Starting phenix.real_space_refine on Sat Jul 4 10:32:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o4n_70108/07_2026/9o4n_70108.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o4n_70108/07_2026/9o4n_70108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o4n_70108/07_2026/9o4n_70108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o4n_70108/07_2026/9o4n_70108.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o4n_70108/07_2026/9o4n_70108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o4n_70108/07_2026/9o4n_70108.map" } resolution = 2.48 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= 0.009 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 Ca 9 9.91 5 S 116 5.16 5 C 12256 2.51 5 N 3288 2.21 5 O 3896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19565 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2980 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 364} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 963 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "L" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 852 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "B" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2980 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 364} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 963 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "I" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 852 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "C" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2980 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 364} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 963 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "J" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 852 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "D" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2980 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 364} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 963 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "K" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 852 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Time building chain proxies: 3.93, per 1000 atoms: 0.20 Number of scatterers: 19565 At special positions: 0 Unit cell: (144.275, 144.275, 99.325, 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) Ca 9 19.99 S 116 16.00 O 3896 8.00 N 3288 7.00 C 12256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.02 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.04 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 336 " distance=2.04 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.02 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.03 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.04 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 336 " distance=2.04 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 417 " distance=2.02 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.03 Simple disulfide: pdb=" SG CYS C 183 " - pdb=" SG CYS C 230 " distance=2.03 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 237 " distance=2.04 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 291 " distance=2.03 Simple disulfide: pdb=" SG CYS C 280 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 336 " distance=2.04 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 447 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.02 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.03 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 230 " distance=2.03 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 237 " distance=2.04 Simple disulfide: pdb=" SG CYS D 278 " - pdb=" SG CYS D 291 " distance=2.03 Simple disulfide: pdb=" SG CYS D 280 " - pdb=" SG CYS D 289 " distance=2.03 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 336 " distance=2.04 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 447 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 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 BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " BETA1-6 " NAG O 1 " - " FUC O 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG R 1 " - " FUC R 3 " " NAG U 1 " - " FUC U 3 " " NAG X 1 " - " FUC X 3 " NAG-ASN " NAG M 1 " - " ASN A 88 " " NAG N 1 " - " ASN A 234 " " NAG O 1 " - " ASN A 146 " " NAG P 1 " - " ASN B 88 " " NAG Q 1 " - " ASN B 234 " " NAG R 1 " - " ASN B 146 " " NAG S 1 " - " ASN C 88 " " NAG T 1 " - " ASN C 234 " " NAG U 1 " - " ASN C 146 " " NAG V 1 " - " ASN D 88 " " NAG W 1 " - " ASN D 234 " " NAG X 1 " - " ASN D 146 " Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 886.4 milliseconds 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4488 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 48 sheets defined 4.5% alpha, 42.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 104 through 110 Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 412A through 414 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'B' and resid 104 through 110 Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 412A through 414 Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'C' and resid 104 through 110 Processing helix chain 'C' and resid 142 through 146 Processing helix chain 'C' and resid 412A through 414 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'D' and resid 104 through 110 Processing helix chain 'D' and resid 142 through 146 Processing helix chain 'D' and resid 412A through 414 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 102 removed outlier: 6.532A pdb=" N SER A 445 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LYS A 102 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N SER A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.667A pdb=" N PHE A 115 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ALA A 138 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ILE A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLN A 136 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N SER A 160 " --> pdb=" O PHE A 173 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N PHE A 173 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 184 removed outlier: 3.582A pdb=" N VAL A 202 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TYR A 207 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ILE A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 224 Processing sheet with id=AA5, first strand: chain 'A' and resid 223 through 224 removed outlier: 3.610A pdb=" N LYS A 264 " --> pdb=" O ARG A 256 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU A 258 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 276 through 283 removed outlier: 5.497A pdb=" N GLU A 277 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ARG A 292 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 353 through 356 removed outlier: 6.390A pdb=" N ASN A 372 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLY A 399 " --> pdb=" O ASN A 372 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N PHE A 374 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 392 " --> pdb=" O TRP A 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.634A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.521A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.570A pdb=" N ASP L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU L 46 " --> pdb=" O LEU L 37 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.570A pdb=" N ASP L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 96 through 102 removed outlier: 6.532A pdb=" N SER B 445 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LYS B 102 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N SER B 443 " --> pdb=" O LYS B 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.667A pdb=" N PHE B 115 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ALA B 138 " --> pdb=" O PHE B 115 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ILE B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLN B 136 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N SER B 160 " --> pdb=" O PHE B 173 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N PHE B 173 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 179 through 184 removed outlier: 3.582A pdb=" N VAL B 202 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TYR B 207 " --> pdb=" O ILE B 211 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ILE B 211 " --> pdb=" O TYR B 207 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 223 through 224 Processing sheet with id=AB8, first strand: chain 'B' and resid 223 through 224 removed outlier: 3.610A pdb=" N LYS B 264 " --> pdb=" O ARG B 256 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU B 258 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE B 262 " --> pdb=" O GLU B 258 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 276 through 283 removed outlier: 5.497A pdb=" N GLU B 277 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ARG B 292 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 353 through 356 removed outlier: 6.390A pdb=" N ASN B 372 " --> pdb=" O GLY B 399 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLY B 399 " --> pdb=" O ASN B 372 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N PHE B 374 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B 392 " --> pdb=" O TRP B 378 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.634A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.521A pdb=" N ASP I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.570A pdb=" N ASP I 105 " --> pdb=" O LEU I 11 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU I 46 " --> pdb=" O LEU I 37 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.570A pdb=" N ASP I 105 " --> pdb=" O LEU I 11 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 96 through 102 removed outlier: 6.532A pdb=" N SER C 445 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LYS C 102 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N SER C 443 " --> pdb=" O LYS C 102 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 115 through 124 removed outlier: 4.667A pdb=" N PHE C 115 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ALA C 138 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ILE C 117 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLN C 136 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLU C 119 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU C 134 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N SER C 160 " --> pdb=" O PHE C 173 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N PHE C 173 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 179 through 184 removed outlier: 3.582A pdb=" N VAL C 202 " --> pdb=" O THR C 195 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TYR C 207 " --> pdb=" O ILE C 211 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ILE C 211 " --> pdb=" O TYR C 207 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 223 through 224 Processing sheet with id=AD2, first strand: chain 'C' and resid 223 through 224 removed outlier: 3.610A pdb=" N LYS C 264 " --> pdb=" O ARG C 256 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU C 258 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE C 262 " --> pdb=" O GLU C 258 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 276 through 283 removed outlier: 5.497A pdb=" N GLU C 277 " --> pdb=" O ARG C 292 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ARG C 292 " --> pdb=" O GLU C 277 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 353 through 356 removed outlier: 6.390A pdb=" N ASN C 372 " --> pdb=" O GLY C 399 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLY C 399 " --> pdb=" O ASN C 372 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N PHE C 374 " --> pdb=" O ILE C 397 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE C 392 " --> pdb=" O TRP C 378 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AD6, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.634A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.521A pdb=" N ASP J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.570A pdb=" N ASP J 105 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU J 46 " --> pdb=" O LEU J 37 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.570A pdb=" N ASP J 105 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR J 97 " --> pdb=" O GLN J 90 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 96 through 102 removed outlier: 6.532A pdb=" N SER D 445 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LYS D 102 " --> pdb=" O SER D 443 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N SER D 443 " --> pdb=" O LYS D 102 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 115 through 124 removed outlier: 4.667A pdb=" N PHE D 115 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ALA D 138 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ILE D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLN D 136 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N SER D 160 " --> pdb=" O PHE D 173 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N PHE D 173 " --> pdb=" O SER D 160 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 179 through 184 removed outlier: 3.582A pdb=" N VAL D 202 " --> pdb=" O THR D 195 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TYR D 207 " --> pdb=" O ILE D 211 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ILE D 211 " --> pdb=" O TYR D 207 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 223 through 224 Processing sheet with id=AE5, first strand: chain 'D' and resid 223 through 224 removed outlier: 3.610A pdb=" N LYS D 264 " --> pdb=" O ARG D 256 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU D 258 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE D 262 " --> pdb=" O GLU D 258 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 276 through 283 removed outlier: 5.497A pdb=" N GLU D 277 " --> pdb=" O ARG D 292 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ARG D 292 " --> pdb=" O GLU D 277 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 353 through 356 removed outlier: 6.390A pdb=" N ASN D 372 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLY D 399 " --> pdb=" O ASN D 372 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N PHE D 374 " --> pdb=" O ILE D 397 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE D 392 " --> pdb=" O TRP D 378 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AE9, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.634A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.521A pdb=" N ASP K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.570A pdb=" N ASP K 105 " --> pdb=" O LEU K 11 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU K 46 " --> pdb=" O LEU K 37 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.570A pdb=" N ASP K 105 " --> pdb=" O LEU K 11 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR K 97 " --> pdb=" O GLN K 90 " (cutoff:3.500A) 720 hydrogen bonds defined for protein. 1812 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: 4.45 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6296 1.34 - 1.47: 5184 1.47 - 1.59: 8412 1.59 - 1.71: 0 1.71 - 1.83: 152 Bond restraints: 20044 Sorted by residual: bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" C1 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" C1 NAG V 1 " pdb=" O5 NAG V 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" N GLU J 1 " pdb=" CA GLU J 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 ... (remaining 20039 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 26264 2.08 - 4.17: 848 4.17 - 6.25: 128 6.25 - 8.33: 20 8.33 - 10.41: 8 Bond angle restraints: 27268 Sorted by residual: angle pdb=" N LEU D 464 " pdb=" CA LEU D 464 " pdb=" C LEU D 464 " ideal model delta sigma weight residual 109.81 120.22 -10.41 2.21e+00 2.05e-01 2.22e+01 angle pdb=" N LEU B 464 " pdb=" CA LEU B 464 " pdb=" C LEU B 464 " ideal model delta sigma weight residual 109.81 120.22 -10.41 2.21e+00 2.05e-01 2.22e+01 angle pdb=" N LEU C 464 " pdb=" CA LEU C 464 " pdb=" C LEU C 464 " ideal model delta sigma weight residual 109.81 120.22 -10.41 2.21e+00 2.05e-01 2.22e+01 angle pdb=" N LEU A 464 " pdb=" CA LEU A 464 " pdb=" C LEU A 464 " ideal model delta sigma weight residual 109.81 120.22 -10.41 2.21e+00 2.05e-01 2.22e+01 angle pdb=" N GLY A 339 " pdb=" CA GLY A 339 " pdb=" C GLY A 339 " ideal model delta sigma weight residual 112.34 103.97 8.37 2.04e+00 2.40e-01 1.68e+01 ... (remaining 27263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 11204 17.69 - 35.38: 776 35.38 - 53.07: 164 53.07 - 70.76: 36 70.76 - 88.45: 20 Dihedral angle restraints: 12200 sinusoidal: 5132 harmonic: 7068 Sorted by residual: dihedral pdb=" CD ARG D 256 " pdb=" NE ARG D 256 " pdb=" CZ ARG D 256 " pdb=" NH1 ARG D 256 " ideal model delta sinusoidal sigma weight residual 0.00 50.05 -50.05 1 1.00e+01 1.00e-02 3.44e+01 dihedral pdb=" CD ARG B 256 " pdb=" NE ARG B 256 " pdb=" CZ ARG B 256 " pdb=" NH1 ARG B 256 " ideal model delta sinusoidal sigma weight residual 0.00 50.05 -50.05 1 1.00e+01 1.00e-02 3.44e+01 dihedral pdb=" CD ARG A 256 " pdb=" NE ARG A 256 " pdb=" CZ ARG A 256 " pdb=" NH1 ARG A 256 " ideal model delta sinusoidal sigma weight residual 0.00 50.05 -50.05 1 1.00e+01 1.00e-02 3.44e+01 ... (remaining 12197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2536 0.074 - 0.148: 460 0.148 - 0.222: 16 0.222 - 0.296: 0 0.296 - 0.370: 4 Chirality restraints: 3016 Sorted by residual: chirality pdb=" CA LEU A 464 " pdb=" N LEU A 464 " pdb=" C LEU A 464 " pdb=" CB LEU A 464 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CA LEU D 464 " pdb=" N LEU D 464 " pdb=" C LEU D 464 " pdb=" CB LEU D 464 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CA LEU B 464 " pdb=" N LEU B 464 " pdb=" C LEU B 464 " pdb=" CB LEU B 464 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.43e+00 ... (remaining 3013 not shown) Planarity restraints: 3520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 256 " -0.690 9.50e-02 1.11e+02 3.11e-01 6.71e+01 pdb=" NE ARG B 256 " 0.059 2.00e-02 2.50e+03 pdb=" CZ ARG B 256 " -0.043 2.00e-02 2.50e+03 pdb=" NH1 ARG B 256 " 0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG B 256 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 256 " -0.690 9.50e-02 1.11e+02 3.11e-01 6.71e+01 pdb=" NE ARG C 256 " 0.059 2.00e-02 2.50e+03 pdb=" CZ ARG C 256 " -0.043 2.00e-02 2.50e+03 pdb=" NH1 ARG C 256 " 0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG C 256 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 256 " 0.690 9.50e-02 1.11e+02 3.11e-01 6.71e+01 pdb=" NE ARG D 256 " -0.059 2.00e-02 2.50e+03 pdb=" CZ ARG D 256 " 0.043 2.00e-02 2.50e+03 pdb=" NH1 ARG D 256 " -0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG D 256 " 0.004 2.00e-02 2.50e+03 ... (remaining 3517 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4240 2.79 - 3.32: 18040 3.32 - 3.84: 34404 3.84 - 4.37: 43668 4.37 - 4.90: 74128 Nonbonded interactions: 174480 Sorted by model distance: nonbonded pdb=" OG SER F 31 " pdb=" OD1 ASN F 98 " model vdw 2.260 3.040 nonbonded pdb=" OG SER E 31 " pdb=" OD1 ASN E 98 " model vdw 2.260 3.040 nonbonded pdb=" OG SER H 31 " pdb=" OD1 ASN H 98 " model vdw 2.260 3.040 nonbonded pdb=" OG SER G 31 " pdb=" OD1 ASN G 98 " model vdw 2.260 3.040 nonbonded pdb=" OD1 ASP C 379 " pdb="CA CA C 502 " model vdw 2.270 3.250 ... (remaining 174475 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 83 through 502) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'X' } 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: 13.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 19.190 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 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:8.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 20112 Z= 0.213 Angle : 0.887 10.413 27432 Z= 0.457 Chirality : 0.056 0.370 3016 Planarity : 0.013 0.311 3508 Dihedral : 13.099 88.447 7592 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 0.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.38 % Allowed : 1.13 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.55 (0.16), residues: 2472 helix: -1.70 (1.03), residues: 24 sheet: 1.07 (0.16), residues: 988 loop : -0.05 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.051 0.003 ARG A 256 TYR 0.035 0.002 TYR C 252 PHE 0.030 0.004 PHE C 410 TRP 0.009 0.001 TRP B 302 HIS 0.007 0.002 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.21 (20044) covalent geometry : angle 0.87298 / 0.45 (27268) SS BOND : bond 0.00550 / 0.36 ( 40) SS BOND : angle 1.93438 / 1.23 ( 80) hydrogen bonds : bond 0.20487 / 13.55 ( 688) hydrogen bonds : angle 9.45657 / 6.53 ( 1812) link_BETA1-4 : bond 0.00216 / 0.14 ( 12) link_BETA1-4 : angle 2.55673 / 1.54 ( 36) link_BETA1-6 : bond 0.00274 / 0.13 ( 4) link_BETA1-6 : angle 1.41520 / 0.79 ( 12) link_NAG-ASN : bond 0.00290 / 0.20 ( 12) link_NAG-ASN : angle 2.56429 / 1.59 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 336 time to evaluate : 0.514 Fit side-chains REVERT: H 10 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8056 (mm-30) REVERT: H 72 ASP cc_start: 0.7262 (t0) cc_final: 0.6807 (t0) REVERT: L 103 LYS cc_start: 0.8690 (tttp) cc_final: 0.8483 (tttp) REVERT: E 10 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8055 (mm-30) REVERT: E 72 ASP cc_start: 0.7262 (t0) cc_final: 0.6807 (t0) REVERT: I 103 LYS cc_start: 0.8690 (tttp) cc_final: 0.8483 (tttp) REVERT: F 10 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8055 (mm-30) REVERT: F 72 ASP cc_start: 0.7261 (t0) cc_final: 0.6807 (t0) REVERT: J 103 LYS cc_start: 0.8692 (tttp) cc_final: 0.8484 (tttp) REVERT: G 10 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8054 (mm-30) REVERT: G 72 ASP cc_start: 0.7261 (t0) cc_final: 0.6807 (t0) REVERT: K 103 LYS cc_start: 0.8691 (tttp) cc_final: 0.8484 (tttp) outliers start: 8 outliers final: 4 residues processed: 344 average time/residue: 0.5925 time to fit residues: 229.8164 Evaluate side-chains 280 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 276 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain D residue 324 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.0770 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 3.9990 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN A 296 HIS H 61 GLN B 226 GLN B 296 HIS E 61 GLN C 226 GLN C 296 HIS F 61 GLN D 226 GLN D 296 HIS D 372 ASN G 61 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.088732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.070171 restraints weight = 32620.013| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 2.28 r_work: 0.2771 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9060 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20112 Z= 0.161 Angle : 0.637 7.493 27432 Z= 0.333 Chirality : 0.048 0.195 3016 Planarity : 0.005 0.049 3508 Dihedral : 6.839 50.460 3276 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.31 % Allowed : 7.88 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.67 (0.17), residues: 2472 helix: -0.72 (0.88), residues: 24 sheet: 0.98 (0.16), residues: 980 loop : 0.17 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 24 TYR 0.015 0.001 TYR D 252 PHE 0.021 0.002 PHE A 410 TRP 0.016 0.001 TRP A 178 HIS 0.002 0.001 HIS A 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (20044) covalent geometry : angle 0.62278 / 0.33 (27268) SS BOND : bond 0.00287 / 0.17 ( 40) SS BOND : angle 1.68069 / 1.04 ( 80) hydrogen bonds : bond 0.04695 / 3.10 ( 688) hydrogen bonds : angle 6.78766 / 4.68 ( 1812) link_BETA1-4 : bond 0.00431 / 0.26 ( 12) link_BETA1-4 : angle 1.83221 / 1.12 ( 36) link_BETA1-6 : bond 0.00195 / 0.09 ( 4) link_BETA1-6 : angle 1.29225 / 0.73 ( 12) link_NAG-ASN : bond 0.00210 / 0.13 ( 12) link_NAG-ASN : angle 2.25853 / 1.41 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 260 time to evaluate : 0.532 Fit side-chains REVERT: A 324 ASP cc_start: 0.8535 (OUTLIER) cc_final: 0.8288 (t0) REVERT: L 24 ARG cc_start: 0.8273 (ttm110) cc_final: 0.7993 (ttm-80) REVERT: B 324 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.8294 (t0) REVERT: I 24 ARG cc_start: 0.8278 (ttm110) cc_final: 0.8000 (ttm-80) REVERT: C 324 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.8290 (t0) REVERT: J 24 ARG cc_start: 0.8277 (ttm110) cc_final: 0.7998 (ttm-80) REVERT: D 324 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8283 (t0) REVERT: K 24 ARG cc_start: 0.8266 (ttm110) cc_final: 0.7985 (ttm-80) outliers start: 28 outliers final: 8 residues processed: 276 average time/residue: 0.5540 time to fit residues: 171.9463 Evaluate side-chains 252 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 240 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain C residue 296 HIS Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain G residue 19 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 53 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 223 optimal weight: 6.9990 chunk 200 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 HIS A 450 ASN H 61 GLN B 184 HIS B 450 ASN E 61 GLN C 184 HIS C 450 ASN F 61 GLN D 184 HIS D 450 ASN G 61 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.082438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.062332 restraints weight = 32834.055| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 2.36 r_work: 0.2646 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9115 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 20112 Z= 0.326 Angle : 0.683 13.967 27432 Z= 0.351 Chirality : 0.051 0.220 3016 Planarity : 0.005 0.043 3508 Dihedral : 6.804 52.793 3276 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.44 % Allowed : 8.07 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.45 (0.17), residues: 2472 helix: -0.22 (0.89), residues: 24 sheet: 0.69 (0.16), residues: 952 loop : 0.13 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 24 TYR 0.015 0.002 TYR D 252 PHE 0.021 0.002 PHE D 121 TRP 0.018 0.002 TRP B 178 HIS 0.009 0.002 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00753 / 0.33 (20044) covalent geometry : angle 0.66824 / 0.35 (27268) SS BOND : bond 0.00450 / 0.28 ( 40) SS BOND : angle 1.77840 / 1.12 ( 80) hydrogen bonds : bond 0.04617 / 3.04 ( 688) hydrogen bonds : angle 6.50591 / 4.50 ( 1812) link_BETA1-4 : bond 0.00398 / 0.26 ( 12) link_BETA1-4 : angle 1.86968 / 1.14 ( 36) link_BETA1-6 : bond 0.00013 / 0.01 ( 4) link_BETA1-6 : angle 1.40378 / 0.77 ( 12) link_NAG-ASN : bond 0.00318 / 0.22 ( 12) link_NAG-ASN : angle 2.41272 / 1.53 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 244 time to evaluate : 0.777 Fit side-chains REVERT: A 324 ASP cc_start: 0.8922 (OUTLIER) cc_final: 0.8619 (t0) REVERT: H 72 ASP cc_start: 0.7554 (t0) cc_final: 0.7153 (t0) REVERT: H 81 ASP cc_start: 0.9081 (t70) cc_final: 0.8679 (t70) REVERT: L 17 GLU cc_start: 0.8026 (pm20) cc_final: 0.7787 (pm20) REVERT: L 24 ARG cc_start: 0.8302 (ttm110) cc_final: 0.8003 (ttm-80) REVERT: B 324 ASP cc_start: 0.8924 (OUTLIER) cc_final: 0.8616 (t0) REVERT: E 72 ASP cc_start: 0.7562 (t0) cc_final: 0.7162 (t0) REVERT: E 81 ASP cc_start: 0.9083 (t70) cc_final: 0.8684 (t70) REVERT: I 17 GLU cc_start: 0.8024 (pm20) cc_final: 0.7783 (pm20) REVERT: I 24 ARG cc_start: 0.8322 (ttm110) cc_final: 0.8025 (ttm-80) REVERT: C 324 ASP cc_start: 0.8921 (OUTLIER) cc_final: 0.8614 (t0) REVERT: F 72 ASP cc_start: 0.7562 (t0) cc_final: 0.7162 (t0) REVERT: F 81 ASP cc_start: 0.9082 (t70) cc_final: 0.8680 (t70) REVERT: J 17 GLU cc_start: 0.8021 (pm20) cc_final: 0.7778 (pm20) REVERT: J 24 ARG cc_start: 0.8307 (ttm110) cc_final: 0.8008 (ttm-80) REVERT: D 324 ASP cc_start: 0.8918 (OUTLIER) cc_final: 0.8608 (t0) REVERT: G 72 ASP cc_start: 0.7555 (t0) cc_final: 0.7153 (t0) REVERT: G 81 ASP cc_start: 0.9083 (t70) cc_final: 0.8683 (t70) REVERT: K 17 GLU cc_start: 0.8015 (pm20) cc_final: 0.7773 (pm20) REVERT: K 24 ARG cc_start: 0.8304 (ttm110) cc_final: 0.8005 (ttm-80) outliers start: 52 outliers final: 16 residues processed: 272 average time/residue: 0.7423 time to fit residues: 224.4419 Evaluate side-chains 260 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 240 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain L residue 45 GLN Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain I residue 45 GLN Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain J residue 45 GLN Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain G residue 19 LYS Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain K residue 45 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 148 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 201 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 chunk 241 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN H 61 GLN B 226 GLN E 61 GLN C 226 GLN F 61 GLN D 226 GLN G 61 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.084545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.064679 restraints weight = 32685.086| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 2.36 r_work: 0.2696 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9083 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20112 Z= 0.166 Angle : 0.611 11.714 27432 Z= 0.311 Chirality : 0.047 0.220 3016 Planarity : 0.004 0.039 3508 Dihedral : 6.429 48.921 3276 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.50 % Allowed : 9.38 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.37 (0.17), residues: 2472 helix: -1.14 (0.71), residues: 24 sheet: 0.59 (0.16), residues: 944 loop : 0.14 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 77 TYR 0.012 0.001 TYR D 252 PHE 0.015 0.002 PHE B 121 TRP 0.015 0.001 TRP D 178 HIS 0.005 0.001 HIS D 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (20044) covalent geometry : angle 0.59556 / 0.31 (27268) SS BOND : bond 0.00329 / 0.21 ( 40) SS BOND : angle 1.72149 / 1.07 ( 80) hydrogen bonds : bond 0.03725 / 2.45 ( 688) hydrogen bonds : angle 6.21505 / 4.30 ( 1812) link_BETA1-4 : bond 0.00367 / 0.23 ( 12) link_BETA1-4 : angle 1.86652 / 1.13 ( 36) link_BETA1-6 : bond 0.00116 / 0.05 ( 4) link_BETA1-6 : angle 1.34198 / 0.73 ( 12) link_NAG-ASN : bond 0.00246 / 0.17 ( 12) link_NAG-ASN : angle 2.28571 / 1.43 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 248 time to evaluate : 0.773 Fit side-chains REVERT: A 324 ASP cc_start: 0.8756 (OUTLIER) cc_final: 0.8401 (t0) REVERT: H 72 ASP cc_start: 0.7488 (t0) cc_final: 0.7101 (t0) REVERT: H 81 ASP cc_start: 0.9060 (t70) cc_final: 0.8664 (t70) REVERT: L 17 GLU cc_start: 0.8096 (pm20) cc_final: 0.7799 (pm20) REVERT: L 24 ARG cc_start: 0.8304 (ttm110) cc_final: 0.7986 (ttm-80) REVERT: L 70 ASP cc_start: 0.8120 (m-30) cc_final: 0.7599 (m-30) REVERT: B 324 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8402 (t0) REVERT: E 72 ASP cc_start: 0.7506 (t0) cc_final: 0.7119 (t0) REVERT: E 81 ASP cc_start: 0.9055 (t70) cc_final: 0.8655 (t70) REVERT: I 17 GLU cc_start: 0.8094 (pm20) cc_final: 0.7798 (pm20) REVERT: I 24 ARG cc_start: 0.8296 (ttm110) cc_final: 0.7978 (ttm-80) REVERT: I 70 ASP cc_start: 0.8113 (m-30) cc_final: 0.7594 (m-30) REVERT: C 324 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8401 (t0) REVERT: F 72 ASP cc_start: 0.7503 (t0) cc_final: 0.7117 (t0) REVERT: F 81 ASP cc_start: 0.9066 (t70) cc_final: 0.8671 (t70) REVERT: J 17 GLU cc_start: 0.8097 (pm20) cc_final: 0.7799 (pm20) REVERT: J 24 ARG cc_start: 0.8291 (ttm110) cc_final: 0.7974 (ttm-80) REVERT: J 70 ASP cc_start: 0.8117 (m-30) cc_final: 0.7597 (m-30) REVERT: D 324 ASP cc_start: 0.8752 (OUTLIER) cc_final: 0.8399 (t0) REVERT: G 72 ASP cc_start: 0.7498 (t0) cc_final: 0.7113 (t0) REVERT: G 81 ASP cc_start: 0.9055 (t70) cc_final: 0.8658 (t70) REVERT: K 17 GLU cc_start: 0.8097 (pm20) cc_final: 0.7799 (pm20) REVERT: K 24 ARG cc_start: 0.8294 (ttm110) cc_final: 0.7977 (ttm-80) REVERT: K 70 ASP cc_start: 0.8134 (m-30) cc_final: 0.7616 (m-30) outliers start: 32 outliers final: 8 residues processed: 264 average time/residue: 0.6892 time to fit residues: 203.5507 Evaluate side-chains 248 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 236 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain G residue 19 LYS Chi-restraints excluded: chain G residue 100 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.7613 > 50: distance: 97 - 255: 7.599 distance: 124 - 264: 26.056 distance: 127 - 261: 17.532 distance: 135 - 248: 23.230 distance: 138 - 245: 28.771 distance: 165 - 213: 16.431 distance: 187 - 192: 27.079 distance: 192 - 193: 39.158 distance: 192 - 198: 34.882 distance: 193 - 194: 24.963 distance: 193 - 196: 26.514 distance: 194 - 195: 32.021 distance: 194 - 199: 25.900 distance: 196 - 197: 12.145 distance: 197 - 198: 19.893 distance: 199 - 200: 6.295 distance: 200 - 201: 26.380 distance: 200 - 203: 30.931 distance: 201 - 202: 19.500 distance: 201 - 210: 25.016 distance: 204 - 205: 22.087 distance: 205 - 206: 12.496 distance: 206 - 207: 18.889 distance: 207 - 208: 18.325 distance: 207 - 209: 10.398 distance: 210 - 211: 16.237 distance: 211 - 212: 19.714 distance: 211 - 214: 8.063 distance: 212 - 213: 28.290 distance: 212 - 217: 18.381 distance: 214 - 215: 22.362 distance: 214 - 216: 17.575 distance: 217 - 218: 17.932 distance: 218 - 219: 9.885 distance: 218 - 221: 18.852 distance: 219 - 220: 31.625 distance: 219 - 228: 20.768 distance: 221 - 222: 6.589 distance: 222 - 223: 14.316 distance: 222 - 224: 18.071 distance: 223 - 225: 18.924 distance: 224 - 226: 25.255 distance: 225 - 227: 19.122 distance: 226 - 227: 11.323 distance: 228 - 229: 9.469 distance: 229 - 230: 26.110 distance: 230 - 231: 17.127 distance: 230 - 232: 17.343 distance: 232 - 233: 14.486 distance: 233 - 234: 13.482 distance: 233 - 236: 20.594 distance: 234 - 235: 10.480 distance: 234 - 241: 21.827 distance: 236 - 237: 16.854 distance: 237 - 238: 9.853 distance: 238 - 239: 6.033 distance: 238 - 240: 6.373 distance: 241 - 242: 16.645 distance: 242 - 243: 33.725 distance: 243 - 244: 47.285 distance: 243 - 245: 28.185 distance: 245 - 246: 23.771 distance: 246 - 247: 10.418 distance: 246 - 249: 28.209 distance: 247 - 248: 25.733 distance: 247 - 252: 15.264 distance: 249 - 250: 4.807 distance: 249 - 251: 8.018 distance: 252 - 253: 6.829 distance: 253 - 254: 25.559 distance: 253 - 256: 25.672 distance: 254 - 255: 5.223 distance: 254 - 261: 23.336 distance: 256 - 257: 12.120 distance: 257 - 258: 9.861 distance: 258 - 259: 8.863 distance: 259 - 260: 8.060 distance: 261 - 262: 31.600 distance: 262 - 263: 27.034 distance: 262 - 265: 22.764 distance: 263 - 264: 24.458 distance: 263 - 268: 16.598 distance: 265 - 266: 25.383 distance: 265 - 267: 18.567