Starting phenix.real_space_refine on Sat Aug 23 10:30:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bto_44894/08_2025/9bto_44894.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bto_44894/08_2025/9bto_44894.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bto_44894/08_2025/9bto_44894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bto_44894/08_2025/9bto_44894.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bto_44894/08_2025/9bto_44894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bto_44894/08_2025/9bto_44894.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.008 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 60 5.16 5 C 7170 2.51 5 N 1965 2.21 5 O 2325 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11520 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2517 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 306} Chain: "B" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1122 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 1, 'TRANS': 145} Chain: "C" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2517 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 306} Chain: "D" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1122 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 1, 'TRANS': 145} Chain: "E" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2517 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 306} Chain: "F" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1122 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 1, 'TRANS': 145} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "J" 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: "K" 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: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "O" 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "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: 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: "A" 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: "C" 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: "E" 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 Time building chain proxies: 3.25, per 1000 atoms: 0.28 Number of scatterers: 11520 At special positions: 0 Unit cell: (90.468, 93.34, 140.01, 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 60 16.00 O 2325 8.00 N 1965 7.00 C 7170 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 57 " distance=2.05 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 72 " distance=2.03 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 143 " distance=2.02 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 294 " - pdb=" SG CYS A 320 " distance=2.02 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 57 " distance=2.05 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 72 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 143 " distance=2.02 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 274 " distance=2.03 Simple disulfide: pdb=" SG CYS C 294 " - pdb=" SG CYS C 320 " distance=2.02 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 57 " distance=2.05 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 94 " - pdb=" SG CYS E 143 " distance=2.02 Simple disulfide: pdb=" SG CYS E 180 " - pdb=" SG CYS E 274 " distance=2.03 Simple disulfide: pdb=" SG CYS E 294 " - pdb=" SG CYS E 320 " distance=2.02 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " 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 BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A 401 " - " ASN A 59 " " NAG A 402 " - " ASN A 232 " " NAG C 401 " - " ASN C 59 " " NAG C 402 " - " ASN C 232 " " NAG E 401 " - " ASN E 59 " " NAG E 402 " - " ASN E 232 " " NAG G 1 " - " ASN A 145 " " NAG H 1 " - " ASN A 196 " " NAG I 1 " - " ASN A 303 " " NAG J 1 " - " ASN A 25 " " NAG K 1 " - " ASN A 332 " " NAG L 1 " - " ASN C 145 " " NAG M 1 " - " ASN C 196 " " NAG N 1 " - " ASN C 303 " " NAG O 1 " - " ASN C 25 " " NAG P 1 " - " ASN C 332 " " NAG Q 1 " - " ASN E 145 " " NAG R 1 " - " ASN E 196 " " NAG S 1 " - " ASN E 303 " " NAG T 1 " - " ASN E 25 " " NAG U 1 " - " ASN E 332 " Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 534.0 milliseconds Enol-peptide restraints added in 1.4 microseconds 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2592 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 30 sheets defined 24.2% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 61 through 67 Processing helix chain 'A' and resid 98 through 102 Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 106 through 112 Processing helix chain 'A' and resid 196 through 204 Processing helix chain 'B' and resid 37 through 57 Processing helix chain 'B' and resid 74 through 109 Processing helix chain 'B' and resid 110 through 127 Processing helix chain 'B' and resid 145 through 154 Processing helix chain 'C' and resid 61 through 67 Processing helix chain 'C' and resid 98 through 102 Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 106 through 112 Processing helix chain 'C' and resid 196 through 204 Processing helix chain 'D' and resid 37 through 57 Processing helix chain 'D' and resid 74 through 109 Processing helix chain 'D' and resid 110 through 127 Processing helix chain 'D' and resid 145 through 154 Processing helix chain 'E' and resid 61 through 67 Processing helix chain 'E' and resid 98 through 102 Processing helix chain 'E' and resid 103 through 105 No H-bonds generated for 'chain 'E' and resid 103 through 105' Processing helix chain 'E' and resid 106 through 112 Processing helix chain 'E' and resid 196 through 204 Processing helix chain 'F' and resid 37 through 57 Processing helix chain 'F' and resid 74 through 109 Processing helix chain 'F' and resid 110 through 127 Processing helix chain 'F' and resid 145 through 154 Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 18 removed outlier: 3.876A pdb=" N GLY A 22 " --> pdb=" O THR A 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 removed outlier: 6.113A pdb=" N ASN A 43 " --> pdb=" O ALA A 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 49 through 50 Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 119 removed outlier: 7.584A pdb=" N VAL A 189 " --> pdb=" O PRO A 269 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE A 266 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N TRP A 158 " --> pdb=" O GLY A 138 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 116 through 119 Processing sheet with id=AA8, first strand: chain 'A' and resid 140 through 144 removed outlier: 4.951A pdb=" N CYS A 143 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 172 through 176 Processing sheet with id=AB1, first strand: chain 'A' and resid 300 through 302 Processing sheet with id=AB2, first strand: chain 'C' and resid 14 through 18 removed outlier: 3.876A pdb=" N GLY C 22 " --> pdb=" O THR C 18 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AB4, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AB5, first strand: chain 'C' and resid 43 through 44 removed outlier: 6.113A pdb=" N ASN C 43 " --> pdb=" O ALA C 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 49 through 50 Processing sheet with id=AB7, first strand: chain 'C' and resid 116 through 119 removed outlier: 7.582A pdb=" N VAL C 189 " --> pdb=" O PRO C 269 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE C 266 " --> pdb=" O ALA C 159 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N TRP C 158 " --> pdb=" O GLY C 138 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 116 through 119 Processing sheet with id=AB9, first strand: chain 'C' and resid 140 through 144 removed outlier: 4.951A pdb=" N CYS C 143 " --> pdb=" O GLY C 151 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 172 through 176 Processing sheet with id=AC2, first strand: chain 'C' and resid 300 through 302 Processing sheet with id=AC3, first strand: chain 'E' and resid 14 through 18 removed outlier: 3.876A pdb=" N GLY E 22 " --> pdb=" O THR E 18 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 29 through 31 Processing sheet with id=AC5, first strand: chain 'E' and resid 33 through 34 Processing sheet with id=AC6, first strand: chain 'E' and resid 43 through 44 removed outlier: 6.113A pdb=" N ASN E 43 " --> pdb=" O ALA E 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 49 through 50 Processing sheet with id=AC8, first strand: chain 'E' and resid 116 through 119 removed outlier: 7.583A pdb=" N VAL E 189 " --> pdb=" O PRO E 269 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE E 266 " --> pdb=" O ALA E 159 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N TRP E 158 " --> pdb=" O GLY E 138 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 116 through 119 Processing sheet with id=AD1, first strand: chain 'E' and resid 140 through 144 removed outlier: 4.951A pdb=" N CYS E 143 " --> pdb=" O GLY E 151 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 172 through 176 Processing sheet with id=AD3, first strand: chain 'E' and resid 300 through 302 459 hydrogen bonds defined for protein. 1242 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: 1.93 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 3223 1.33 - 1.47: 3353 1.47 - 1.61: 5082 1.61 - 1.74: 3 1.74 - 1.88: 78 Bond restraints: 11739 Sorted by residual: bond pdb=" CB HIS B 22 " pdb=" CG HIS B 22 " ideal model delta sigma weight residual 1.497 1.400 0.097 1.40e-02 5.10e+03 4.84e+01 bond pdb=" CB HIS F 22 " pdb=" CG HIS F 22 " ideal model delta sigma weight residual 1.497 1.400 0.097 1.40e-02 5.10e+03 4.78e+01 bond pdb=" CB HIS D 22 " pdb=" CG HIS D 22 " ideal model delta sigma weight residual 1.497 1.400 0.097 1.40e-02 5.10e+03 4.77e+01 bond pdb=" CB LEU C 330 " pdb=" CG LEU C 330 " ideal model delta sigma weight residual 1.530 1.398 0.132 2.00e-02 2.50e+03 4.36e+01 bond pdb=" CB HIS E 296 " pdb=" CG HIS E 296 " ideal model delta sigma weight residual 1.497 1.405 0.092 1.40e-02 5.10e+03 4.35e+01 ... (remaining 11734 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 12452 1.92 - 3.84: 2780 3.84 - 5.75: 556 5.75 - 7.67: 101 7.67 - 9.59: 26 Bond angle restraints: 15915 Sorted by residual: angle pdb=" CA ASP F 90 " pdb=" CB ASP F 90 " pdb=" CG ASP F 90 " ideal model delta sigma weight residual 112.60 120.90 -8.30 1.00e+00 1.00e+00 6.89e+01 angle pdb=" CA ASP D 90 " pdb=" CB ASP D 90 " pdb=" CG ASP D 90 " ideal model delta sigma weight residual 112.60 120.89 -8.29 1.00e+00 1.00e+00 6.87e+01 angle pdb=" CA ASP B 90 " pdb=" CB ASP B 90 " pdb=" CG ASP B 90 " ideal model delta sigma weight residual 112.60 120.88 -8.28 1.00e+00 1.00e+00 6.85e+01 angle pdb=" C PHE A 230 " pdb=" N PRO A 231 " pdb=" CA PRO A 231 " ideal model delta sigma weight residual 119.92 127.20 -7.28 1.07e+00 8.73e-01 4.63e+01 angle pdb=" C PHE E 230 " pdb=" N PRO E 231 " pdb=" CA PRO E 231 " ideal model delta sigma weight residual 119.92 127.18 -7.26 1.07e+00 8.73e-01 4.60e+01 ... (remaining 15910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.09: 7377 21.09 - 42.19: 165 42.19 - 63.28: 54 63.28 - 84.37: 57 84.37 - 105.47: 45 Dihedral angle restraints: 7698 sinusoidal: 3639 harmonic: 4059 Sorted by residual: dihedral pdb=" O4 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C5 BMA M 3 " pdb=" O5 BMA M 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.76 105.47 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" O4 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C5 BMA H 3 " pdb=" O5 BMA H 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.76 105.47 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" O4 BMA R 3 " pdb=" C4 BMA R 3 " pdb=" C5 BMA R 3 " pdb=" O5 BMA R 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.74 105.45 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 7695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1218 0.093 - 0.187: 446 0.187 - 0.280: 145 0.280 - 0.374: 84 0.374 - 0.467: 45 Chirality restraints: 1938 Sorted by residual: chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.52e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.49e+02 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.44e+02 ... (remaining 1935 not shown) Planarity restraints: 2013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 25 " -0.052 2.00e-02 2.50e+03 5.39e-02 3.63e+01 pdb=" CG ASN C 25 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN C 25 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN C 25 " 0.083 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 25 " -0.052 2.00e-02 2.50e+03 5.37e-02 3.60e+01 pdb=" CG ASN E 25 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN E 25 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN E 25 " 0.083 2.00e-02 2.50e+03 pdb=" C1 NAG T 1 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 25 " -0.052 2.00e-02 2.50e+03 5.33e-02 3.55e+01 pdb=" CG ASN A 25 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN A 25 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 25 " 0.082 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " -0.064 2.00e-02 2.50e+03 ... (remaining 2010 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 5261 2.93 - 3.42: 10513 3.42 - 3.91: 19675 3.91 - 4.41: 22081 4.41 - 4.90: 35560 Nonbonded interactions: 93090 Sorted by model distance: nonbonded pdb=" NZ LYS B 61 " pdb=" OD2 ASP D 86 " model vdw 2.436 3.120 nonbonded pdb=" NZ LYS D 61 " pdb=" OD2 ASP F 86 " model vdw 2.437 3.120 nonbonded pdb=" OD2 ASP B 86 " pdb=" NZ LYS F 61 " model vdw 2.438 3.120 nonbonded pdb=" O5 NAG J 1 " pdb=" O6 NAG J 1 " model vdw 2.444 2.432 nonbonded pdb=" O5 NAG T 1 " pdb=" O6 NAG T 1 " model vdw 2.444 2.432 ... (remaining 93085 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'T' selection = chain 'U' } 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: 8.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.340 Find NCS groups from input model: 0.250 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: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 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 : 0.024 0.132 11802 Z= 1.289 Angle : 1.776 9.589 16086 Z= 1.141 Chirality : 0.136 0.467 1938 Planarity : 0.008 0.038 1992 Dihedral : 15.344 105.468 5052 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 0.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 aren not related in a simple way. whole: 0.65 (0.20), residues: 1425 helix: 0.94 (0.27), residues: 321 sheet: 0.60 (0.33), residues: 234 loop : 0.30 (0.19), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 88 TYR 0.061 0.010 TYR A 135 PHE 0.020 0.006 PHE A 192 TRP 0.048 0.008 TRP F 21 HIS 0.013 0.002 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.02324 (11739) covalent geometry : angle 1.74309 (15915) SS BOND : bond 0.01175 ( 18) SS BOND : angle 3.01052 ( 36) hydrogen bonds : bond 0.15987 ( 435) hydrogen bonds : angle 7.48181 ( 1242) link_BETA1-4 : bond 0.07015 ( 24) link_BETA1-4 : angle 4.79440 ( 72) link_NAG-ASN : bond 0.07604 ( 21) link_NAG-ASN : angle 2.51805 ( 63) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.386 Fit side-chains REVERT: B 22 HIS cc_start: 0.4073 (t-90) cc_final: 0.3859 (p-80) REVERT: B 47 LYS cc_start: 0.8254 (tttt) cc_final: 0.8034 (ttmt) REVERT: B 50 LYS cc_start: 0.8664 (mttt) cc_final: 0.8347 (mmmt) REVERT: B 86 ASP cc_start: 0.8555 (t70) cc_final: 0.8296 (t0) REVERT: B 125 MET cc_start: 0.7565 (mtm) cc_final: 0.7347 (mtp) REVERT: D 22 HIS cc_start: 0.4279 (t-90) cc_final: 0.3889 (p-80) REVERT: D 50 LYS cc_start: 0.8665 (mttt) cc_final: 0.8347 (mmmt) REVERT: D 86 ASP cc_start: 0.8627 (t70) cc_final: 0.8010 (t0) REVERT: F 50 LYS cc_start: 0.8700 (mttt) cc_final: 0.8317 (mmmt) REVERT: F 86 ASP cc_start: 0.8567 (t70) cc_final: 0.8045 (t0) REVERT: F 125 MET cc_start: 0.7550 (mtm) cc_final: 0.7312 (mtp) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.1288 time to fit residues: 39.8415 Evaluate side-chains 97 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN B 74 HIS ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 ASN D 74 HIS ** D 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 ASN F 74 HIS ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.115390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.081416 restraints weight = 20649.210| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.68 r_work: 0.2988 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11802 Z= 0.177 Angle : 0.755 6.458 16086 Z= 0.358 Chirality : 0.045 0.194 1938 Planarity : 0.004 0.033 1992 Dihedral : 11.341 64.743 2442 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.08 % Allowed : 5.32 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 aren not related in a simple way. whole: 0.65 (0.21), residues: 1425 helix: 2.07 (0.28), residues: 327 sheet: 0.05 (0.30), residues: 258 loop : -0.04 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 278 TYR 0.021 0.002 TYR A 135 PHE 0.010 0.002 PHE A 192 TRP 0.011 0.001 TRP F 21 HIS 0.006 0.001 HIS D 22 Details of bonding type rmsd covalent geometry : bond 0.00389 (11739) covalent geometry : angle 0.69445 (15915) SS BOND : bond 0.00216 ( 18) SS BOND : angle 1.20670 ( 36) hydrogen bonds : bond 0.05188 ( 435) hydrogen bonds : angle 5.62527 ( 1242) link_BETA1-4 : bond 0.00805 ( 24) link_BETA1-4 : angle 3.40996 ( 72) link_NAG-ASN : bond 0.00429 ( 21) link_NAG-ASN : angle 3.08238 ( 63) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 253 LYS cc_start: 0.9139 (mmtt) cc_final: 0.8855 (mmtp) REVERT: B 50 LYS cc_start: 0.8536 (mttt) cc_final: 0.8220 (mmmt) REVERT: B 86 ASP cc_start: 0.8967 (t70) cc_final: 0.8465 (t0) REVERT: B 125 MET cc_start: 0.8213 (mtm) cc_final: 0.7978 (mtp) REVERT: C 253 LYS cc_start: 0.9114 (mmtt) cc_final: 0.8807 (mmtm) REVERT: D 50 LYS cc_start: 0.8511 (mttt) cc_final: 0.8228 (mmmt) REVERT: D 85 ASP cc_start: 0.8430 (m-30) cc_final: 0.8222 (m-30) REVERT: D 86 ASP cc_start: 0.8896 (t70) cc_final: 0.8173 (t0) REVERT: F 21 TRP cc_start: 0.6797 (m100) cc_final: 0.6499 (m100) REVERT: F 50 LYS cc_start: 0.8530 (mttt) cc_final: 0.8187 (mmmt) REVERT: F 61 LYS cc_start: 0.9092 (mtpp) cc_final: 0.8757 (mtpp) REVERT: F 81 ASP cc_start: 0.9043 (t0) cc_final: 0.8792 (t0) REVERT: F 85 ASP cc_start: 0.8357 (m-30) cc_final: 0.8084 (m-30) REVERT: F 86 ASP cc_start: 0.8907 (t70) cc_final: 0.8492 (t0) REVERT: F 125 MET cc_start: 0.8248 (mtm) cc_final: 0.8000 (mtp) outliers start: 13 outliers final: 6 residues processed: 136 average time/residue: 0.1411 time to fit residues: 26.2306 Evaluate side-chains 95 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain E residue 48 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 17 optimal weight: 0.5980 chunk 7 optimal weight: 5.9990 chunk 111 optimal weight: 0.2980 chunk 31 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 ASN C 99 HIS D 46 ASN E 99 HIS F 22 HIS F 46 ASN F 64 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.113930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.079229 restraints weight = 20521.012| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.72 r_work: 0.2953 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11802 Z= 0.164 Angle : 0.632 8.101 16086 Z= 0.300 Chirality : 0.043 0.174 1938 Planarity : 0.004 0.031 1992 Dihedral : 6.706 33.848 2442 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.16 % Allowed : 6.48 % Favored : 92.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 aren not related in a simple way. whole: 0.69 (0.21), residues: 1425 helix: 2.59 (0.28), residues: 327 sheet: -0.09 (0.30), residues: 258 loop : -0.19 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 278 TYR 0.017 0.001 TYR A 135 PHE 0.008 0.001 PHE A 192 TRP 0.008 0.001 TRP D 14 HIS 0.011 0.001 HIS B 22 Details of bonding type rmsd covalent geometry : bond 0.00375 (11739) covalent geometry : angle 0.58794 (15915) SS BOND : bond 0.00212 ( 18) SS BOND : angle 0.72976 ( 36) hydrogen bonds : bond 0.04085 ( 435) hydrogen bonds : angle 5.14155 ( 1242) link_BETA1-4 : bond 0.00833 ( 24) link_BETA1-4 : angle 2.43129 ( 72) link_NAG-ASN : bond 0.00553 ( 21) link_NAG-ASN : angle 2.74210 ( 63) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.536 Fit side-chains REVERT: B 50 LYS cc_start: 0.8496 (mttt) cc_final: 0.8185 (mmmt) REVERT: B 86 ASP cc_start: 0.8980 (t0) cc_final: 0.8521 (t0) REVERT: B 125 MET cc_start: 0.8185 (mtm) cc_final: 0.7813 (mtp) REVERT: C 164 ASN cc_start: 0.8240 (t0) cc_final: 0.7985 (t0) REVERT: D 50 LYS cc_start: 0.8474 (mttt) cc_final: 0.8191 (mmmt) REVERT: D 81 ASP cc_start: 0.8909 (t0) cc_final: 0.8643 (t0) REVERT: D 86 ASP cc_start: 0.8948 (t70) cc_final: 0.8497 (t0) REVERT: F 50 LYS cc_start: 0.8529 (mttt) cc_final: 0.8171 (mmmt) REVERT: F 64 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8381 (mt0) REVERT: F 86 ASP cc_start: 0.8896 (t70) cc_final: 0.8501 (t0) outliers start: 14 outliers final: 9 residues processed: 116 average time/residue: 0.1386 time to fit residues: 22.2993 Evaluate side-chains 103 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain F residue 64 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 59 optimal weight: 0.0870 chunk 90 optimal weight: 0.9980 chunk 139 optimal weight: 20.0000 chunk 89 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 HIS B 75 ASN D 75 ASN F 75 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.113644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.078901 restraints weight = 20445.441| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.69 r_work: 0.2949 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11802 Z= 0.147 Angle : 0.586 8.631 16086 Z= 0.277 Chirality : 0.041 0.220 1938 Planarity : 0.004 0.032 1992 Dihedral : 5.241 26.710 2442 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.16 % Allowed : 7.48 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 aren not related in a simple way. whole: 0.64 (0.21), residues: 1425 helix: 2.67 (0.28), residues: 327 sheet: -0.10 (0.30), residues: 258 loop : -0.29 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 278 TYR 0.014 0.001 TYR E 135 PHE 0.009 0.001 PHE A 192 TRP 0.008 0.001 TRP B 21 HIS 0.006 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00341 (11739) covalent geometry : angle 0.54540 (15915) SS BOND : bond 0.00207 ( 18) SS BOND : angle 0.57057 ( 36) hydrogen bonds : bond 0.03769 ( 435) hydrogen bonds : angle 4.97514 ( 1242) link_BETA1-4 : bond 0.00626 ( 24) link_BETA1-4 : angle 2.13434 ( 72) link_NAG-ASN : bond 0.00476 ( 21) link_NAG-ASN : angle 2.68906 ( 63) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.530 Fit side-chains REVERT: B 50 LYS cc_start: 0.8510 (mttt) cc_final: 0.8198 (mmmt) REVERT: B 86 ASP cc_start: 0.8976 (t0) cc_final: 0.8508 (t0) REVERT: C 164 ASN cc_start: 0.8194 (t0) cc_final: 0.7935 (t0) REVERT: D 50 LYS cc_start: 0.8504 (mttt) cc_final: 0.8216 (mmmt) REVERT: D 86 ASP cc_start: 0.8955 (t70) cc_final: 0.8503 (t0) REVERT: F 50 LYS cc_start: 0.8536 (mttt) cc_final: 0.8180 (mmmt) REVERT: F 86 ASP cc_start: 0.8899 (t70) cc_final: 0.8462 (t0) REVERT: F 125 MET cc_start: 0.7839 (mtm) cc_final: 0.7331 (ptp) outliers start: 14 outliers final: 12 residues processed: 112 average time/residue: 0.1358 time to fit residues: 20.9226 Evaluate side-chains 105 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 250 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 ASN ** D 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 ASN F 75 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.111502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.076666 restraints weight = 20548.126| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.73 r_work: 0.2892 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11802 Z= 0.182 Angle : 0.581 8.971 16086 Z= 0.277 Chirality : 0.041 0.173 1938 Planarity : 0.004 0.033 1992 Dihedral : 4.687 25.826 2442 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.08 % Allowed : 7.81 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 aren not related in a simple way. whole: 0.58 (0.21), residues: 1425 helix: 2.75 (0.28), residues: 327 sheet: -0.15 (0.31), residues: 258 loop : -0.38 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 278 TYR 0.017 0.001 TYR A 135 PHE 0.010 0.001 PHE A 192 TRP 0.010 0.001 TRP F 21 HIS 0.010 0.001 HIS D 22 Details of bonding type rmsd covalent geometry : bond 0.00433 (11739) covalent geometry : angle 0.54720 (15915) SS BOND : bond 0.00257 ( 18) SS BOND : angle 0.60127 ( 36) hydrogen bonds : bond 0.03714 ( 435) hydrogen bonds : angle 4.88632 ( 1242) link_BETA1-4 : bond 0.00592 ( 24) link_BETA1-4 : angle 1.78168 ( 72) link_NAG-ASN : bond 0.00404 ( 21) link_NAG-ASN : angle 2.60956 ( 63) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.624 Fit side-chains REVERT: A 48 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7497 (pm20) REVERT: A 164 ASN cc_start: 0.7915 (t0) cc_final: 0.7674 (t0) REVERT: B 50 LYS cc_start: 0.8460 (mttt) cc_final: 0.8141 (mmmt) REVERT: B 64 GLN cc_start: 0.8812 (mp10) cc_final: 0.8539 (mt0) REVERT: B 86 ASP cc_start: 0.9033 (t0) cc_final: 0.8558 (t0) REVERT: B 125 MET cc_start: 0.8107 (mtm) cc_final: 0.7339 (ptp) REVERT: C 164 ASN cc_start: 0.8206 (t0) cc_final: 0.7960 (t0) REVERT: D 50 LYS cc_start: 0.8408 (mttt) cc_final: 0.8119 (mmmt) REVERT: D 86 ASP cc_start: 0.8951 (t70) cc_final: 0.8461 (t0) REVERT: F 50 LYS cc_start: 0.8433 (mttt) cc_final: 0.8077 (mmmt) REVERT: F 86 ASP cc_start: 0.8942 (t70) cc_final: 0.8498 (t0) REVERT: F 125 MET cc_start: 0.7847 (mtm) cc_final: 0.7409 (ptp) outliers start: 13 outliers final: 10 residues processed: 102 average time/residue: 0.1489 time to fit residues: 20.7264 Evaluate side-chains 97 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 250 MET Chi-restraints excluded: chain F residue 60 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 64 optimal weight: 0.9980 chunk 91 optimal weight: 0.0030 chunk 53 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 HIS D 75 ASN E 14 HIS F 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.112598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.078128 restraints weight = 20698.947| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.74 r_work: 0.2949 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 11802 Z= 0.127 Angle : 0.527 9.186 16086 Z= 0.250 Chirality : 0.040 0.187 1938 Planarity : 0.004 0.032 1992 Dihedral : 4.457 23.777 2442 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.33 % Allowed : 8.40 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 aren not related in a simple way. whole: 0.69 (0.22), residues: 1425 helix: 3.00 (0.28), residues: 324 sheet: -0.11 (0.31), residues: 258 loop : -0.37 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 278 TYR 0.012 0.001 TYR E 135 PHE 0.008 0.001 PHE A 192 TRP 0.005 0.001 TRP F 14 HIS 0.006 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00295 (11739) covalent geometry : angle 0.49650 (15915) SS BOND : bond 0.00195 ( 18) SS BOND : angle 0.47133 ( 36) hydrogen bonds : bond 0.03348 ( 435) hydrogen bonds : angle 4.72462 ( 1242) link_BETA1-4 : bond 0.00583 ( 24) link_BETA1-4 : angle 1.50398 ( 72) link_NAG-ASN : bond 0.00443 ( 21) link_NAG-ASN : angle 2.44184 ( 63) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.478 Fit side-chains REVERT: A 48 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7517 (pm20) REVERT: A 164 ASN cc_start: 0.7936 (t0) cc_final: 0.7699 (t0) REVERT: B 50 LYS cc_start: 0.8518 (mttt) cc_final: 0.8191 (mmmt) REVERT: B 64 GLN cc_start: 0.8728 (mp10) cc_final: 0.8444 (mt0) REVERT: B 86 ASP cc_start: 0.9013 (t0) cc_final: 0.8554 (t0) REVERT: B 125 MET cc_start: 0.8086 (mtm) cc_final: 0.7307 (ptp) REVERT: C 164 ASN cc_start: 0.8231 (t0) cc_final: 0.7991 (t0) REVERT: D 50 LYS cc_start: 0.8487 (mttt) cc_final: 0.8197 (mmmt) REVERT: D 86 ASP cc_start: 0.8950 (t70) cc_final: 0.8502 (t0) REVERT: F 50 LYS cc_start: 0.8518 (mttt) cc_final: 0.8165 (mmmt) REVERT: F 64 GLN cc_start: 0.8218 (mt0) cc_final: 0.7967 (mt0) REVERT: F 86 ASP cc_start: 0.8948 (t70) cc_final: 0.8504 (t0) REVERT: F 88 ARG cc_start: 0.8182 (tmt170) cc_final: 0.7939 (tpt170) REVERT: F 125 MET cc_start: 0.7826 (mtm) cc_final: 0.7507 (ptp) outliers start: 16 outliers final: 9 residues processed: 109 average time/residue: 0.1511 time to fit residues: 22.1875 Evaluate side-chains 100 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain E residue 250 MET Chi-restraints excluded: chain F residue 56 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.1205 > 50: distance: 20 - 106: 8.739 distance: 47 - 117: 11.703 distance: 84 - 89: 22.847 distance: 89 - 90: 12.024 distance: 90 - 91: 31.875 distance: 91 - 92: 18.662 distance: 91 - 93: 38.964 distance: 93 - 94: 25.694 distance: 94 - 95: 29.597 distance: 94 - 97: 25.077 distance: 95 - 96: 41.439 distance: 95 - 101: 58.121 distance: 97 - 98: 13.761 distance: 98 - 99: 25.144 distance: 98 - 100: 8.581 distance: 101 - 102: 50.639 distance: 102 - 103: 20.035 distance: 102 - 105: 17.652 distance: 103 - 104: 31.999 distance: 103 - 107: 24.090 distance: 105 - 106: 22.770 distance: 107 - 108: 5.472 distance: 107 - 113: 19.478 distance: 108 - 109: 4.762 distance: 108 - 111: 5.735 distance: 109 - 110: 22.488 distance: 109 - 114: 5.493 distance: 111 - 112: 13.907 distance: 112 - 113: 9.906 distance: 114 - 115: 4.795 distance: 116 - 117: 14.353 distance: 116 - 122: 9.898 distance: 118 - 119: 4.393 distance: 118 - 120: 5.865 distance: 119 - 121: 7.921 distance: 122 - 123: 10.315 distance: 123 - 124: 8.238 distance: 123 - 126: 9.712 distance: 124 - 125: 8.066 distance: 124 - 136: 7.250 distance: 126 - 127: 3.564 distance: 127 - 128: 3.021 distance: 127 - 129: 5.254 distance: 128 - 130: 4.174 distance: 132 - 134: 4.030 distance: 136 - 137: 9.096 distance: 137 - 138: 16.940 distance: 137 - 140: 7.631 distance: 138 - 139: 7.045 distance: 138 - 143: 24.977 distance: 140 - 141: 12.055 distance: 140 - 142: 28.096 distance: 143 - 144: 7.781 distance: 144 - 145: 24.791 distance: 144 - 147: 18.669 distance: 145 - 146: 11.798 distance: 145 - 152: 11.627 distance: 147 - 148: 14.006 distance: 148 - 149: 13.380 distance: 150 - 151: 11.875 distance: 152 - 153: 13.260 distance: 153 - 154: 35.482 distance: 153 - 156: 27.472 distance: 154 - 155: 8.871 distance: 154 - 159: 19.064 distance: 156 - 157: 32.394 distance: 156 - 158: 45.741 distance: 159 - 160: 12.490 distance: 159 - 165: 18.139 distance: 160 - 161: 13.961 distance: 160 - 163: 25.692 distance: 161 - 162: 12.468 distance: 161 - 166: 27.481 distance: 163 - 164: 21.136 distance: 164 - 165: 21.330