00e-02 2.50e+03 pdb=" O SER E 422 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG E 423 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 422 " -0.014 2.00e-02 2.50e+03 2.93e-02 8.57e+00 pdb=" C SER A 422 " 0.051 2.00e-02 2.50e+03 pdb=" O SER A 422 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG A 423 " -0.017 2.00e-02 2.50e+03 ... (remaining 2492 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4025 2.81 - 3.34: 12897 3.34 - 3.86: 24074 3.86 - 4.38: 29290 4.38 - 4.90: 50179 Nonbonded interactions: 120465 Sorted by model distance: nonbonded pdb=" OE1 GLU E 203 " pdb=" OH TYR E 231 " model vdw 2.293 3.040 nonbonded pdb=" OE1 GLU B 203 " pdb=" OH TYR B 231 " model vdw 2.293 3.040 nonbonded pdb=" OE1 GLU D 203 " pdb=" OH TYR D 231 " model vdw 2.293 3.040 nonbonded pdb=" OE1 GLU A 203 " pdb=" OH TYR A 231 " model vdw 2.293 3.040 nonbonded pdb=" OE1 GLU C 203 " pdb=" OH TYR C 231 " model vdw 2.293 3.040 ... (remaining 120460 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 42 through 450 or resid 503 or (resid 505 and (name C23 or \ name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 \ 0 or name C31 or name C32 or name O7 or name O8 )) or resid 506 through 507 or r \ esid 510)) selection = (chain 'B' and (resid 42 through 450 or resid 502 or (resid 504 and (name C23 or \ name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 \ 0 or name C31 or name C32 or name O7 or name O8 )) or resid 505 through 506 or r \ esid 509)) selection = (chain 'C' and (resid 42 through 450 or resid 502 or (resid 504 and (name C23 or \ name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 \ 0 or name C31 or name C32 or name O7 or name O8 )) or resid 505 through 506 or r \ esid 509)) selection = (chain 'D' and (resid 42 through 450 or resid 502 or (resid 504 and (name C23 or \ name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 \ 0 or name C31 or name C32 or name O7 or name O8 )) or resid 505 through 506 or r \ esid 509)) selection = (chain 'E' and (resid 42 through 450 or resid 503 or resid 505 through 507 or (r \ esid 508 and (name C23 or name C24 or name C25 or name C26 or name C27 or name C \ 28 or name C29 or name C30 or name C31 or name C32 or name O7 or name O8 )))) } 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: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 14.850 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 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:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 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 : 0.004 0.035 15005 Z= 0.245 Angle : 0.712 5.642 20225 Z= 0.425 Chirality : 0.045 0.134 2250 Planarity : 0.009 0.103 2485 Dihedral : 13.608 65.752 5775 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.19), residues: 1715 helix: 0.33 (0.19), residues: 605 sheet: -0.19 (0.24), residues: 405 loop : -0.44 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG B 445 TYR 0.014 0.002 TYR B 257 PHE 0.021 0.001 PHE D 327 TRP 0.009 0.001 TRP C 273 HIS 0.002 0.001 HIS E 446 Details of bonding type rmsd covalent geometry : bond 0.00380 (14985) covalent geometry : angle 0.69963 (20175) SS BOND : bond 0.00414 ( 10) SS BOND : angle 2.18329 ( 20) hydrogen bonds : bond 0.16664 ( 725) hydrogen bonds : angle 7.27755 ( 2400) link_NAG-ASN : bond 0.00847 ( 10) link_NAG-ASN : angle 3.13681 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8755 (tmmt) cc_final: 0.8456 (tttm) REVERT: A 111 GLU cc_start: 0.8528 (mp0) cc_final: 0.8261 (mp0) REVERT: A 177 LYS cc_start: 0.9096 (ttmm) cc_final: 0.8630 (ttpt) REVERT: A 207 ASP cc_start: 0.8517 (t70) cc_final: 0.8072 (p0) REVERT: A 251 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8110 (mt-10) REVERT: B 207 ASP cc_start: 0.8532 (t70) cc_final: 0.8075 (p0) REVERT: B 416 LYS cc_start: 0.8746 (mtpt) cc_final: 0.8390 (mttp) REVERT: C 116 SER cc_start: 0.8900 (p) cc_final: 0.8548 (t) REVERT: C 203 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8648 (mm-30) REVERT: C 207 ASP cc_start: 0.8419 (t70) cc_final: 0.8129 (p0) REVERT: C 416 LYS cc_start: 0.8690 (mtpt) cc_final: 0.8424 (mtpp) REVERT: D 116 SER cc_start: 0.8963 (p) cc_final: 0.8569 (t) REVERT: D 207 ASP cc_start: 0.8514 (t70) cc_final: 0.8109 (p0) REVERT: E 101 GLN cc_start: 0.8910 (mt0) cc_final: 0.8695 (mt0) REVERT: E 207 ASP cc_start: 0.8592 (t70) cc_final: 0.8269 (p0) REVERT: E 228 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7988 (mt-10) REVERT: E 416 LYS cc_start: 0.8681 (mtpt) cc_final: 0.8240 (mttm) outliers start: 0 outliers final: 3 residues processed: 295 average time/residue: 0.8184 time to fit residues: 258.5918 Evaluate side-chains 249 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 246 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain D residue 157 ASN Chi-restraints excluded: chain E residue 157 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN C 220 GLN C 300 GLN D 220 GLN D 300 GLN E 220 GLN E 300 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.103121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.074833 restraints weight = 20689.970| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 2.49 r_work: 0.2673 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15005 Z= 0.130 Angle : 0.580 5.408 20225 Z= 0.297 Chirality : 0.042 0.146 2250 Planarity : 0.004 0.033 2485 Dihedral : 9.640 56.912 2421 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.92 % Allowed : 8.43 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.20), residues: 1715 helix: 2.23 (0.20), residues: 605 sheet: 0.35 (0.25), residues: 400 loop : -0.15 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 417 TYR 0.018 0.001 TYR C 335 PHE 0.011 0.001 PHE A 134 TRP 0.011 0.001 TRP A 102 HIS 0.002 0.001 HIS C 235 Details of bonding type rmsd covalent geometry : bond 0.00272 (14985) covalent geometry : angle 0.56441 (20175) SS BOND : bond 0.00121 ( 10) SS BOND : angle 0.90445 ( 20) hydrogen bonds : bond 0.04730 ( 725) hydrogen bonds : angle 5.03576 ( 2400) link_NAG-ASN : bond 0.00749 ( 10) link_NAG-ASN : angle 3.48234 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 253 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8745 (tmmt) cc_final: 0.8476 (tttm) REVERT: A 111 GLU cc_start: 0.8631 (mp0) cc_final: 0.8295 (mp0) REVERT: A 116 SER cc_start: 0.8923 (p) cc_final: 0.8528 (t) REVERT: A 177 LYS cc_start: 0.9089 (ttmm) cc_final: 0.8514 (ttpt) REVERT: A 207 ASP cc_start: 0.8691 (t70) cc_final: 0.7995 (p0) REVERT: A 214 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8480 (mm-30) REVERT: A 225 GLU cc_start: 0.7960 (pm20) cc_final: 0.7716 (pm20) REVERT: A 251 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8549 (mt-10) REVERT: B 111 GLU cc_start: 0.8749 (mp0) cc_final: 0.8370 (mp0) REVERT: B 116 SER cc_start: 0.8895 (p) cc_final: 0.8443 (t) REVERT: B 207 ASP cc_start: 0.8749 (t70) cc_final: 0.8047 (p0) REVERT: B 214 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8602 (mm-30) REVERT: B 225 GLU cc_start: 0.8007 (pm20) cc_final: 0.7734 (pm20) REVERT: B 416 LYS cc_start: 0.8666 (mtpt) cc_final: 0.8458 (mtpp) REVERT: C 111 GLU cc_start: 0.8718 (mp0) cc_final: 0.8369 (mp0) REVERT: C 116 SER cc_start: 0.8824 (p) cc_final: 0.8432 (t) REVERT: C 207 ASP cc_start: 0.8691 (t70) cc_final: 0.8110 (p0) REVERT: C 225 GLU cc_start: 0.7969 (pm20) cc_final: 0.7669 (pm20) REVERT: C 416 LYS cc_start: 0.8583 (mtpt) cc_final: 0.8381 (mtpp) REVERT: D 116 SER cc_start: 0.8886 (p) cc_final: 0.8401 (t) REVERT: D 123 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.7699 (mpp) REVERT: D 207 ASP cc_start: 0.8684 (t70) cc_final: 0.8033 (p0) REVERT: D 343 ARG cc_start: 0.7394 (mtp-110) cc_final: 0.7057 (mtm-85) REVERT: E 50 LYS cc_start: 0.8707 (tttm) cc_final: 0.8478 (tttm) REVERT: E 101 GLN cc_start: 0.9182 (mt0) cc_final: 0.8973 (mt0) REVERT: E 111 GLU cc_start: 0.8523 (mp0) cc_final: 0.8271 (mp0) REVERT: E 116 SER cc_start: 0.8827 (p) cc_final: 0.8326 (t) REVERT: E 207 ASP cc_start: 0.8817 (t70) cc_final: 0.8209 (p0) REVERT: E 416 LYS cc_start: 0.8556 (mtpt) cc_final: 0.8108 (mttm) outliers start: 30 outliers final: 9 residues processed: 259 average time/residue: 0.8069 time to fit residues: 224.2035 Evaluate side-chains 245 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 235 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 181 MET Chi-restraints excluded: chain E residue 254 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/iotbx/cli_parser.py", line 995, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.2896 > 50: distance: 6 - 63: 9.823 distance: 17 - 66: 3.762 distance: 58 - 63: 6.249 distance: 63 - 64: 7.891 distance: 64 - 65: 16.281 distance: 64 - 67: 27.060 distance: 65 - 66: 14.591 distance: 65 - 72: 8.114 distance: 67 - 68: 27.957 distance: 68 - 69: 9.775 distance: 69 - 70: 4.063 distance: 72 - 73: 23.141 distance: 73 - 74: 21.444 distance: 73 - 76: 21.468 distance: 74 - 75: 11.549 distance: 74 - 79: 15.203 distance: 76 - 77: 24.325 distance: 76 - 78: 29.319 distance: 79 - 80: 24.209 distance: 80 - 81: 11.603 distance: 80 - 83: 23.687 distance: 81 - 82: 22.206 distance: 81 - 84: 16.373 distance: 84 - 85: 18.069 distance: 85 - 86: 22.381 distance: 85 - 88: 17.282 distance: 86 - 87: 17.451 distance: 86 - 93: 11.883 distance: 88 - 89: 31.943 distance: 89 - 90: 15.009 distance: 90 - 91: 19.492 distance: 90 - 92: 17.775 distance: 93 - 94: 14.974 distance: 94 - 95: 10.203 distance: 95 - 96: 20.582 distance: 95 - 97: 7.333 distance: 97 - 98: 18.703 distance: 98 - 99: 29.900 distance: 98 - 101: 28.845 distance: 99 - 100: 10.323 distance: 99 - 105: 17.710 distance: 101 - 102: 21.154 distance: 102 - 103: 9.243 distance: 102 - 104: 5.267 distance: 105 - 106: 35.349 distance: 106 - 107: 28.032 distance: 106 - 109: 20.799 distance: 107 - 108: 39.187 distance: 107 - 112: 53.290 distance: 109 - 110: 21.184 distance: 109 - 111: 28.395 distance: 112 - 113: 39.186 distance: 113 - 114: 26.649 distance: 113 - 116: 33.336 distance: 114 - 115: 8.650 distance: 114 - 120: 23.253 distance: 116 - 117: 25.110 distance: 117 - 118: 22.912 distance: 117 - 119: 23.317 distance: 120 - 121: 11.062 distance: 120 - 126: 21.653 distance: 121 - 122: 8.268 distance: 121 - 124: 16.627 distance: 122 - 123: 12.543 distance: 122 - 127: 3.938 distance: 124 - 125: 16.087 distance: 125 - 126: 25.599 distance: 127 - 128: 6.758 distance: 128 - 129: 3.871 distance: 128 - 131: 6.138 distance: 129 - 130: 11.448 distance: 129 - 136: 7.475 distance: 131 - 132: 11.003 distance: 132 - 133: 5.098