Starting phenix.real_space_refine on Wed Aug 27 02:55:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z15_14441/08_2025/7z15_14441_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z15_14441/08_2025/7z15_14441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7z15_14441/08_2025/7z15_14441_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z15_14441/08_2025/7z15_14441_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z15_14441/08_2025/7z15_14441.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z15_14441/08_2025/7z15_14441.map" } resolution = 1.93 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= 0.069 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: 8 Type Number sf(0) Gaussians Zn 4 6.06 5 P 16 5.49 5 Mg 4 5.21 5 S 96 5.16 5 C 14134 2.51 5 N 4020 2.21 5 O 5481 1.98 5 H 22357 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 46112 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2195 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "B" Number of atoms: 2961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 2961 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 178} Chain: "C" Number of atoms: 5412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 5412 Classifications: {'peptide': 353} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 332} Chain: "D" Number of atoms: 4365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 4365 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 20, 'TRANS': 257} Chain: "E" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2195 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "F" Number of atoms: 2961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 2961 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 178} Chain: "G" Number of atoms: 5413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 5413 Classifications: {'peptide': 353} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 332} Chain: "H" Number of atoms: 4365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 4365 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 20, 'TRANS': 257} Chain: "I" Number of atoms: 3950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 3950 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 3950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 3950 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 3503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3503 Classifications: {'peptide': 224} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 212} Chain: "L" Number of atoms: 3503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3503 Classifications: {'peptide': 224} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 212} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {' ZN': 1, 'I9X': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {' ZN': 1, 'I9X': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "B" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 210 Classifications: {'water': 210} Link IDs: {None: 209} Chain: "D" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 170 Classifications: {'water': 170} Link IDs: {None: 169} Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "F" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "G" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 220 Classifications: {'water': 220} Link IDs: {None: 219} Chain: "H" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 162 Classifications: {'water': 162} Link IDs: {None: 161} Chain: "I" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "J" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "K" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "L" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14374 SG CYS D 241 84.847 38.738 104.685 1.00 19.21 S ATOM 14413 SG CYS D 244 84.335 35.032 104.151 1.00 21.52 S ATOM 14733 SG CYS D 266 81.721 37.434 103.090 1.00 15.69 S ATOM 14813 SG CYS D 272 82.451 37.045 106.927 1.00 18.26 S ATOM 29308 SG CYS H 241 18.783 99.997 104.669 1.00 19.24 S ATOM 29347 SG CYS H 244 19.296 103.703 104.134 1.00 21.67 S ATOM 29667 SG CYS H 266 21.909 101.300 103.075 1.00 15.74 S ATOM 29747 SG CYS H 272 21.178 101.691 106.912 1.00 18.34 S Time building chain proxies: 6.75, per 1000 atoms: 0.15 Number of scatterers: 46112 At special positions: 0 Unit cell: (104.462, 139.562, 156.276, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 S 96 16.00 P 16 15.00 Mg 4 11.99 O 5481 8.00 N 4020 7.00 C 14134 6.00 H 22357 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 Time building additional restraints: 3.28 Conformation dependent library (CDL) restraints added in 869.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C1000 " pdb="ZN ZN C1000 " - pdb=" NE2 HIS C 333 " pdb="ZN ZN C1000 " - pdb=" NE2 HIS C 328 " pdb=" ZN D1000 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 241 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 244 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 266 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 272 " pdb=" ZN G1000 " pdb="ZN ZN G1000 " - pdb=" NE2 HIS G 333 " pdb="ZN ZN G1000 " - pdb=" NE2 HIS G 328 " pdb=" ZN H1000 " pdb="ZN ZN H1000 " - pdb=" SG CYS H 241 " pdb="ZN ZN H1000 " - pdb=" SG CYS H 244 " pdb="ZN ZN H1000 " - pdb=" SG CYS H 266 " pdb="ZN ZN H1000 " - pdb=" SG CYS H 272 " Number of angles added : 12 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5368 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 26 sheets defined 46.2% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 3 through 18 Processing helix chain 'A' and resid 19 through 31 Processing helix chain 'A' and resid 54 through 56 No H-bonds generated for 'chain 'A' and resid 54 through 56' Processing helix chain 'A' and resid 88 through 103 removed outlier: 3.621A pdb=" N GLN A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 115 removed outlier: 4.677A pdb=" N GLN A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ASN A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 136 Processing helix chain 'B' and resid 9 through 27 Processing helix chain 'B' and resid 45 through 56 Processing helix chain 'B' and resid 66 through 69 Processing helix chain 'B' and resid 70 through 82 Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'B' and resid 102 through 109 Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.863A pdb=" N GLY B 120 " --> pdb=" O PRO B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 164 Processing helix chain 'C' and resid 7 through 25 Processing helix chain 'C' and resid 33 through 41 Processing helix chain 'C' and resid 41 through 53 Processing helix chain 'C' and resid 56 through 67 Processing helix chain 'C' and resid 70 through 84 removed outlier: 3.684A pdb=" N THR C 83 " --> pdb=" O ARG C 79 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 130 through 135 Processing helix chain 'C' and resid 154 through 162 Processing helix chain 'C' and resid 188 through 198 Processing helix chain 'C' and resid 200 through 213 Processing helix chain 'C' and resid 281 through 295 Processing helix chain 'C' and resid 295 through 300 Processing helix chain 'C' and resid 305 through 308 Processing helix chain 'C' and resid 309 through 316 removed outlier: 3.772A pdb=" N HIS C 316 " --> pdb=" O PHE C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 333 through 353 Processing helix chain 'D' and resid 13 through 30 Processing helix chain 'D' and resid 49 through 60 Processing helix chain 'D' and resid 76 through 90 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 137 through 147 removed outlier: 4.242A pdb=" N THR D 143 " --> pdb=" O THR D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 165 Processing helix chain 'D' and resid 189 through 197 Proline residue: D 194 - end of helix Processing helix chain 'D' and resid 268 through 279 Processing helix chain 'E' and resid 4 through 18 Processing helix chain 'E' and resid 19 through 31 Processing helix chain 'E' and resid 54 through 56 No H-bonds generated for 'chain 'E' and resid 54 through 56' Processing helix chain 'E' and resid 88 through 103 removed outlier: 3.620A pdb=" N GLN E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 115 removed outlier: 4.678A pdb=" N GLN E 109 " --> pdb=" O SER E 105 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ASN E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 136 Processing helix chain 'F' and resid 9 through 27 Processing helix chain 'F' and resid 45 through 56 Processing helix chain 'F' and resid 66 through 69 Processing helix chain 'F' and resid 70 through 82 Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 102 through 109 Processing helix chain 'F' and resid 116 through 120 removed outlier: 3.863A pdb=" N GLY F 120 " --> pdb=" O PRO F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 164 Processing helix chain 'G' and resid 7 through 25 Processing helix chain 'G' and resid 33 through 41 Processing helix chain 'G' and resid 41 through 53 Processing helix chain 'G' and resid 56 through 67 Processing helix chain 'G' and resid 70 through 84 removed outlier: 3.684A pdb=" N THR G 83 " --> pdb=" O ARG G 79 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR G 84 " --> pdb=" O ALA G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 99 Processing helix chain 'G' and resid 130 through 135 Processing helix chain 'G' and resid 154 through 162 Processing helix chain 'G' and resid 188 through 198 Processing helix chain 'G' and resid 200 through 213 Processing helix chain 'G' and resid 281 through 295 Processing helix chain 'G' and resid 295 through 300 Processing helix chain 'G' and resid 305 through 308 Processing helix chain 'G' and resid 309 through 316 removed outlier: 3.772A pdb=" N HIS G 316 " --> pdb=" O PHE G 312 " (cutoff:3.500A) Processing helix chain 'G' and resid 318 through 328 Processing helix chain 'G' and resid 329 through 331 No H-bonds generated for 'chain 'G' and resid 329 through 331' Processing helix chain 'G' and resid 333 through 353 Processing helix chain 'H' and resid 13 through 30 Processing helix chain 'H' and resid 49 through 60 Processing helix chain 'H' and resid 76 through 90 Processing helix chain 'H' and resid 97 through 101 Processing helix chain 'H' and resid 137 through 147 removed outlier: 4.242A pdb=" N THR H 143 " --> pdb=" O THR H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 165 Processing helix chain 'H' and resid 189 through 197 Proline residue: H 194 - end of helix Processing helix chain 'H' and resid 268 through 279 Processing helix chain 'I' and resid 43 through 52 Processing helix chain 'I' and resid 73 through 84 Processing helix chain 'I' and resid 91 through 96 Processing helix chain 'I' and resid 101 through 113 removed outlier: 4.395A pdb=" N ARG I 109 " --> pdb=" O ASN I 105 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU I 110 " --> pdb=" O ILE I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 132 Processing helix chain 'I' and resid 135 through 139 Processing helix chain 'I' and resid 142 through 146 Processing helix chain 'I' and resid 147 through 161 Processing helix chain 'I' and resid 177 through 196 Processing helix chain 'I' and resid 205 through 213 Processing helix chain 'I' and resid 230 through 236 Processing helix chain 'I' and resid 239 through 248 Processing helix chain 'J' and resid 43 through 52 Processing helix chain 'J' and resid 73 through 84 Processing helix chain 'J' and resid 91 through 96 Processing helix chain 'J' and resid 101 through 113 removed outlier: 4.396A pdb=" N ARG J 109 " --> pdb=" O ASN J 105 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU J 110 " --> pdb=" O ILE J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 132 Processing helix chain 'J' and resid 135 through 139 Processing helix chain 'J' and resid 142 through 146 Processing helix chain 'J' and resid 147 through 161 Processing helix chain 'J' and resid 177 through 196 Processing helix chain 'J' and resid 205 through 213 Processing helix chain 'J' and resid 230 through 236 Processing helix chain 'J' and resid 239 through 248 Processing helix chain 'K' and resid 46 through 55 Processing helix chain 'K' and resid 80 through 91 Processing helix chain 'K' and resid 106 through 117 Proline residue: K 114 - end of helix Processing helix chain 'K' and resid 121 through 136 Processing helix chain 'K' and resid 139 through 143 Processing helix chain 'K' and resid 146 through 150 Processing helix chain 'K' and resid 151 through 165 Processing helix chain 'K' and resid 181 through 198 Processing helix chain 'K' and resid 208 through 216 Processing helix chain 'L' and resid 46 through 55 Processing helix chain 'L' and resid 80 through 91 Processing helix chain 'L' and resid 106 through 117 Proline residue: L 114 - end of helix Processing helix chain 'L' and resid 121 through 136 Processing helix chain 'L' and resid 139 through 143 Processing helix chain 'L' and resid 146 through 150 Processing helix chain 'L' and resid 151 through 165 Processing helix chain 'L' and resid 181 through 198 Processing helix chain 'L' and resid 208 through 216 Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 85 removed outlier: 4.926A pdb=" N ILE A 49 " --> pdb=" O ALA A 62 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ASP A 64 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL A 47 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR A 66 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY A 45 " --> pdb=" O THR A 66 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR A 68 " --> pdb=" O GLU A 43 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLU A 43 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ALA A 70 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ALA A 41 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL A 72 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ILE A 39 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU A 74 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLU A 37 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LYS C 87 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU A 46 " --> pdb=" O LYS C 87 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 89 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139 removed outlier: 4.621A pdb=" N GLN C 116 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 144 Processing sheet with id=AA4, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.308A pdb=" N LEU B 123 " --> pdb=" O ILE B 175 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N THR B 177 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU B 125 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ALA B 95 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLN B 126 " --> pdb=" O ALA B 95 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR B 97 " --> pdb=" O GLN B 126 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP B 63 " --> pdb=" O VAL B 96 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 147 through 149 Processing sheet with id=AA6, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AA7, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.519A pdb=" N SER C 227 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG C 104 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE C 225 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ALA C 222 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL C 256 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY C 246 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE C 234 " --> pdb=" O ASN C 244 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASN C 244 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE C 259 " --> pdb=" O HIS C 268 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N HIS C 268 " --> pdb=" O PHE C 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 35 through 36 removed outlier: 6.447A pdb=" N ILE D 104 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLN D 124 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N THR D 106 " --> pdb=" O GLN D 124 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AB1, first strand: chain 'D' and resid 251 through 255 Processing sheet with id=AB2, first strand: chain 'E' and resid 79 through 85 removed outlier: 4.926A pdb=" N ILE E 49 " --> pdb=" O ALA E 62 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ASP E 64 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL E 47 " --> pdb=" O ASP E 64 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N THR E 66 " --> pdb=" O GLY E 45 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY E 45 " --> pdb=" O THR E 66 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR E 68 " --> pdb=" O GLU E 43 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLU E 43 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ALA E 70 " --> pdb=" O ALA E 41 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ALA E 41 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL E 72 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ILE E 39 " --> pdb=" O VAL E 72 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU E 74 " --> pdb=" O GLU E 37 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLU E 37 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LYS G 87 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU E 46 " --> pdb=" O LYS G 87 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA G 89 " --> pdb=" O LEU E 46 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 138 through 139 removed outlier: 4.616A pdb=" N GLN G 116 " --> pdb=" O VAL E 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 32 through 33 removed outlier: 6.308A pdb=" N LEU F 123 " --> pdb=" O ILE F 175 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N THR F 177 " --> pdb=" O LEU F 123 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU F 125 " --> pdb=" O THR F 177 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ALA F 95 " --> pdb=" O ILE F 124 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N GLN F 126 " --> pdb=" O ALA F 95 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR F 97 " --> pdb=" O GLN F 126 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TRP F 63 " --> pdb=" O VAL F 96 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 147 through 149 Processing sheet with id=AB6, first strand: chain 'G' and resid 100 through 105 removed outlier: 6.519A pdb=" N SER G 227 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG G 104 " --> pdb=" O ILE G 225 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE G 225 " --> pdb=" O ARG G 104 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ALA G 222 " --> pdb=" O VAL G 256 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL G 256 " --> pdb=" O ALA G 222 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY G 246 " --> pdb=" O VAL G 232 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE G 234 " --> pdb=" O ASN G 244 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ASN G 244 " --> pdb=" O ILE G 234 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR G 270 " --> pdb=" O ASN G 257 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE G 259 " --> pdb=" O HIS G 268 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N HIS G 268 " --> pdb=" O PHE G 259 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 35 through 36 removed outlier: 6.447A pdb=" N ILE H 104 " --> pdb=" O ILE H 122 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLN H 124 " --> pdb=" O ILE H 104 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N THR H 106 " --> pdb=" O GLN H 124 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 181 through 183 Processing sheet with id=AB9, first strand: chain 'H' and resid 251 through 255 Processing sheet with id=AC1, first strand: chain 'I' and resid 19 through 28 removed outlier: 7.684A pdb=" N GLY I 20 " --> pdb=" O TYR I 15 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N TYR I 15 " --> pdb=" O GLY I 20 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N SER I 22 " --> pdb=" O HIS I 13 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N HIS I 13 " --> pdb=" O SER I 22 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N PHE I 26 " --> pdb=" O ASN I 9 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASN I 9 " --> pdb=" O PHE I 26 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU I 28 " --> pdb=" O SER I 7 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N SER I 7 " --> pdb=" O LEU I 28 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU I 11 " --> pdb=" O GLN I 59 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLN I 59 " --> pdb=" O LEU I 11 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 85 through 88 removed outlier: 6.193A pdb=" N GLY I 86 " --> pdb=" O PHE I 168 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ASP I 170 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL I 88 " --> pdb=" O ASP I 170 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU I 216 " --> pdb=" O SER I 227 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N SER I 227 " --> pdb=" O LEU I 216 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL I 218 " --> pdb=" O VAL I 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 19 through 28 removed outlier: 6.734A pdb=" N GLY J 20 " --> pdb=" O LEU J 14 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU J 14 " --> pdb=" O GLY J 20 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N SER J 22 " --> pdb=" O THR J 12 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N THR J 12 " --> pdb=" O SER J 22 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N VAL J 24 " --> pdb=" O ASN J 10 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU J 11 " --> pdb=" O GLN J 59 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLN J 59 " --> pdb=" O LEU J 11 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 85 through 88 removed outlier: 6.194A pdb=" N GLY J 86 " --> pdb=" O PHE J 168 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ASP J 170 " --> pdb=" O GLY J 86 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL J 88 " --> pdb=" O ASP J 170 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU J 226 " --> pdb=" O VAL J 218 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LYS J 220 " --> pdb=" O VAL J 224 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N VAL J 224 " --> pdb=" O LYS J 220 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 20 through 31 removed outlier: 7.047A pdb=" N LEU K 21 " --> pdb=" O ILE K 12 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ILE K 12 " --> pdb=" O LEU K 21 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL K 23 " --> pdb=" O THR K 10 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N THR K 10 " --> pdb=" O VAL K 23 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASN K 25 " --> pdb=" O SER K 8 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N SER K 8 " --> pdb=" O ASN K 25 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ALA K 27 " --> pdb=" O ASN K 6 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL K 7 " --> pdb=" O GLU K 62 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLU K 62 " --> pdb=" O VAL K 7 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 92 through 95 Processing sheet with id=AC7, first strand: chain 'L' and resid 20 through 31 removed outlier: 7.046A pdb=" N LEU L 21 " --> pdb=" O ILE L 12 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ILE L 12 " --> pdb=" O LEU L 21 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL L 23 " --> pdb=" O THR L 10 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N THR L 10 " --> pdb=" O VAL L 23 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASN L 25 " --> pdb=" O SER L 8 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N SER L 8 " --> pdb=" O ASN L 25 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ALA L 27 " --> pdb=" O ASN L 6 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL L 7 " --> pdb=" O GLU L 62 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLU L 62 " --> pdb=" O VAL L 7 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 92 through 95 1111 hydrogen bonds defined for protein. 3075 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: 10.26 Time building geometry restraints manager: 4.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.14: 22388 1.14 - 1.44: 9617 1.44 - 1.74: 13196 1.74 - 2.04: 168 2.04 - 2.34: 4 Bond restraints: 45373 Sorted by residual: bond pdb=" C HIS G 219 " pdb=" O HIS G 219 " ideal model delta sigma weight residual 1.235 1.137 0.098 4.70e-03 4.53e+04 4.35e+02 bond pdb=" C HIS C 219 " pdb=" O HIS C 219 " ideal model delta sigma weight residual 1.235 1.140 0.095 4.70e-03 4.53e+04 4.04e+02 bond pdb=" C VAL G 245 " pdb=" O VAL G 245 " ideal model delta sigma weight residual 1.239 1.017 0.222 1.13e-02 7.83e+03 3.86e+02 bond pdb=" C VAL C 245 " pdb=" O VAL C 245 " ideal model delta sigma weight residual 1.239 1.017 0.222 1.13e-02 7.83e+03 3.86e+02 bond pdb=" C GLY D 151 " pdb=" O GLY D 151 " ideal model delta sigma weight residual 1.234 1.008 0.225 1.20e-02 6.94e+03 3.52e+02 ... (remaining 45368 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.48: 81367 3.48 - 6.96: 628 6.96 - 10.44: 64 10.44 - 13.92: 5 13.92 - 17.40: 10 Bond angle restraints: 82074 Sorted by residual: angle pdb=" C TYR H 171 " pdb=" CA TYR H 171 " pdb=" CB TYR H 171 " ideal model delta sigma weight residual 110.67 127.35 -16.68 2.23e+00 2.01e-01 5.60e+01 angle pdb=" C TYR D 171 " pdb=" CA TYR D 171 " pdb=" CB TYR D 171 " ideal model delta sigma weight residual 110.67 127.22 -16.55 2.23e+00 2.01e-01 5.51e+01 angle pdb=" N PRO G 220 " pdb=" CA PRO G 220 " pdb=" CB PRO G 220 " ideal model delta sigma weight residual 103.19 110.14 -6.95 9.50e-01 1.11e+00 5.35e+01 angle pdb=" CA GLU C 340 " pdb=" C GLU C 340 " pdb=" O GLU C 340 " ideal model delta sigma weight residual 120.90 113.11 7.79 1.07e+00 8.73e-01 5.29e+01 angle pdb=" N ALA G 339 " pdb=" CA ALA G 339 " pdb=" C ALA G 339 " ideal model delta sigma weight residual 111.14 103.46 7.68 1.08e+00 8.57e-01 5.05e+01 ... (remaining 82069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.12: 20656 35.12 - 70.25: 640 70.25 - 105.37: 51 105.37 - 140.49: 8 140.49 - 175.62: 2 Dihedral angle restraints: 21357 sinusoidal: 11932 harmonic: 9425 Sorted by residual: dihedral pdb=" C5' ADP J1000 " pdb=" O5' ADP J1000 " pdb=" PA ADP J1000 " pdb=" O2A ADP J1000 " ideal model delta sinusoidal sigma weight residual -60.00 -170.73 110.73 1 2.00e+01 2.50e-03 3.25e+01 dihedral pdb=" C5' ADP I1000 " pdb=" O5' ADP I1000 " pdb=" PA ADP I1000 " pdb=" O2A ADP I1000 " ideal model delta sinusoidal sigma weight residual -60.00 -170.68 110.68 1 2.00e+01 2.50e-03 3.25e+01 dihedral pdb=" C PHE G 221 " pdb=" N PHE G 221 " pdb=" CA PHE G 221 " pdb=" CB PHE G 221 " ideal model delta harmonic sigma weight residual -122.60 -109.18 -13.42 0 2.50e+00 1.60e-01 2.88e+01 ... (remaining 21354 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3167 0.079 - 0.158: 333 0.158 - 0.238: 37 0.238 - 0.317: 28 0.317 - 0.396: 11 Chirality restraints: 3576 Sorted by residual: chirality pdb=" C04 I9X D1001 " pdb=" C03 I9X D1001 " pdb=" O10 I9X D1001 " pdb=" P08 I9X D1001 " both_signs ideal model delta sigma weight residual True 1.45 -1.84 -0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" C04 I9X H1001 " pdb=" C03 I9X H1001 " pdb=" O10 I9X H1001 " pdb=" P08 I9X H1001 " both_signs ideal model delta sigma weight residual True 1.45 -1.84 -0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" CA THR F 162 " pdb=" N THR F 162 " pdb=" C THR F 162 " pdb=" CB THR F 162 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.37 2.00e-01 2.50e+01 3.42e+00 ... (remaining 3573 not shown) Planarity restraints: 6818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN K 6 " -0.015 2.00e-02 2.50e+03 4.42e-01 2.93e+03 pdb=" CG ASN K 6 " 0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN K 6 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN K 6 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN K 6 " 0.763 2.00e-02 2.50e+03 pdb="HD22 ASN K 6 " -0.768 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN K 25 " -0.097 2.00e-02 2.50e+03 4.37e-01 2.87e+03 pdb=" CG ASN K 25 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN K 25 " 0.090 2.00e-02 2.50e+03 pdb=" ND2 ASN K 25 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN K 25 " 0.744 2.00e-02 2.50e+03 pdb="HD22 ASN K 25 " -0.759 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 244 " 0.119 2.00e-02 2.50e+03 4.33e-01 2.82e+03 pdb=" CG ASN C 244 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN C 244 " -0.106 2.00e-02 2.50e+03 pdb=" ND2 ASN C 244 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN C 244 " 0.749 2.00e-02 2.50e+03 pdb="HD22 ASN C 244 " -0.735 2.00e-02 2.50e+03 ... (remaining 6815 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 2269 2.16 - 2.77: 90403 2.77 - 3.38: 145217 3.38 - 3.99: 194915 3.99 - 4.60: 294903 Nonbonded interactions: 727707 Sorted by model distance: nonbonded pdb=" H GLY J 41 " pdb=" O2B ADP J1000 " model vdw 1.549 2.450 nonbonded pdb=" H GLY I 41 " pdb=" O2B ADP I1000 " model vdw 1.549 2.450 nonbonded pdb=" HG1 THR J 45 " pdb="MG MG J1002 " model vdw 1.565 1.700 nonbonded pdb=" HG1 THR I 45 " pdb="MG MG I1002 " model vdw 1.565 1.700 nonbonded pdb=" O PHE C 325 " pdb=" HD1 HIS C 328 " model vdw 1.592 2.450 ... (remaining 727702 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and (resid 1 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE \ 1)) or resid 17 through 1000)) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } 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=0.00 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: 6.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.360 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 45.970 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.110 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:6.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 : 0.013 0.328 23028 Z= 0.885 Angle : 1.010 17.402 31334 Z= 0.626 Chirality : 0.057 0.396 3576 Planarity : 0.009 0.258 4098 Dihedral : 15.882 175.618 8644 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.83 % Allowed : 7.88 % Favored : 91.29 % Cbeta Deviations : 0.34 % 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: 1.32 (0.16), residues: 2864 helix: 1.76 (0.16), residues: 1134 sheet: 0.04 (0.24), residues: 492 loop : 0.55 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG D 18 TYR 0.044 0.003 TYR H 158 PHE 0.099 0.003 PHE L 98 TRP 0.032 0.002 TRP A 83 HIS 0.020 0.001 HIS G 219 Details of bonding type rmsd covalent geometry : bond 0.01215 (23016) covalent geometry : angle 1.00698 (31322) hydrogen bonds : bond 0.12462 ( 1111) hydrogen bonds : angle 6.16783 ( 3075) metal coordination : bond 0.13004 ( 12) metal coordination : angle 3.97031 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 338 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 318 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 7 residues processed: 334 average time/residue: 1.4840 time to fit residues: 560.2489 Evaluate side-chains 288 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 281 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain D residue 262 ARG Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 194 CYS Chi-restraints excluded: chain H residue 262 ARG Chi-restraints excluded: chain H residue 276 SER 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: 62.9389 > 50: distance: 250 - 451: 4.677 distance: 253 - 484: 7.575 distance: 284 - 487: 9.367 distance: 287 - 523: 5.473 distance: 426 - 438: 3.433 distance: 438 - 439: 3.529 distance: 438 - 443: 4.302 distance: 439 - 440: 4.063 distance: 439 - 442: 5.425 distance: 439 - 444: 10.360 distance: 440 - 441: 16.671 distance: 440 - 448: 5.808 distance: 442 - 445: 9.777 distance: 442 - 446: 15.366 distance: 442 - 447: 14.950 distance: 448 - 449: 4.629 distance: 448 - 456: 7.477 distance: 449 - 452: 4.752 distance: 449 - 457: 4.753 distance: 450 - 467: 4.822 distance: 452 - 453: 3.935 distance: 452 - 458: 6.497 distance: 452 - 459: 4.118 distance: 453 - 454: 5.024 distance: 453 - 455: 6.665 distance: 453 - 460: 6.542 distance: 454 - 461: 3.094 distance: 454 - 463: 5.172 distance: 455 - 464: 11.643 distance: 455 - 465: 7.173 distance: 455 - 466: 3.632 distance: 467 - 476: 6.194 distance: 467 - 676: 6.113 distance: 468 - 477: 10.442 distance: 469 - 470: 8.795 distance: 469 - 484: 4.825 distance: 470 - 673: 12.645 distance: 471 - 472: 3.633 distance: 471 - 478: 7.066 distance: 471 - 479: 3.294 distance: 472 - 473: 5.349 distance: 472 - 480: 7.669 distance: 472 - 481: 4.605 distance: 473 - 474: 5.813 distance: 475 - 482: 6.888 distance: 484 - 485: 4.628 distance: 484 - 492: 7.203 distance: 485 - 486: 3.594 distance: 485 - 493: 3.645 distance: 486 - 487: 5.984 distance: 486 - 503: 4.505 distance: 488 - 489: 4.096 distance: 488 - 494: 6.811 distance: 488 - 495: 9.002 distance: 489 - 490: 4.429 distance: 489 - 496: 3.130 distance: 490 - 497: 3.827 distance: 490 - 498: 6.611 distance: 490 - 499: 6.069 distance: 491 - 500: 5.351 distance: 491 - 501: 6.373 distance: 503 - 645: 3.866 distance: 504 - 505: 3.459 distance: 504 - 507: 5.916 distance: 504 - 515: 6.301 distance: 505 - 506: 6.949 distance: 505 - 523: 4.689 distance: 506 - 642: 3.716 distance: 507 - 508: 3.905 distance: 507 - 516: 3.462 distance: 507 - 517: 9.746 distance: 508 - 509: 5.201 distance: 508 - 510: 5.312 distance: 509 - 518: 4.394 distance: 511 - 520: 4.263 distance: 512 - 521: 3.812 distance: 513 - 522: 3.179 distance: 523 - 524: 4.306 distance: 523 - 527: 9.187 distance: 524 - 525: 4.622 distance: 524 - 528: 12.753 distance: 524 - 529: 11.197 distance: 525 - 526: 7.606 distance: 525 - 530: 4.249 distance: 530 - 531: 4.116 distance: 530 - 535: 5.312 distance: 530 - 609: 6.299 distance: 531 - 532: 6.782 distance: 531 - 536: 4.281 distance: 532 - 533: 6.121 distance: 534 - 537: 3.563 distance: 534 - 538: 3.312 distance: 534 - 539: 3.349 distance: 540 - 541: 5.838 distance: 540 - 544: 3.787 distance: 541 - 542: 8.562 distance: 541 - 545: 15.614 distance: 541 - 546: 13.602 distance: 542 - 543: 5.024 distance: 542 - 547: 7.309 distance: 547 - 548: 10.043 distance: 547 - 558: 15.635 distance: 548 - 549: 4.009 distance: 548 - 551: 3.970 distance: 548 - 559: 5.447 distance: 549 - 550: 24.916 distance: 549 - 571: 19.510 distance: 551 - 552: 12.954 distance: 551 - 560: 4.854 distance: 551 - 561: 5.578 distance: 552 - 553: 4.926 distance: 552 - 562: 5.089 distance: 552 - 563: 13.379 distance: 553 - 554: 6.556 distance: 553 - 564: 7.061 distance: 553 - 565: 5.439 distance: 554 - 555: 12.419 distance: 554 - 566: 4.989 distance: 555 - 556: 6.859 distance: 555 - 557: 9.084 distance: 556 - 567: 3.905 distance: 556 - 568: 4.429 distance: 557 - 569: 3.160 distance: 557 - 570: 5.872 distance: 571 - 572: 9.420 distance: 571 - 580: 25.403 distance: 572 - 573: 7.418 distance: 572 - 575: 12.361 distance: 572 - 581: 26.851 distance: 573 - 574: 15.986 distance: 573 - 586: 5.545 distance: 575 - 576: 11.679 distance: 575 - 582: 13.787 distance: 575 - 583: 10.654 distance: 576 - 577: 5.313 distance: 576 - 584: 11.571 distance: 576 - 585: 6.590 distance: 577 - 578: 4.711 distance: 577 - 579: 6.368