Starting phenix.real_space_refine on Mon Aug 25 10:41:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mgb_48248/08_2025/9mgb_48248.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mgb_48248/08_2025/9mgb_48248.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mgb_48248/08_2025/9mgb_48248.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mgb_48248/08_2025/9mgb_48248.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mgb_48248/08_2025/9mgb_48248.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mgb_48248/08_2025/9mgb_48248.map" } resolution = 2.1 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= -0.002 sd= 0.098 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 150 5.16 5 C 16914 2.51 5 N 4464 2.21 5 O 5328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 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: 26856 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1242 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 157} Chain: "B" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1279 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 172} Chain: "C" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1242 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 157} Chain: "D" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1279 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 172} Chain: "F" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1242 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 157} Chain: "G" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1279 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 172} Chain: "I" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1242 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 157} Chain: "J" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1279 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 172} Chain: "L" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1242 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 157} Chain: "M" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1279 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 172} Chain: "O" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1242 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 157} Chain: "Q" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1279 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 172} Chain: "a" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1740 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 218} Chain breaks: 1 Chain: "c" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1740 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 218} Chain breaks: 1 Chain: "e" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1740 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 218} Chain breaks: 1 Chain: "g" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1740 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 218} Chain breaks: 1 Chain: "i" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1740 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 218} Chain breaks: 1 Chain: "k" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1740 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 218} Chain breaks: 1 Chain: "A" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PEB': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'PEB': 2, 'PUB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PEB': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'PEB': 2, 'PUB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PEB': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'PEB': 2, 'PUB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PEB': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'PEB': 2, 'PUB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PEB': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'PEB': 2, 'PUB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PEB': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'PEB': 2, 'PUB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.45, per 1000 atoms: 0.20 Number of scatterers: 26856 At special positions: 0 Unit cell: (173.9, 172.96, 93.06, 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 150 16.00 O 5328 8.00 N 4464 7.00 C 16914 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS a 26 " - pdb=" SG CYS a 100 " distance=2.03 Simple disulfide: pdb=" SG CYS a 167 " - pdb=" SG CYS a 232 " distance=2.03 Simple disulfide: pdb=" SG CYS c 26 " - pdb=" SG CYS c 100 " distance=2.03 Simple disulfide: pdb=" SG CYS c 167 " - pdb=" SG CYS c 232 " distance=2.03 Simple disulfide: pdb=" SG CYS e 26 " - pdb=" SG CYS e 100 " distance=2.03 Simple disulfide: pdb=" SG CYS e 167 " - pdb=" SG CYS e 232 " distance=2.03 Simple disulfide: pdb=" SG CYS g 26 " - pdb=" SG CYS g 100 " distance=2.03 Simple disulfide: pdb=" SG CYS g 167 " - pdb=" SG CYS g 232 " distance=2.04 Simple disulfide: pdb=" SG CYS i 26 " - pdb=" SG CYS i 100 " distance=2.03 Simple disulfide: pdb=" SG CYS i 167 " - pdb=" SG CYS i 232 " distance=2.03 Simple disulfide: pdb=" SG CYS k 26 " - pdb=" SG CYS k 100 " distance=2.03 Simple disulfide: pdb=" SG CYS k 167 " - pdb=" SG CYS k 232 " 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 971.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6228 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 35 sheets defined 53.4% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 Processing helix chain 'A' and resid 20 through 47 removed outlier: 4.444A pdb=" N ALA A 35 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N SER A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 63 Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 75 through 100 Processing helix chain 'A' and resid 102 through 109 Processing helix chain 'A' and resid 112 through 120 Processing helix chain 'A' and resid 123 through 138 removed outlier: 4.002A pdb=" N TYR A 127 " --> pdb=" O PRO A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 164 Processing helix chain 'B' and resid 3 through 14 Processing helix chain 'B' and resid 20 through 33 Processing helix chain 'B' and resid 33 through 46 Processing helix chain 'B' and resid 47 through 63 Processing helix chain 'B' and resid 64 through 68 Processing helix chain 'B' and resid 75 through 100 Processing helix chain 'B' and resid 102 through 109 Processing helix chain 'B' and resid 112 through 121 Processing helix chain 'B' and resid 123 through 143 Processing helix chain 'B' and resid 158 through 176 Processing helix chain 'C' and resid 3 through 15 Processing helix chain 'C' and resid 20 through 47 removed outlier: 4.407A pdb=" N ALA C 35 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N SER C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 63 Processing helix chain 'C' and resid 64 through 68 Processing helix chain 'C' and resid 75 through 100 Processing helix chain 'C' and resid 102 through 109 Processing helix chain 'C' and resid 112 through 120 Processing helix chain 'C' and resid 123 through 138 removed outlier: 3.930A pdb=" N TYR C 127 " --> pdb=" O PRO C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 164 Processing helix chain 'D' and resid 3 through 15 removed outlier: 4.055A pdb=" N LYS D 15 " --> pdb=" O ASN D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 33 Processing helix chain 'D' and resid 33 through 46 Processing helix chain 'D' and resid 47 through 63 Processing helix chain 'D' and resid 64 through 67 Processing helix chain 'D' and resid 75 through 100 Processing helix chain 'D' and resid 102 through 110 Processing helix chain 'D' and resid 112 through 121 Processing helix chain 'D' and resid 123 through 143 Processing helix chain 'D' and resid 158 through 176 Processing helix chain 'F' and resid 3 through 15 Processing helix chain 'F' and resid 20 through 47 removed outlier: 4.362A pdb=" N ALA F 35 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N SER F 36 " --> pdb=" O GLN F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 63 Processing helix chain 'F' and resid 64 through 68 Processing helix chain 'F' and resid 75 through 100 Processing helix chain 'F' and resid 102 through 109 Processing helix chain 'F' and resid 112 through 120 Processing helix chain 'F' and resid 123 through 138 removed outlier: 4.007A pdb=" N TYR F 127 " --> pdb=" O PRO F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 164 Processing helix chain 'G' and resid 3 through 14 Processing helix chain 'G' and resid 20 through 33 Processing helix chain 'G' and resid 33 through 47 removed outlier: 3.515A pdb=" N ASN G 47 " --> pdb=" O SER G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 63 Processing helix chain 'G' and resid 64 through 67 Processing helix chain 'G' and resid 75 through 100 Processing helix chain 'G' and resid 102 through 110 Processing helix chain 'G' and resid 112 through 121 Processing helix chain 'G' and resid 123 through 143 Processing helix chain 'G' and resid 158 through 176 Processing helix chain 'I' and resid 3 through 15 Processing helix chain 'I' and resid 20 through 47 removed outlier: 4.415A pdb=" N ALA I 35 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N SER I 36 " --> pdb=" O GLN I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 63 Processing helix chain 'I' and resid 64 through 68 Processing helix chain 'I' and resid 75 through 100 Processing helix chain 'I' and resid 102 through 109 Processing helix chain 'I' and resid 112 through 120 Processing helix chain 'I' and resid 123 through 138 removed outlier: 3.975A pdb=" N TYR I 127 " --> pdb=" O PRO I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 164 Processing helix chain 'J' and resid 3 through 14 Processing helix chain 'J' and resid 20 through 33 Processing helix chain 'J' and resid 33 through 46 Processing helix chain 'J' and resid 47 through 63 Processing helix chain 'J' and resid 64 through 67 Processing helix chain 'J' and resid 75 through 100 Processing helix chain 'J' and resid 102 through 110 Processing helix chain 'J' and resid 112 through 121 Processing helix chain 'J' and resid 123 through 143 Processing helix chain 'J' and resid 158 through 176 Processing helix chain 'L' and resid 3 through 15 Processing helix chain 'L' and resid 20 through 47 removed outlier: 4.413A pdb=" N ALA L 35 " --> pdb=" O ILE L 31 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N SER L 36 " --> pdb=" O GLN L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 63 Processing helix chain 'L' and resid 64 through 68 Processing helix chain 'L' and resid 75 through 100 Processing helix chain 'L' and resid 102 through 109 Processing helix chain 'L' and resid 112 through 120 Processing helix chain 'L' and resid 123 through 138 removed outlier: 3.927A pdb=" N TYR L 127 " --> pdb=" O PRO L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 164 Processing helix chain 'M' and resid 3 through 15 removed outlier: 4.043A pdb=" N LYS M 15 " --> pdb=" O ASN M 11 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 33 Processing helix chain 'M' and resid 33 through 46 Processing helix chain 'M' and resid 47 through 63 Processing helix chain 'M' and resid 64 through 67 Processing helix chain 'M' and resid 75 through 100 Processing helix chain 'M' and resid 102 through 110 Processing helix chain 'M' and resid 112 through 121 Processing helix chain 'M' and resid 123 through 143 Processing helix chain 'M' and resid 158 through 176 Processing helix chain 'O' and resid 3 through 15 Processing helix chain 'O' and resid 20 through 47 removed outlier: 4.396A pdb=" N ALA O 35 " --> pdb=" O ILE O 31 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N SER O 36 " --> pdb=" O GLN O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 47 through 63 Processing helix chain 'O' and resid 64 through 68 Processing helix chain 'O' and resid 75 through 100 Processing helix chain 'O' and resid 102 through 109 Processing helix chain 'O' and resid 112 through 120 Processing helix chain 'O' and resid 123 through 138 removed outlier: 3.939A pdb=" N TYR O 127 " --> pdb=" O PRO O 123 " (cutoff:3.500A) Processing helix chain 'O' and resid 145 through 164 Processing helix chain 'Q' and resid 3 through 14 Processing helix chain 'Q' and resid 20 through 33 Processing helix chain 'Q' and resid 33 through 46 Processing helix chain 'Q' and resid 47 through 63 Processing helix chain 'Q' and resid 64 through 68 Processing helix chain 'Q' and resid 75 through 100 Processing helix chain 'Q' and resid 102 through 110 Processing helix chain 'Q' and resid 112 through 121 Processing helix chain 'Q' and resid 123 through 143 Processing helix chain 'Q' and resid 158 through 176 Processing helix chain 'a' and resid 32 through 36 removed outlier: 3.539A pdb=" N TYR a 36 " --> pdb=" O PHE a 33 " (cutoff:3.500A) Processing helix chain 'a' and resid 66 through 69 Processing helix chain 'a' and resid 91 through 95 Processing helix chain 'a' and resid 223 through 227 Processing helix chain 'c' and resid 32 through 36 removed outlier: 3.504A pdb=" N TYR c 36 " --> pdb=" O PHE c 33 " (cutoff:3.500A) Processing helix chain 'c' and resid 223 through 227 Processing helix chain 'e' and resid 32 through 36 Processing helix chain 'e' and resid 223 through 227 Processing helix chain 'g' and resid 32 through 36 removed outlier: 3.521A pdb=" N TYR g 36 " --> pdb=" O PHE g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 223 through 227 Processing helix chain 'i' and resid 32 through 36 Processing helix chain 'i' and resid 91 through 95 Processing helix chain 'i' and resid 223 through 227 Processing helix chain 'k' and resid 32 through 36 Processing helix chain 'k' and resid 91 through 95 Processing helix chain 'k' and resid 223 through 227 Processing sheet with id=AA1, first strand: chain 'a' and resid 9 through 10 Processing sheet with id=AA2, first strand: chain 'a' and resid 14 through 15 removed outlier: 6.670A pdb=" N GLU a 14 " --> pdb=" O THR a 121 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE a 38 " --> pdb=" O GLU a 54 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU a 54 " --> pdb=" O ILE a 38 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TRP a 40 " --> pdb=" O ILE a 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 14 through 15 removed outlier: 6.670A pdb=" N GLU a 14 " --> pdb=" O THR a 121 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N TYR a 113 " --> pdb=" O ARG a 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 148 through 149 Processing sheet with id=AA5, first strand: chain 'a' and resid 154 through 156 removed outlier: 6.175A pdb=" N GLN a 181 " --> pdb=" O LEU a 190 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LEU a 190 " --> pdb=" O GLN a 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 154 through 156 removed outlier: 3.776A pdb=" N THR a 241 " --> pdb=" O GLN a 234 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'c' and resid 9 through 10 Processing sheet with id=AA8, first strand: chain 'c' and resid 62 through 64 removed outlier: 6.682A pdb=" N TRP c 40 " --> pdb=" O ILE c 52 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLU c 54 " --> pdb=" O ILE c 38 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE c 38 " --> pdb=" O GLU c 54 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N TYR c 113 " --> pdb=" O ARG c 102 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'c' and resid 62 through 64 removed outlier: 6.682A pdb=" N TRP c 40 " --> pdb=" O ILE c 52 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLU c 54 " --> pdb=" O ILE c 38 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE c 38 " --> pdb=" O GLU c 54 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'c' and resid 148 through 149 Processing sheet with id=AB2, first strand: chain 'c' and resid 154 through 156 removed outlier: 6.884A pdb=" N LEU c 155 " --> pdb=" O GLU c 249 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLN c 181 " --> pdb=" O LEU c 190 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU c 190 " --> pdb=" O GLN c 181 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'c' and resid 154 through 156 removed outlier: 6.884A pdb=" N LEU c 155 " --> pdb=" O GLU c 249 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR c 241 " --> pdb=" O GLN c 234 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'e' and resid 9 through 10 Processing sheet with id=AB5, first strand: chain 'e' and resid 14 through 15 removed outlier: 6.888A pdb=" N GLU e 14 " --> pdb=" O THR e 121 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE e 38 " --> pdb=" O GLU e 54 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLU e 54 " --> pdb=" O ILE e 38 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP e 40 " --> pdb=" O ILE e 52 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'e' and resid 14 through 15 removed outlier: 6.888A pdb=" N GLU e 14 " --> pdb=" O THR e 121 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TYR e 113 " --> pdb=" O ARG e 102 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'e' and resid 148 through 149 Processing sheet with id=AB8, first strand: chain 'e' and resid 197 through 198 removed outlier: 6.368A pdb=" N TRP e 179 " --> pdb=" O LEU e 191 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TYR e 193 " --> pdb=" O LEU e 177 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU e 177 " --> pdb=" O TYR e 193 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR e 241 " --> pdb=" O GLN e 234 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'e' and resid 197 through 198 removed outlier: 6.368A pdb=" N TRP e 179 " --> pdb=" O LEU e 191 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TYR e 193 " --> pdb=" O LEU e 177 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU e 177 " --> pdb=" O TYR e 193 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'g' and resid 9 through 10 Processing sheet with id=AC2, first strand: chain 'g' and resid 14 through 15 removed outlier: 7.215A pdb=" N GLU g 14 " --> pdb=" O THR g 121 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE g 38 " --> pdb=" O GLU g 54 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU g 54 " --> pdb=" O ILE g 38 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TRP g 40 " --> pdb=" O ILE g 52 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'g' and resid 14 through 15 removed outlier: 7.215A pdb=" N GLU g 14 " --> pdb=" O THR g 121 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TYR g 113 " --> pdb=" O ARG g 102 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'g' and resid 148 through 149 Processing sheet with id=AC5, first strand: chain 'g' and resid 154 through 156 removed outlier: 5.961A pdb=" N GLN g 181 " --> pdb=" O LEU g 190 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LEU g 190 " --> pdb=" O GLN g 181 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'g' and resid 154 through 156 removed outlier: 3.793A pdb=" N THR g 241 " --> pdb=" O GLN g 234 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'i' and resid 9 through 10 Processing sheet with id=AC8, first strand: chain 'i' and resid 14 through 15 removed outlier: 3.730A pdb=" N THR i 121 " --> pdb=" O GLU i 14 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE i 38 " --> pdb=" O GLU i 54 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU i 54 " --> pdb=" O ILE i 38 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N TRP i 40 " --> pdb=" O ILE i 52 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'i' and resid 14 through 15 removed outlier: 3.730A pdb=" N THR i 121 " --> pdb=" O GLU i 14 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR i 113 " --> pdb=" O ARG i 102 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'i' and resid 148 through 149 Processing sheet with id=AD2, first strand: chain 'i' and resid 154 through 156 removed outlier: 3.518A pdb=" N GLU i 249 " --> pdb=" O LEU i 155 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLN i 181 " --> pdb=" O LEU i 190 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU i 190 " --> pdb=" O GLN i 181 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'i' and resid 154 through 156 removed outlier: 3.518A pdb=" N GLU i 249 " --> pdb=" O LEU i 155 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR i 241 " --> pdb=" O GLN i 234 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'k' and resid 9 through 10 Processing sheet with id=AD5, first strand: chain 'k' and resid 62 through 64 removed outlier: 6.593A pdb=" N TRP k 40 " --> pdb=" O ILE k 52 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU k 54 " --> pdb=" O ILE k 38 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE k 38 " --> pdb=" O GLU k 54 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TYR k 113 " --> pdb=" O ARG k 102 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'k' and resid 148 through 150 Processing sheet with id=AD7, first strand: chain 'k' and resid 154 through 156 removed outlier: 6.192A pdb=" N GLN k 181 " --> pdb=" O LEU k 190 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N LEU k 190 " --> pdb=" O GLN k 181 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'k' and resid 154 through 156 removed outlier: 3.805A pdb=" N THR k 241 " --> pdb=" O GLN k 234 " (cutoff:3.500A) 1704 hydrogen bonds defined for protein. 4731 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: 4.65 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4501 1.30 - 1.43: 7291 1.43 - 1.56: 15376 1.56 - 1.69: 0 1.69 - 1.82: 210 Bond restraints: 27378 Sorted by residual: bond pdb=" C1B PEB F 202 " pdb=" CHA PEB F 202 " ideal model delta sigma weight residual 1.441 1.362 0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C1B PEB I 202 " pdb=" CHA PEB I 202 " ideal model delta sigma weight residual 1.441 1.363 0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C1B PEB O 202 " pdb=" CHA PEB O 202 " ideal model delta sigma weight residual 1.441 1.366 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C3C PUB G 201 " pdb=" C4C PUB G 201 " ideal model delta sigma weight residual 1.450 1.376 0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C3C PUB B 201 " pdb=" C4C PUB B 201 " ideal model delta sigma weight residual 1.450 1.376 0.074 2.00e-02 2.50e+03 1.36e+01 ... (remaining 27373 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 36343 2.06 - 4.13: 802 4.13 - 6.19: 73 6.19 - 8.26: 11 8.26 - 10.32: 1 Bond angle restraints: 37230 Sorted by residual: angle pdb=" C2A PEB A 202 " pdb=" C3A PEB A 202 " pdb=" CAA PEB A 202 " ideal model delta sigma weight residual 114.07 103.75 10.32 3.00e+00 1.11e-01 1.18e+01 angle pdb=" N ASN C 80 " pdb=" CA ASN C 80 " pdb=" C ASN C 80 " ideal model delta sigma weight residual 111.28 107.95 3.33 1.09e+00 8.42e-01 9.35e+00 angle pdb=" CA LEU k 119 " pdb=" C LEU k 119 " pdb=" O LEU k 119 " ideal model delta sigma weight residual 120.51 116.21 4.30 1.43e+00 4.89e-01 9.03e+00 angle pdb=" CA THR k 118 " pdb=" CB THR k 118 " pdb=" OG1 THR k 118 " ideal model delta sigma weight residual 109.60 105.24 4.36 1.50e+00 4.44e-01 8.46e+00 angle pdb=" N ASN A 80 " pdb=" CA ASN A 80 " pdb=" C ASN A 80 " ideal model delta sigma weight residual 111.28 108.15 3.13 1.09e+00 8.42e-01 8.23e+00 ... (remaining 37225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 14866 17.94 - 35.89: 1819 35.89 - 53.83: 419 53.83 - 71.77: 103 71.77 - 89.72: 61 Dihedral angle restraints: 17268 sinusoidal: 7482 harmonic: 9786 Sorted by residual: dihedral pdb=" CB CYS k 26 " pdb=" SG CYS k 26 " pdb=" SG CYS k 100 " pdb=" CB CYS k 100 " ideal model delta sinusoidal sigma weight residual 93.00 57.00 36.00 1 1.00e+01 1.00e-02 1.83e+01 dihedral pdb=" CB CYS i 26 " pdb=" SG CYS i 26 " pdb=" SG CYS i 100 " pdb=" CB CYS i 100 " ideal model delta sinusoidal sigma weight residual 93.00 58.43 34.57 1 1.00e+01 1.00e-02 1.69e+01 dihedral pdb=" CB CYS c 26 " pdb=" SG CYS c 26 " pdb=" SG CYS c 100 " pdb=" CB CYS c 100 " ideal model delta sinusoidal sigma weight residual 93.00 59.40 33.60 1 1.00e+01 1.00e-02 1.60e+01 ... (remaining 17265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3393 0.051 - 0.102: 530 0.102 - 0.153: 108 0.153 - 0.203: 15 0.203 - 0.254: 16 Chirality restraints: 4062 Sorted by residual: chirality pdb=" C1D PEB G 203 " pdb=" ND PEB G 203 " pdb=" C2D PEB G 203 " pdb=" CHC PEB G 203 " both_signs ideal model delta sigma weight residual False -2.56 -2.82 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C1D PEB J 203 " pdb=" ND PEB J 203 " pdb=" C2D PEB J 203 " pdb=" CHC PEB J 203 " both_signs ideal model delta sigma weight residual False -2.56 -2.81 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" C1D PEB D 203 " pdb=" ND PEB D 203 " pdb=" C2D PEB D 203 " pdb=" CHC PEB D 203 " both_signs ideal model delta sigma weight residual False -2.56 -2.81 0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 4059 not shown) Planarity restraints: 4728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB PEB I 202 " 0.376 2.00e-02 2.50e+03 2.81e-01 1.78e+03 pdb=" C1B PEB I 202 " -0.013 2.00e-02 2.50e+03 pdb=" C2B PEB I 202 " 0.110 2.00e-02 2.50e+03 pdb=" C3B PEB I 202 " -0.045 2.00e-02 2.50e+03 pdb=" C4B PEB I 202 " 0.123 2.00e-02 2.50e+03 pdb=" CAB PEB I 202 " -0.380 2.00e-02 2.50e+03 pdb=" CHA PEB I 202 " -0.518 2.00e-02 2.50e+03 pdb=" CHB PEB I 202 " -0.010 2.00e-02 2.50e+03 pdb=" CMB PEB I 202 " 0.358 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB PEB D 202 " -0.365 2.00e-02 2.50e+03 2.62e-01 1.55e+03 pdb=" C1B PEB D 202 " -0.117 2.00e-02 2.50e+03 pdb=" C2B PEB D 202 " 0.037 2.00e-02 2.50e+03 pdb=" C3B PEB D 202 " -0.105 2.00e-02 2.50e+03 pdb=" C4B PEB D 202 " 0.010 2.00e-02 2.50e+03 pdb=" CAB PEB D 202 " -0.327 2.00e-02 2.50e+03 pdb=" CHA PEB D 202 " 0.040 2.00e-02 2.50e+03 pdb=" CHB PEB D 202 " 0.484 2.00e-02 2.50e+03 pdb=" CMB PEB D 202 " 0.342 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB PEB L 202 " -0.249 2.00e-02 2.50e+03 2.60e-01 1.52e+03 pdb=" C1B PEB L 202 " -0.106 2.00e-02 2.50e+03 pdb=" C2B PEB L 202 " 0.063 2.00e-02 2.50e+03 pdb=" C3B PEB L 202 " -0.103 2.00e-02 2.50e+03 pdb=" C4B PEB L 202 " 0.044 2.00e-02 2.50e+03 pdb=" CAB PEB L 202 " -0.403 2.00e-02 2.50e+03 pdb=" CHA PEB L 202 " -0.081 2.00e-02 2.50e+03 pdb=" CHB PEB L 202 " 0.436 2.00e-02 2.50e+03 pdb=" CMB PEB L 202 " 0.399 2.00e-02 2.50e+03 ... (remaining 4725 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 338 2.62 - 3.19: 24080 3.19 - 3.76: 49962 3.76 - 4.33: 67093 4.33 - 4.90: 106533 Nonbonded interactions: 248006 Sorted by model distance: nonbonded pdb=" OD2 ASP I 87 " pdb=" OH TYR g 106 " model vdw 2.045 3.040 nonbonded pdb=" OD2 ASP F 87 " pdb=" OH TYR a 106 " model vdw 2.061 3.040 nonbonded pdb=" OH TYR J 95 " pdb=" O ARG L 17 " model vdw 2.168 3.040 nonbonded pdb=" O TYR i 194 " pdb=" OG1 THR i 195 " model vdw 2.171 3.040 nonbonded pdb=" O ARG C 17 " pdb=" OH TYR G 95 " model vdw 2.173 3.040 ... (remaining 248001 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'Q' } ncs_group { reference = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'i' selection = chain 'k' } 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: 4.000 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: 0.030 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 21.820 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.080 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:8.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 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 : 0.006 0.079 27400 Z= 0.301 Angle : 0.653 10.324 37254 Z= 0.317 Chirality : 0.042 0.254 4062 Planarity : 0.018 0.281 4728 Dihedral : 16.961 89.715 11004 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.90 % Favored : 97.07 % Rotamer: Outliers : 0.47 % Allowed : 16.45 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 1.39 (0.14), residues: 3342 helix: 1.74 (0.12), residues: 1626 sheet: 0.20 (0.19), residues: 678 loop : 0.29 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG e 58 TYR 0.011 0.001 TYR e 235 PHE 0.009 0.002 PHE a 99 TRP 0.007 0.001 TRP k 240 HIS 0.006 0.001 HIS I 48 Details of bonding type rmsd covalent geometry : bond 0.00538 (27378) covalent geometry : angle 0.65305 (37230) SS BOND : bond 0.00219 ( 12) SS BOND : angle 0.53961 ( 24) hydrogen bonds : bond 0.13502 ( 1644) hydrogen bonds : angle 5.61642 ( 4731) Misc. bond : bond 0.06860 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 685 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 1 MET cc_start: 0.8042 (ptp) cc_final: 0.7772 (ptp) REVERT: c 22 VAL cc_start: 0.9018 (t) cc_final: 0.8714 (p) REVERT: c 221 ASN cc_start: 0.8351 (p0) cc_final: 0.7892 (p0) REVERT: g 155 LEU cc_start: 0.8668 (mt) cc_final: 0.8350 (tp) REVERT: k 221 ASN cc_start: 0.7999 (t0) cc_final: 0.7646 (p0) outliers start: 13 outliers final: 6 residues processed: 695 average time/residue: 0.7003 time to fit residues: 552.0714 Evaluate side-chains 618 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 612 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain G residue 50 CYS Chi-restraints excluded: chain I residue 139 CYS Chi-restraints excluded: chain M residue 50 CYS Chi-restraints excluded: chain Q residue 50 CYS Chi-restraints excluded: chain k residue 108 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- 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: 61.6533 > 50: distance: 20 - 37: 18.099 distance: 24 - 42: 19.508 distance: 29 - 49: 4.796 distance: 32 - 37: 16.064 distance: 33 - 57: 11.196 distance: 37 - 38: 13.352 distance: 38 - 39: 9.759 distance: 38 - 41: 11.168 distance: 39 - 40: 4.312 distance: 39 - 42: 24.185 distance: 40 - 63: 18.430 distance: 42 - 43: 14.854 distance: 43 - 44: 13.102 distance: 43 - 46: 14.118 distance: 44 - 45: 10.773 distance: 44 - 49: 17.718 distance: 45 - 71: 13.990 distance: 46 - 47: 17.518 distance: 46 - 48: 20.280 distance: 49 - 50: 15.043 distance: 50 - 51: 5.306 distance: 50 - 53: 13.697 distance: 51 - 52: 10.195 distance: 51 - 57: 9.788 distance: 52 - 78: 11.576 distance: 53 - 54: 3.866 distance: 54 - 55: 4.328 distance: 54 - 56: 5.739 distance: 57 - 58: 17.162 distance: 58 - 59: 7.243 distance: 58 - 61: 8.646 distance: 59 - 60: 3.397 distance: 59 - 63: 8.174 distance: 61 - 62: 10.824 distance: 63 - 64: 7.690 distance: 64 - 65: 5.384 distance: 64 - 67: 17.096 distance: 65 - 66: 5.490 distance: 65 - 71: 7.203 distance: 67 - 68: 18.599 distance: 67 - 69: 18.281 distance: 68 - 70: 17.971 distance: 71 - 72: 4.078 distance: 72 - 73: 7.562 distance: 72 - 75: 7.592 distance: 73 - 74: 18.437 distance: 73 - 78: 12.702 distance: 75 - 76: 9.830 distance: 75 - 77: 14.231 distance: 78 - 79: 19.225 distance: 79 - 80: 6.274 distance: 79 - 82: 19.934 distance: 80 - 81: 11.427 distance: 80 - 84: 12.824 distance: 82 - 83: 23.264 distance: 84 - 85: 11.993 distance: 85 - 86: 13.567 distance: 85 - 88: 12.242 distance: 86 - 87: 17.583 distance: 86 - 92: 11.539 distance: 87 - 109: 19.342 distance: 88 - 89: 23.414 distance: 89 - 90: 12.232 distance: 89 - 91: 13.772 distance: 92 - 93: 6.138 distance: 93 - 94: 7.385 distance: 93 - 96: 31.169 distance: 94 - 95: 51.926 distance: 94 - 97: 20.271 distance: 95 - 117: 30.842 distance: 97 - 98: 20.277 distance: 98 - 99: 26.585 distance: 98 - 101: 16.471 distance: 99 - 100: 21.321 distance: 99 - 103: 11.889 distance: 100 - 123: 26.051 distance: 101 - 102: 37.077