Starting phenix.real_space_refine (version: 1.21rc1) on Wed May 17 02:54:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czl_30511/05_2023/7czl_30511_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czl_30511/05_2023/7czl_30511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czl_30511/05_2023/7czl_30511.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czl_30511/05_2023/7czl_30511.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czl_30511/05_2023/7czl_30511_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czl_30511/05_2023/7czl_30511_updated.pdb" } resolution = 3.78 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2658 atoms to isotropic. 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: 9 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 4 7.16 5 P 2 5.49 5 Mg 70 5.21 5 S 140 5.16 5 Cl 2 4.86 5 C 28272 2.51 5 N 5784 2.21 5 O 6583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 16": "NH1" <-> "NH2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B ARG 384": "NH1" <-> "NH2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B ARG 472": "NH1" <-> "NH2" Residue "C ARG 207": "NH1" <-> "NH2" Residue "C ARG 261": "NH1" <-> "NH2" Residue "C ARG 320": "NH1" <-> "NH2" Residue "C ARG 362": "NH1" <-> "NH2" Residue "C ARG 390": "NH1" <-> "NH2" Residue "D ARG 24": "NH1" <-> "NH2" Residue "E ARG 51": "NH1" <-> "NH2" Residue "I ARG 34": "NH1" <-> "NH2" Residue "K ARG 46": "NH1" <-> "NH2" Residue "T ARG 28": "NH1" <-> "NH2" Residue "a ARG 5016": "NH1" <-> "NH2" Residue "a PHE 5300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 5057": "NH1" <-> "NH2" Residue "b ARG 5068": "NH1" <-> "NH2" Residue "b ARG 5384": "NH1" <-> "NH2" Residue "b ARG 5385": "NH1" <-> "NH2" Residue "b ARG 5472": "NH1" <-> "NH2" Residue "c ARG 5207": "NH1" <-> "NH2" Residue "c ARG 5261": "NH1" <-> "NH2" Residue "c ARG 5320": "NH1" <-> "NH2" Residue "c ARG 5362": "NH1" <-> "NH2" Residue "c ARG 5390": "NH1" <-> "NH2" Residue "c ARG 5461": "NH1" <-> "NH2" Residue "e ARG 5051": "NH1" <-> "NH2" Residue "i ARG 5034": "NH1" <-> "NH2" Residue "t ARG 5028": "NH1" <-> "NH2" Residue "n ARG 45": "NH1" <-> "NH2" Residue "n ARG 76": "NH1" <-> "NH2" Residue "n ARG 82": "NH1" <-> "NH2" Residue "n ARG 107": "NH1" <-> "NH2" Residue "n ARG 130": "NH1" <-> "NH2" Residue "N ARG 45": "NH1" <-> "NH2" Residue "N ARG 82": "NH1" <-> "NH2" Residue "N ARG 107": "NH1" <-> "NH2" Residue "N ARG 130": "NH1" <-> "NH2" Residue "y ARG 42": "NH1" <-> "NH2" Residue "y ARG 43": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 40859 Number of models: 1 Model: "" Number of chains: 55 Chain: "A" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2533 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 310} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3784 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 31, 'TRANS': 452} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 3412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3412 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 24, 'TRANS': 421} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "D" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2693 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 323} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 522 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 60} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 242 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 29} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 482 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 58} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 277 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Chain: "K" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 289 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 32} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 301 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "M" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 258 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "T" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 254 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 27} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Z" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 442 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 59} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "a" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2523 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 308} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "b" Number of atoms: 3780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3780 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 31, 'TRANS': 452} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "c" Number of atoms: 3412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3412 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 24, 'TRANS': 421} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "d" Number of atoms: 2687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2687 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 323} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "e" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 522 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 60} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "f" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 219 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "h" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 482 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 58} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "i" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 277 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Chain: "k" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 264 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 3, 'TRANS': 30} Chain: "l" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 301 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "m" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 258 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "t" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 254 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 27} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "z" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 442 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 59} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "Y" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 215 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "n" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 860 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "N" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 860 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "y" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 215 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "X" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 254 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "x" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 254 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "A" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 551 Unusual residues: {'BCR': 1, 'BCT': 1, 'CLA': 4, 'LHG': 1, 'LMT': 1, 'MGE': 1, 'PHO': 1, 'PQ9': 1, 'SQD': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 1170 Unusual residues: {'BCR': 2, 'CLA': 16, 'LMT': 1, 'MGE': 1} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'CLA:plan-4': 1, 'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 1100 Unusual residues: {' CA': 1, 'BCR': 3, 'CLA': 13, 'DGD': 3, 'MGE': 1} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'CLA:plan-5': 2} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 455 Unusual residues: {'BCR': 1, 'CLA': 2, 'FE2': 1, 'MGE': 3, 'PHO': 1, 'PQ9': 1, 'SQD': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 94 Unusual residues: {'BCR': 1, 'DGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "L" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'SQD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "M" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'BCR': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 545 Unusual residues: {'BCR': 1, 'BCT': 1, 'CLA': 4, 'DGD': 1, 'LHG': 1, 'LMT': 1, 'PHO': 1, 'PQ9': 1, 'SQD': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PQ9:plan-4': 1, 'PQ9:plan-2': 1, 'PQ9:plan-3': 1} Unresolved non-hydrogen planarities: 15 Chain: "b" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 1153 Unusual residues: {'BCR': 3, 'CLA': 16, 'MGE': 1} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'CLA:plan-4': 2, 'CLA:plan-5': 2} Unresolved non-hydrogen planarities: 16 Chain: "c" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 938 Unusual residues: {' CA': 1, 'BCR': 2, 'CLA': 12, 'DGD': 2, 'MGE': 1} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'CLA:plan-5': 2} Unresolved non-hydrogen planarities: 7 Chain: "d" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 455 Unusual residues: {'BCR': 1, 'CLA': 2, 'FE2': 1, 'MGE': 3, 'PHO': 1, 'PQ9': 1, 'SQD': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 94 Unusual residues: {'BCR': 1, 'DGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "k" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 105 Unusual residues: {'BCR': 1, 'CLA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "l" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 95 Unusual residues: {'MGE': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "m" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 131 Unusual residues: {'LMT': 1, 'MGE': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "t" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'BCR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "z" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1 PQ9 a5407 " occ=0.50 ... (28 atoms not shown) pdb=" O4 PQ9 a5407 " occ=0.50 Time building chain proxies: 21.10, per 1000 atoms: 0.52 Number of scatterers: 40859 At special positions: 0 Unit cell: (199.901, 160.704, 109.749, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Fe 4 26.01 Ca 2 19.99 Cl 2 17.00 S 140 16.00 P 2 15.00 Mg 70 11.99 O 6583 8.00 N 5784 7.00 C 28272 6.00 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 - 3.50 Amino acid : False - 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=71, symmetry=0 Number of additional bonds: simple=71, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.17 Conformation dependent library (CDL) restraints added in 5.1 seconds 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7784 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 173 helices and 6 sheets defined 57.5% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.72 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 Processing helix chain 'A' and resid 32 through 53 removed outlier: 3.922A pdb=" N ILE A 36 " --> pdb=" O TRP A 32 " (cutoff:3.500A) Proline residue: A 39 - end of helix removed outlier: 3.554A pdb=" N ALA A 51 " --> pdb=" O CYS A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 110 through 134 removed outlier: 3.847A pdb=" N PHE A 117 " --> pdb=" O GLN A 113 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TRP A 131 " --> pdb=" O MET A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 157 removed outlier: 4.131A pdb=" N ALA A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Proline residue: A 150 - end of helix Processing helix chain 'A' and resid 160 through 165 Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 176 through 190 removed outlier: 3.757A pdb=" N PHE A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 221 removed outlier: 3.879A pdb=" N ALA A 203 " --> pdb=" O GLN A 199 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL A 219 " --> pdb=" O HIS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 258 removed outlier: 3.649A pdb=" N GLY A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 263 No H-bonds generated for 'chain 'A' and resid 261 through 263' Processing helix chain 'A' and resid 268 through 294 removed outlier: 3.767A pdb=" N PHE A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) Proline residue: A 279 - end of helix removed outlier: 3.560A pdb=" N PHE A 285 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 332 removed outlier: 3.721A pdb=" N VAL A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 12 removed outlier: 3.507A pdb=" N VAL B 11 " --> pdb=" O VAL B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 43 removed outlier: 3.503A pdb=" N ALA B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 69 Processing helix chain 'B' and resid 93 through 116 Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 135 through 155 removed outlier: 3.627A pdb=" N ILE B 141 " --> pdb=" O LYS B 137 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS B 142 " --> pdb=" O MET B 138 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 148 " --> pdb=" O PHE B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 190 removed outlier: 3.680A pdb=" N PHE B 190 " --> pdb=" O PRO B 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 187 through 190' Processing helix chain 'B' and resid 195 through 218 removed outlier: 3.873A pdb=" N ALA B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 207 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 229 Processing helix chain 'B' and resid 234 through 257 removed outlier: 3.729A pdb=" N PHE B 250 " --> pdb=" O PHE B 246 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 251 " --> pdb=" O PHE B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 276 removed outlier: 3.630A pdb=" N ASP B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 272 through 276' Processing helix chain 'B' and resid 279 through 294 removed outlier: 4.274A pdb=" N ARG B 287 " --> pdb=" O GLU B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 307 through 312 Processing helix chain 'B' and resid 330 through 334 removed outlier: 3.575A pdb=" N ASP B 334 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 395 No H-bonds generated for 'chain 'B' and resid 392 through 395' Processing helix chain 'B' and resid 414 through 426 removed outlier: 3.696A pdb=" N ILE B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N PHE B 426 " --> pdb=" O ARG B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 476 removed outlier: 3.702A pdb=" N THR B 452 " --> pdb=" O ARG B 448 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 474 " --> pdb=" O GLY B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 480 No H-bonds generated for 'chain 'B' and resid 478 through 480' Processing helix chain 'C' and resid 38 through 42 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.696A pdb=" N GLY C 51 " --> pdb=" O GLY C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 84 No H-bonds generated for 'chain 'C' and resid 82 through 84' Processing helix chain 'C' and resid 89 through 95 Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 108 through 133 removed outlier: 3.514A pdb=" N VAL C 114 " --> pdb=" O PHE C 111 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C 116 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY C 126 " --> pdb=" O ALA C 123 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS C 132 " --> pdb=" O GLY C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 143 No H-bonds generated for 'chain 'C' and resid 140 through 143' Processing helix chain 'C' and resid 156 through 180 removed outlier: 3.634A pdb=" N PHE C 163 " --> pdb=" O THR C 159 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 213 No H-bonds generated for 'chain 'C' and resid 210 through 213' Processing helix chain 'C' and resid 230 through 252 removed outlier: 3.771A pdb=" N VAL C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP C 239 " --> pdb=" O GLY C 235 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 268 through 292 removed outlier: 3.800A pdb=" N LEU C 272 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL C 290 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP C 291 " --> pdb=" O THR C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 302 No H-bonds generated for 'chain 'C' and resid 299 through 302' Processing helix chain 'C' and resid 306 through 323 removed outlier: 3.649A pdb=" N SER C 310 " --> pdb=" O GLY C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 357 Processing helix chain 'C' and resid 364 through 369 Proline residue: C 368 - end of helix No H-bonds generated for 'chain 'C' and resid 364 through 369' Processing helix chain 'C' and resid 377 through 383 removed outlier: 3.664A pdb=" N ASN C 382 " --> pdb=" O ASN C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 397 removed outlier: 3.679A pdb=" N ARG C 390 " --> pdb=" O PRO C 386 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET C 396 " --> pdb=" O ALA C 392 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR C 397 " --> pdb=" O ALA C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 453 removed outlier: 3.864A pdb=" N ALA C 427 " --> pdb=" O ARG C 423 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 457 No H-bonds generated for 'chain 'C' and resid 455 through 457' Processing helix chain 'D' and resid 14 through 22 Processing helix chain 'D' and resid 32 through 53 removed outlier: 3.821A pdb=" N LEU D 36 " --> pdb=" O TRP D 32 " (cutoff:3.500A) Proline residue: D 39 - end of helix removed outlier: 3.853A pdb=" N THR D 50 " --> pdb=" O GLY D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 109 through 136 removed outlier: 4.615A pdb=" N ALA D 133 " --> pdb=" O GLN D 129 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG D 134 " --> pdb=" O PHE D 130 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU D 135 " --> pdb=" O GLU D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 157 removed outlier: 4.498A pdb=" N ALA D 148 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Proline residue: D 149 - end of helix Processing helix chain 'D' and resid 159 through 163 Processing helix chain 'D' and resid 175 through 188 removed outlier: 3.851A pdb=" N PHE D 179 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE D 184 " --> pdb=" O ARG D 180 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE D 185 " --> pdb=" O PHE D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 220 removed outlier: 3.632A pdb=" N GLY D 200 " --> pdb=" O PHE D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 256 removed outlier: 3.501A pdb=" N ILE D 256 " --> pdb=" O PHE D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 290 Proline residue: D 275 - end of helix removed outlier: 3.829A pdb=" N GLY D 285 " --> pdb=" O MET D 281 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL D 287 " --> pdb=" O ALA D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 307 Processing helix chain 'D' and resid 316 through 333 removed outlier: 3.575A pdb=" N LEU D 320 " --> pdb=" O THR D 316 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG D 326 " --> pdb=" O ASN D 322 " (cutoff:3.500A) Proline residue: D 331 - end of helix Processing helix chain 'E' and resid 22 through 24 No H-bonds generated for 'chain 'E' and resid 22 through 24' Processing helix chain 'E' and resid 26 through 39 removed outlier: 3.678A pdb=" N ALA E 33 " --> pdb=" O ALA E 29 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY E 34 " --> pdb=" O LEU E 30 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 47 Processing helix chain 'E' and resid 72 through 82 removed outlier: 3.895A pdb=" N GLU E 77 " --> pdb=" O LYS E 73 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR E 78 " --> pdb=" O GLN E 74 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE E 79 " --> pdb=" O GLN E 75 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU E 81 " --> pdb=" O GLU E 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 41 removed outlier: 4.393A pdb=" N VAL F 28 " --> pdb=" O HIS F 24 " (cutoff:3.500A) Proline residue: F 29 - end of helix removed outlier: 3.700A pdb=" N GLY F 35 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA F 36 " --> pdb=" O PHE F 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 12 removed outlier: 3.543A pdb=" N ARG H 12 " --> pdb=" O GLY H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 49 Processing helix chain 'I' and resid 2 through 24 removed outlier: 3.874A pdb=" N PHE I 21 " --> pdb=" O LEU I 17 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE I 23 " --> pdb=" O PHE I 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 23 Processing helix chain 'K' and resid 28 through 43 removed outlier: 4.025A pdb=" N LEU K 33 " --> pdb=" O PRO K 29 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE K 37 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL K 43 " --> pdb=" O TRP K 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 36 removed outlier: 3.983A pdb=" N GLY L 20 " --> pdb=" O SER L 16 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU L 25 " --> pdb=" O LEU L 21 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N SER L 33 " --> pdb=" O LEU L 29 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TYR L 34 " --> pdb=" O LEU L 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 31 removed outlier: 3.659A pdb=" N THR M 11 " --> pdb=" O GLY M 7 " (cutoff:3.500A) Proline residue: M 18 - end of helix removed outlier: 3.648A pdb=" N LEU M 25 " --> pdb=" O PHE M 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 22 removed outlier: 3.854A pdb=" N TYR T 6 " --> pdb=" O GLU T 2 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE T 19 " --> pdb=" O ALA T 15 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE T 22 " --> pdb=" O PHE T 18 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2 through 28 removed outlier: 3.684A pdb=" N VAL Z 13 " --> pdb=" O LEU Z 9 " (cutoff:3.500A) Proline residue: Z 24 - end of helix Processing helix chain 'Z' and resid 33 through 36 No H-bonds generated for 'chain 'Z' and resid 33 through 36' Processing helix chain 'Z' and resid 39 through 61 removed outlier: 3.854A pdb=" N GLY Z 45 " --> pdb=" O PHE Z 41 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU Z 46 " --> pdb=" O LEU Z 42 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA Z 49 " --> pdb=" O GLY Z 45 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU Z 50 " --> pdb=" O LEU Z 46 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL Z 51 " --> pdb=" O TRP Z 47 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU Z 52 " --> pdb=" O ILE Z 48 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL Z 54 " --> pdb=" O LEU Z 50 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY Z 55 " --> pdb=" O VAL Z 51 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL Z 56 " --> pdb=" O LEU Z 52 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU Z 57 " --> pdb=" O VAL Z 53 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE Z 60 " --> pdb=" O VAL Z 56 " (cutoff:3.500A) Processing helix chain 'a' and resid 5013 through 5022 Processing helix chain 'a' and resid 5032 through 5053 removed outlier: 3.922A pdb=" N ILE a5036 " --> pdb=" O TRP a5032 " (cutoff:3.500A) Proline residue: a5039 - end of helix removed outlier: 3.554A pdb=" N ALA a5051 " --> pdb=" O CYS a5047 " (cutoff:3.500A) Processing helix chain 'a' and resid 5102 through 5107 Processing helix chain 'a' and resid 5110 through 5134 removed outlier: 3.846A pdb=" N PHE a5117 " --> pdb=" O GLN a5113 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N CYS a5125 " --> pdb=" O LEU a5121 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TRP a5131 " --> pdb=" O MET a5127 " (cutoff:3.500A) Processing helix chain 'a' and resid 5143 through 5157 removed outlier: 4.131A pdb=" N ALA a5149 " --> pdb=" O VAL a5145 " (cutoff:3.500A) Proline residue: a5150 - end of helix Processing helix chain 'a' and resid 5160 through 5165 Processing helix chain 'a' and resid 5168 through 5170 No H-bonds generated for 'chain 'a' and resid 5168 through 5170' Processing helix chain 'a' and resid 5176 through 5190 removed outlier: 3.757A pdb=" N PHE a5180 " --> pdb=" O ILE a5176 " (cutoff:3.500A) Processing helix chain 'a' and resid 5196 through 5221 removed outlier: 3.878A pdb=" N ALA a5203 " --> pdb=" O GLN a5199 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL a5219 " --> pdb=" O HIS a5215 " (cutoff:3.500A) Processing helix chain 'a' and resid 5248 through 5258 removed outlier: 3.649A pdb=" N GLY a5253 " --> pdb=" O VAL a5249 " (cutoff:3.500A) Processing helix chain 'a' and resid 5261 through 5263 No H-bonds generated for 'chain 'a' and resid 5261 through 5263' Processing helix chain 'a' and resid 5268 through 5294 removed outlier: 3.767A pdb=" N PHE a5273 " --> pdb=" O ARG a5269 " (cutoff:3.500A) Proline residue: a5279 - end of helix removed outlier: 3.561A pdb=" N PHE a5285 " --> pdb=" O VAL a5281 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR a5286 " --> pdb=" O GLY a5282 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER a5291 " --> pdb=" O ALA a5287 " (cutoff:3.500A) Processing helix chain 'a' and resid 5317 through 5332 removed outlier: 3.721A pdb=" N VAL a5330 " --> pdb=" O LEU a5326 " (cutoff:3.500A) Processing helix chain 'b' and resid 5008 through 5012 removed outlier: 3.506A pdb=" N VAL b5011 " --> pdb=" O VAL b5008 " (cutoff:3.500A) Processing helix chain 'b' and resid 5016 through 5043 removed outlier: 3.503A pdb=" N ALA b5038 " --> pdb=" O ALA b5034 " (cutoff:3.500A) Processing helix chain 'b' and resid 5063 through 5069 Processing helix chain 'b' and resid 5093 through 5116 Processing helix chain 'b' and resid 5121 through 5123 No H-bonds generated for 'chain 'b' and resid 5121 through 5123' Processing helix chain 'b' and resid 5135 through 5155 removed outlier: 3.627A pdb=" N ILE b5141 " --> pdb=" O LYS b5137 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS b5142 " --> pdb=" O MET b5138 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU b5148 " --> pdb=" O PHE b5144 " (cutoff:3.500A) Processing helix chain 'b' and resid 5187 through 5190 removed outlier: 3.679A pdb=" N PHE b5190 " --> pdb=" O PRO b5187 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 5187 through 5190' Processing helix chain 'b' and resid 5195 through 5218 removed outlier: 3.872A pdb=" N ALA b5200 " --> pdb=" O GLY b5196 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE b5207 " --> pdb=" O ILE b5203 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE b5217 " --> pdb=" O GLY b5213 " (cutoff:3.500A) Processing helix chain 'b' and resid 5223 through 5229 Processing helix chain 'b' and resid 5234 through 5257 removed outlier: 3.730A pdb=" N PHE b5250 " --> pdb=" O PHE b5246 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL b5251 " --> pdb=" O PHE b5247 " (cutoff:3.500A) Processing helix chain 'b' and resid 5272 through 5276 removed outlier: 3.629A pdb=" N ASP b5276 " --> pdb=" O ARG b5272 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 5272 through 5276' Processing helix chain 'b' and resid 5279 through 5294 removed outlier: 4.273A pdb=" N ARG b5287 " --> pdb=" O GLU b5283 " (cutoff:3.500A) Processing helix chain 'b' and resid 5298 through 5303 Processing helix chain 'b' and resid 5307 through 5312 Processing helix chain 'b' and resid 5330 through 5334 removed outlier: 3.576A pdb=" N ASP b5334 " --> pdb=" O ASN b5331 " (cutoff:3.500A) Processing helix chain 'b' and resid 5392 through 5395 No H-bonds generated for 'chain 'b' and resid 5392 through 5395' Processing helix chain 'b' and resid 5414 through 5426 removed outlier: 3.696A pdb=" N ILE b5425 " --> pdb=" O ALA b5421 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N PHE b5426 " --> pdb=" O ARG b5422 " (cutoff:3.500A) Processing helix chain 'b' and resid 5447 through 5476 removed outlier: 3.703A pdb=" N THR b5452 " --> pdb=" O ARG b5448 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE b5464 " --> pdb=" O LEU b5460 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS b5469 " --> pdb=" O GLY b5465 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU b5474 " --> pdb=" O GLY b5470 " (cutoff:3.500A) Processing helix chain 'b' and resid 5478 through 5480 No H-bonds generated for 'chain 'b' and resid 5478 through 5480' Processing helix chain 'c' and resid 5038 through 5042 Processing helix chain 'c' and resid 5046 through 5073 removed outlier: 3.697A pdb=" N GLY c5051 " --> pdb=" O GLY c5047 " (cutoff:3.500A) Processing helix chain 'c' and resid 5082 through 5084 No H-bonds generated for 'chain 'c' and resid 5082 through 5084' Processing helix chain 'c' and resid 5089 through 5095 Processing helix chain 'c' and resid 5101 through 5103 No H-bonds generated for 'chain 'c' and resid 5101 through 5103' Processing helix chain 'c' and resid 5108 through 5133 removed outlier: 3.514A pdb=" N VAL c5114 " --> pdb=" O PHE c5111 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL c5116 " --> pdb=" O VAL c5113 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY c5126 " --> pdb=" O ALA c5123 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS c5132 " --> pdb=" O GLY c5129 " (cutoff:3.500A) Processing helix chain 'c' and resid 5140 through 5143 No H-bonds generated for 'chain 'c' and resid 5140 through 5143' Processing helix chain 'c' and resid 5156 through 5180 removed outlier: 3.634A pdb=" N PHE c5163 " --> pdb=" O THR c5159 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA c5172 " --> pdb=" O LEU c5168 " (cutoff:3.500A) Processing helix chain 'c' and resid 5210 through 5213 No H-bonds generated for 'chain 'c' and resid 5210 through 5213' Processing helix chain 'c' and resid 5230 through 5252 removed outlier: 3.770A pdb=" N VAL c5234 " --> pdb=" O LEU c5230 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP c5239 " --> pdb=" O GLY c5235 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA c5246 " --> pdb=" O LEU c5242 " (cutoff:3.500A) Processing helix chain 'c' and resid 5258 through 5262 Processing helix chain 'c' and resid 5268 through 5292 removed outlier: 3.799A pdb=" N LEU c5272 " --> pdb=" O GLY c5268 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL c5290 " --> pdb=" O ALA c5286 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP c5291 " --> pdb=" O THR c5287 " (cutoff:3.500A) Processing helix chain 'c' and resid 5299 through 5302 No H-bonds generated for 'chain 'c' and resid 5299 through 5302' Processing helix chain 'c' and resid 5306 through 5323 removed outlier: 3.650A pdb=" N SER c5310 " --> pdb=" O GLY c5306 " (cutoff:3.500A) Processing helix chain 'c' and resid 5353 through 5357 Processing helix chain 'c' and resid 5364 through 5369 Proline residue: c5368 - end of helix No H-bonds generated for 'chain 'c' and resid 5364 through 5369' Processing helix chain 'c' and resid 5377 through 5383 removed outlier: 3.663A pdb=" N ASN c5382 " --> pdb=" O ASN c5378 " (cutoff:3.500A) Processing helix chain 'c' and resid 5386 through 5397 removed outlier: 3.677A pdb=" N ARG c5390 " --> pdb=" O PRO c5386 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET c5396 " --> pdb=" O ALA c5392 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR c5397 " --> pdb=" O ALA c5393 " (cutoff:3.500A) Processing helix chain 'c' and resid 5422 through 5453 removed outlier: 3.864A pdb=" N ALA c5427 " --> pdb=" O ARG c5423 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY c5446 " --> pdb=" O LEU c5442 " (cutoff:3.500A) Processing helix chain 'c' and resid 5455 through 5457 No H-bonds generated for 'chain 'c' and resid 5455 through 5457' Processing helix chain 'd' and resid 5014 through 5022 Processing helix chain 'd' and resid 5032 through 5053 removed outlier: 3.822A pdb=" N LEU d5036 " --> pdb=" O TRP d5032 " (cutoff:3.500A) Proline residue: d5039 - end of helix removed outlier: 3.853A pdb=" N THR d5050 " --> pdb=" O GLY d5046 " (cutoff:3.500A) Processing helix chain 'd' and resid 5101 through 5106 Processing helix chain 'd' and resid 5109 through 5136 removed outlier: 4.616A pdb=" N ALA d5133 " --> pdb=" O GLN d5129 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG d5134 " --> pdb=" O PHE d5130 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU d5135 " --> pdb=" O GLU d5131 " (cutoff:3.500A) Processing helix chain 'd' and resid 5141 through 5157 removed outlier: 4.498A pdb=" N ALA d5148 " --> pdb=" O ILE d5144 " (cutoff:3.500A) Proline residue: d5149 - end of helix Processing helix chain 'd' and resid 5159 through 5163 Processing helix chain 'd' and resid 5175 through 5188 removed outlier: 3.851A pdb=" N PHE d5179 " --> pdb=" O VAL d5175 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE d5184 " --> pdb=" O ARG d5180 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE d5185 " --> pdb=" O PHE d5181 " (cutoff:3.500A) Processing helix chain 'd' and resid 5195 through 5220 removed outlier: 3.632A pdb=" N GLY d5200 " --> pdb=" O PHE d5196 " (cutoff:3.500A) Processing helix chain 'd' and resid 5246 through 5256 removed outlier: 3.501A pdb=" N ILE d5256 " --> pdb=" O PHE d5252 " (cutoff:3.500A) Processing helix chain 'd' and resid 5264 through 5290 Proline residue: d5275 - end of helix removed outlier: 3.829A pdb=" N GLY d5285 " --> pdb=" O MET d5281 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL d5287 " --> pdb=" O ALA d5283 " (cutoff:3.500A) Processing helix chain 'd' and resid 5299 through 5307 Processing helix chain 'd' and resid 5316 through 5333 removed outlier: 3.577A pdb=" N LEU d5320 " --> pdb=" O THR d5316 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG d5326 " --> pdb=" O ASN d5322 " (cutoff:3.500A) Proline residue: d5331 - end of helix Processing helix chain 'e' and resid 5022 through 5024 No H-bonds generated for 'chain 'e' and resid 5022 through 5024' Processing helix chain 'e' and resid 5026 through 5039 removed outlier: 3.679A pdb=" N ALA e5033 " --> pdb=" O ALA e5029 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY e5034 " --> pdb=" O LEU e5030 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL e5038 " --> pdb=" O GLY e5034 " (cutoff:3.500A) Processing helix chain 'e' and resid 5042 through 5047 Processing helix chain 'e' and resid 5072 through 5082 removed outlier: 3.842A pdb=" N GLU e5077 " --> pdb=" O LYS e5073 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR e5078 " --> pdb=" O GLN e5074 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE e5079 " --> pdb=" O GLN e5075 " (cutoff:3.500A) Processing helix chain 'f' and resid 5018 through 5041 removed outlier: 3.538A pdb=" N ALA f5022 " --> pdb=" O VAL f5018 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL f5023 " --> pdb=" O ARG f5019 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL f5028 " --> pdb=" O HIS f5024 " (cutoff:3.500A) Proline residue: f5029 - end of helix removed outlier: 3.701A pdb=" N GLY f5035 " --> pdb=" O ILE f5031 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA f5036 " --> pdb=" O PHE f5032 " (cutoff:3.500A) Processing helix chain 'h' and resid 5006 through 5012 removed outlier: 3.543A pdb=" N ARG h5012 " --> pdb=" O GLY h5008 " (cutoff:3.500A) Processing helix chain 'h' and resid 5029 through 5049 Processing helix chain 'i' and resid 5002 through 5024 removed outlier: 3.874A pdb=" N PHE i5021 " --> pdb=" O LEU i5017 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY i5022 " --> pdb=" O LEU i5018 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE i5023 " --> pdb=" O PHE i5019 " (cutoff:3.500A) Processing helix chain 'k' and resid 5019 through 5023 Processing helix chain 'k' and resid 5028 through 5043 removed outlier: 4.026A pdb=" N LEU k5033 " --> pdb=" O PRO k5029 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE k5037 " --> pdb=" O LEU k5033 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL k5043 " --> pdb=" O TRP k5039 " (cutoff:3.500A) Processing helix chain 'l' and resid 5014 through 5036 removed outlier: 3.984A pdb=" N GLY l5020 " --> pdb=" O SER l5016 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU l5025 " --> pdb=" O LEU l5021 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N SER l5033 " --> pdb=" O LEU l5029 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TYR l5034 " --> pdb=" O LEU l5030 " (cutoff:3.500A) Processing helix chain 'm' and resid 5007 through 5031 removed outlier: 3.659A pdb=" N THR m5011 " --> pdb=" O GLY m5007 " (cutoff:3.500A) Proline residue: m5018 - end of helix removed outlier: 3.647A pdb=" N LEU m5025 " --> pdb=" O PHE m5021 " (cutoff:3.500A) Processing helix chain 't' and resid 5002 through 5022 removed outlier: 3.853A pdb=" N TYR t5006 " --> pdb=" O GLU t5002 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE t5019 " --> pdb=" O ALA t5015 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE t5022 " --> pdb=" O PHE t5018 " (cutoff:3.500A) Processing helix chain 'z' and resid 5002 through 5028 removed outlier: 3.683A pdb=" N VAL z5013 " --> pdb=" O LEU z5009 " (cutoff:3.500A) Proline residue: z5024 - end of helix Processing helix chain 'z' and resid 5033 through 5036 No H-bonds generated for 'chain 'z' and resid 5033 through 5036' Processing helix chain 'z' and resid 5039 through 5061 removed outlier: 3.854A pdb=" N GLY z5045 " --> pdb=" O PHE z5041 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU z5046 " --> pdb=" O LEU z5042 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA z5049 " --> pdb=" O GLY z5045 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU z5050 " --> pdb=" O LEU z5046 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL z5051 " --> pdb=" O TRP z5047 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU z5052 " --> pdb=" O ILE z5048 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL z5054 " --> pdb=" O LEU z5050 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLY z5055 " --> pdb=" O VAL z5051 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL z5056 " --> pdb=" O LEU z5052 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU z5057 " --> pdb=" O VAL z5053 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE z5060 " --> pdb=" O VAL z5056 " (cutoff:3.500A) Processing helix chain 'Y' and resid 21 through 41 removed outlier: 3.558A pdb=" N GLY Y 32 " --> pdb=" O ILE Y 28 " (cutoff:3.500A) Proline residue: Y 33 - end of helix removed outlier: 3.805A pdb=" N ILE Y 36 " --> pdb=" O GLY Y 32 " (cutoff:3.500A) Processing helix chain 'n' and resid 33 through 47 removed outlier: 3.652A pdb=" N SER n 43 " --> pdb=" O ALA n 39 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU n 46 " --> pdb=" O SER n 42 " (cutoff:3.500A) Processing helix chain 'n' and resid 58 through 76 removed outlier: 3.558A pdb=" N LYS n 67 " --> pdb=" O GLU n 63 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU n 68 " --> pdb=" O ALA n 64 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN n 69 " --> pdb=" O ARG n 65 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU n 74 " --> pdb=" O ASP n 70 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR n 75 " --> pdb=" O PHE n 71 " (cutoff:3.500A) Processing helix chain 'n' and resid 85 through 104 removed outlier: 4.014A pdb=" N HIS n 100 " --> pdb=" O SER n 96 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TYR n 101 " --> pdb=" O LEU n 97 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER n 102 " --> pdb=" O ALA n 98 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER n 103 " --> pdb=" O GLY n 99 " (cutoff:3.500A) Processing helix chain 'n' and resid 111 through 132 removed outlier: 3.730A pdb=" N ARG n 116 " --> pdb=" O LYS n 112 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU n 117 " --> pdb=" O LEU n 113 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU n 118 " --> pdb=" O LYS n 114 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU n 126 " --> pdb=" O LYS n 122 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA n 132 " --> pdb=" O LEU n 128 " (cutoff:3.500A) Processing helix chain 'N' and resid 33 through 47 removed outlier: 3.653A pdb=" N SER N 43 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU N 46 " --> pdb=" O SER N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 58 through 77 removed outlier: 3.558A pdb=" N LYS N 67 " --> pdb=" O GLU N 63 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU N 68 " --> pdb=" O ALA N 64 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN N 69 " --> pdb=" O ARG N 65 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU N 74 " --> pdb=" O ASP N 70 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR N 75 " --> pdb=" O PHE N 71 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG N 77 " --> pdb=" O ALA N 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 104 removed outlier: 4.014A pdb=" N HIS N 100 " --> pdb=" O SER N 96 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TYR N 101 " --> pdb=" O LEU N 97 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER N 102 " --> pdb=" O ALA N 98 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER N 103 " --> pdb=" O GLY N 99 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 132 removed outlier: 3.645A pdb=" N LEU N 117 " --> pdb=" O LEU N 113 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU N 118 " --> pdb=" O LYS N 114 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN N 119 " --> pdb=" O ALA N 115 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU N 120 " --> pdb=" O ARG N 116 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU N 126 " --> pdb=" O LYS N 122 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA N 132 " --> pdb=" O LEU N 128 " (cutoff:3.500A) Processing helix chain 'y' and resid 20 through 28 Processing helix chain 'y' and resid 31 through 42 Processing helix chain 'X' and resid 5 through 34 Processing helix chain 'x' and resid 5 through 34 removed outlier: 3.643A pdb=" N PHE x 25 " --> pdb=" O LEU x 21 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 343 through 347 removed outlier: 3.683A pdb=" N VAL B 345 " --> pdb=" O SER B 400 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 369 through 371 Processing sheet with id= C, first strand: chain 'C' and resid 341 through 343 Processing sheet with id= D, first strand: chain 'b' and resid 5343 through 5347 removed outlier: 3.684A pdb=" N VAL b5345 " --> pdb=" O SER b5400 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'b' and resid 5369 through 5371 Processing sheet with id= F, first strand: chain 'c' and resid 5341 through 5343 1506 hydrogen bonds defined for protein. 4356 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: 12.05 Time building geometry restraints manager: 22.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.37: 12861 1.37 - 1.55: 29030 1.55 - 1.73: 97 1.73 - 1.91: 246 1.91 - 2.08: 288 Bond restraints: 42522 Sorted by residual: bond pdb=" C10 PQ9 A 406 " pdb=" C5 PQ9 A 406 " ideal model delta sigma weight residual 1.346 1.480 -0.134 2.00e-02 2.50e+03 4.46e+01 bond pdb=" C10 PQ9 a5407 " pdb=" C5 PQ9 a5407 " ideal model delta sigma weight residual 1.346 1.479 -0.133 2.00e-02 2.50e+03 4.46e+01 bond pdb=" C1A MGE D 409 " pdb=" O1G MGE D 409 " ideal model delta sigma weight residual 1.330 1.452 -0.122 2.00e-02 2.50e+03 3.69e+01 bond pdb=" C1A MGE b5620 " pdb=" O1G MGE b5620 " ideal model delta sigma weight residual 1.330 1.452 -0.122 2.00e-02 2.50e+03 3.69e+01 bond pdb=" C1A MGE d5408 " pdb=" O1G MGE d5408 " ideal model delta sigma weight residual 1.330 1.451 -0.121 2.00e-02 2.50e+03 3.68e+01 ... (remaining 42517 not shown) Histogram of bond angle deviations from ideal: 85.28 - 103.77: 1090 103.77 - 122.25: 49323 122.25 - 140.73: 8128 140.73 - 159.21: 74 159.21 - 177.69: 144 Bond angle restraints: 58759 Sorted by residual: angle pdb=" C ILE y 28 " pdb=" N GLY y 29 " pdb=" CA GLY y 29 " ideal model delta sigma weight residual 121.41 104.23 17.18 1.96e+00 2.60e-01 7.68e+01 angle pdb=" CG1 VAL A 249 " pdb=" CB VAL A 249 " pdb=" CG2 VAL A 249 " ideal model delta sigma weight residual 110.80 94.98 15.82 2.20e+00 2.07e-01 5.17e+01 angle pdb=" N ALA y 20 " pdb=" CA ALA y 20 " pdb=" C ALA y 20 " ideal model delta sigma weight residual 111.14 103.51 7.63 1.08e+00 8.57e-01 4.99e+01 angle pdb=" N ILE y 28 " pdb=" CA ILE y 28 " pdb=" C ILE y 28 " ideal model delta sigma weight residual 110.62 116.91 -6.29 1.02e+00 9.61e-01 3.81e+01 angle pdb=" N ARG A 64 " pdb=" CA ARG A 64 " pdb=" C ARG A 64 " ideal model delta sigma weight residual 110.80 123.94 -13.14 2.13e+00 2.20e-01 3.80e+01 ... (remaining 58754 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.90: 20932 34.90 - 69.81: 709 69.81 - 104.71: 76 104.71 - 139.62: 21 139.62 - 174.52: 4 Dihedral angle restraints: 21742 sinusoidal: 9562 harmonic: 12180 Sorted by residual: dihedral pdb=" CA ARG A 64 " pdb=" C ARG A 64 " pdb=" N GLU A 65 " pdb=" CA GLU A 65 " ideal model delta harmonic sigma weight residual 180.00 134.97 45.03 0 5.00e+00 4.00e-02 8.11e+01 dihedral pdb=" CA ILE k5017 " pdb=" C ILE k5017 " pdb=" N PHE k5018 " pdb=" CA PHE k5018 " ideal model delta harmonic sigma weight residual 180.00 136.44 43.56 0 5.00e+00 4.00e-02 7.59e+01 dihedral pdb=" CA ILE K 17 " pdb=" C ILE K 17 " pdb=" N PHE K 18 " pdb=" CA PHE K 18 " ideal model delta harmonic sigma weight residual 180.00 136.50 43.50 0 5.00e+00 4.00e-02 7.57e+01 ... (remaining 21739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 5611 0.147 - 0.294: 164 0.294 - 0.441: 5 0.441 - 0.588: 2 0.588 - 0.736: 1 Chirality restraints: 5783 Sorted by residual: chirality pdb=" CB VAL a5249 " pdb=" CA VAL a5249 " pdb=" CG1 VAL a5249 " pdb=" CG2 VAL a5249 " both_signs ideal model delta sigma weight residual False -2.63 -1.89 -0.74 2.00e-01 2.50e+01 1.35e+01 chirality pdb=" CB VAL C 410 " pdb=" CA VAL C 410 " pdb=" CG1 VAL C 410 " pdb=" CG2 VAL C 410 " both_signs ideal model delta sigma weight residual False -2.63 -2.05 -0.58 2.00e-01 2.50e+01 8.53e+00 chirality pdb=" CA ILE y 28 " pdb=" N ILE y 28 " pdb=" C ILE y 28 " pdb=" CB ILE y 28 " both_signs ideal model delta sigma weight residual False 2.43 1.90 0.53 2.00e-01 2.50e+01 7.08e+00 ... (remaining 5780 not shown) Planarity restraints: 7335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 BCR C 516 " 0.248 2.00e-02 2.50e+03 3.07e-01 1.18e+03 pdb=" C13 BCR C 516 " -0.197 2.00e-02 2.50e+03 pdb=" C14 BCR C 516 " -0.486 2.00e-02 2.50e+03 pdb=" C15 BCR C 516 " 0.360 2.00e-02 2.50e+03 pdb=" C35 BCR C 516 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 BCR c5514 " -0.248 2.00e-02 2.50e+03 3.07e-01 1.18e+03 pdb=" C13 BCR c5514 " 0.197 2.00e-02 2.50e+03 pdb=" C14 BCR c5514 " 0.486 2.00e-02 2.50e+03 pdb=" C15 BCR c5514 " -0.360 2.00e-02 2.50e+03 pdb=" C35 BCR c5514 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C14 BCR Y 101 " 0.153 2.00e-02 2.50e+03 2.80e-01 7.85e+02 pdb=" C15 BCR Y 101 " -0.409 2.00e-02 2.50e+03 pdb=" C16 BCR Y 101 " 0.341 2.00e-02 2.50e+03 pdb=" C17 BCR Y 101 " -0.086 2.00e-02 2.50e+03 ... (remaining 7332 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 18 1.99 - 2.72: 3153 2.72 - 3.44: 62375 3.44 - 4.17: 99603 4.17 - 4.90: 177374 Nonbonded interactions: 342523 Sorted by model distance: nonbonded pdb=" OE2 GLU m5002 " pdb=" O4' LMT m5102 " model vdw 1.261 2.440 nonbonded pdb=" OD2 ASP k5019 " pdb=" CD GLN y 21 " model vdw 1.491 3.270 nonbonded pdb=" OE1 GLU H 47 " pdb=" CD2 PHE X 10 " model vdw 1.497 3.340 nonbonded pdb=" OD2 ASP k5019 " pdb=" CG GLN y 21 " model vdw 1.561 3.440 nonbonded pdb=" OE2 GLU H 47 " pdb=" CD2 PHE X 10 " model vdw 1.630 3.340 ... (remaining 342518 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 333 or resid 402 through 403)) selection = (chain 'a' and (resid 5012 through 5333 or resid 5402 through 5403)) } ncs_group { reference = (chain 'B' and (resid 2 through 484 or (resid 485 and (name N or name CA or name \ C or name O or name CB )) or resid 601 through 605 or (resid 606 and (name NB o \ r name ND or name C1 or name C1A or name C1B or name C1C or name C1D or name C2A \ or name C2B or name C2C or name C2D or name C3A or name C3B or name C3C or name \ C3D or name C4A or name C4B or name C4C or name C4D or name CAA or name CAB or \ name CAC or name CAD or name CBA or name CBB or name CBC or name CBD or name CED \ or name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name \ CMB or name CMC or name CMD or name NA or name NC or name O1D or name O2D or na \ me OBD or name MG )) or resid 607 through 618)) selection = (chain 'b' and (resid 5002 through 5485 or resid 5601 through 5618)) } ncs_group { reference = (chain 'C' and (resid 27 through 472 or resid 501 through 510 or (resid 511 and \ (name NB or name ND or name C1 or name C1A or name C1B or name C1C or name C1D o \ r name C2 or name C2A or name C2B or name C2C or name C2D or name C3 or name C3A \ or name C3B or name C3C or name C3D or name C4 or name C4A or name C4B or name \ C4C or name C4D or name C5 or name C6 or name CAA or name CAB or name CAC or nam \ e CAD or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or \ name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name CM \ B or name CMC or name CMD or name NA or name NC or name O1A or name O1D or name \ O2A or name O2D or name OBD or name MG )) or (resid 512 and (name NB or name ND \ or name C1 or name C1A or name C1B or name C1C or name C1D or name C2 or name C2 \ A or name C2B or name C2C or name C2D or name C3 or name C3A or name C3B or name \ C3C or name C3D or name C4 or name C4A or name C4B or name C4C or name C4D or n \ ame C5 or name CAA or name CAB or name CAC or name CAD or name CBA or name CBB o \ r name CBC or name CBD or name CED or name CGA or name CGD or name CHA or name C \ HB or name CHC or name CHD or name CMA or name CMB or name CMC or name CMD or na \ me NA or name NC or name O1A or name O1D or name O2A or name O2D or name OBD or \ name MG )) or resid 514)) selection = (chain 'c' and (resid 5027 through 5472 or resid 5501 through 5512 or resid 5514 \ )) } ncs_group { reference = (chain 'D' and (resid 13 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 351 or resid 401 through 402 or (r \ esid 404 and (name NB or name ND or name C1 or name C1A or name C1B or name C1C \ or name C1D or name C2 or name C2A or name C2B or name C2C or name C2D or name C \ 3 or name C3A or name C3B or name C3C or name C3D or name C4 or name C4A or name \ C4B or name C4C or name C4D or name C5 or name CAA or name CAB or name CAC or n \ ame CAD or name CBA or name CBB or name CBC or name CBD or name CED or name CGA \ or name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name \ CMB or name CMC or name CMD or name NA or name NC or name O1A or name O1D or nam \ e O2A or name O2D or name OBD or name MG )) or resid 408 through 410)) selection = (chain 'd' and (resid 5013 through 5351 or resid 5401 through 5402 or resid 5404 \ or resid 5408 through 5410)) } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = (chain 'F' and (resid 17 through 44 or resid 101)) selection = chain 'f' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'I' selection = chain 'i' } ncs_group { reference = (chain 'K' and resid 12 through 45) selection = (chain 'k' and resid 5012 through 5045) } ncs_group { reference = (chain 'L' and resid 1 through 37) selection = (chain 'l' and resid 5001 through 5037) } ncs_group { reference = (chain 'M' and resid 1 through 33) selection = (chain 'm' and resid 5001 through 5033) } ncs_group { reference = chain 'N' selection = chain 'n' } ncs_group { reference = (chain 'T' and (resid 1 through 30 or resid 102)) selection = (chain 't' and (resid 5001 through 5030 or resid 5102)) } ncs_group { reference = chain 'X' selection = chain 'x' } ncs_group { reference = (chain 'Y' and resid 18 through 46) selection = chain 'y' } ncs_group { reference = chain 'Z' selection = (chain 'z' and resid 5001 through 5062) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.290 Construct map_model_manager: 0.050 Extract box with map and model: 7.430 Check model and map are aligned: 0.510 Set scattering table: 0.310 Process input model: 101.740 Find NCS groups from input model: 3.200 Set up NCS constraints: 0.540 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 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 : 0.012 0.135 42522 Z= 0.691 Angle : 1.232 17.176 58759 Z= 0.531 Chirality : 0.063 0.736 5783 Planarity : 0.023 0.307 7335 Dihedral : 16.461 174.524 13958 Min Nonbonded Distance : 1.261 Molprobity Statistics. All-atom Clashscore : 28.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.47 % Favored : 91.39 % Rotamer Outliers : 1.63 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.41 (0.10), residues: 4240 helix: -3.34 (0.07), residues: 2299 sheet: -1.11 (1.01), residues: 20 loop : -2.25 (0.12), residues: 1921 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 3493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 991 time to evaluate : 4.611 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 34 residues processed: 1024 average time/residue: 0.5436 time to fit residues: 914.4727 Evaluate side-chains 639 residues out of total 3493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 605 time to evaluate : 4.376 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.4590 time to fit residues: 32.4015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 350 optimal weight: 5.9990 chunk 314 optimal weight: 0.9990 chunk 174 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 212 optimal weight: 0.9990 chunk 168 optimal weight: 9.9990 chunk 325 optimal weight: 10.0000 chunk 125 optimal weight: 0.2980 chunk 197 optimal weight: 6.9990 chunk 242 optimal weight: 2.9990 chunk 376 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 322 ASN A 325 ASN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 338 GLN ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN C 84 GLN C 311 GLN D 61 HIS ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN E 23 HIS H 59 ASN K 40 GLN L 8 GLN Z 58 ASN a5075 ASN a5087 ASN ** a5187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a5296 ASN a5322 ASN ** b5058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b5274 GLN ** b5281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b5289 GLN b5317 ASN b5343 HIS c5084 GLN c5311 GLN c5382 ASN d5061 HIS d5129 GLN d5334 GLN e5023 HIS h5059 ASN k5040 GLN l5008 GLN ** m5032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 21 GLN n 100 HIS N 100 HIS Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 42522 Z= 0.232 Angle : 0.874 17.571 58759 Z= 0.387 Chirality : 0.046 0.347 5783 Planarity : 0.006 0.063 7335 Dihedral : 19.089 177.832 6770 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.55 % Favored : 95.35 % Rotamer Outliers : 3.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.12), residues: 4240 helix: -0.54 (0.10), residues: 2344 sheet: -1.78 (1.01), residues: 24 loop : -1.56 (0.14), residues: 1872 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 963 residues out of total 3493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 836 time to evaluate : 4.420 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 127 outliers final: 64 residues processed: 901 average time/residue: 0.5020 time to fit residues: 772.0847 Evaluate side-chains 724 residues out of total 3493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 660 time to evaluate : 4.468 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 0 residues processed: 64 average time/residue: 0.3861 time to fit residues: 51.8078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 209 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 chunk 313 optimal weight: 5.9990 chunk 256 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 377 optimal weight: 0.8980 chunk 407 optimal weight: 9.9990 chunk 336 optimal weight: 4.9990 chunk 374 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 302 optimal weight: 8.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS C 441 HIS D 224 GLN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a5234 ASN a5315 ASN ** b5058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b5281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c5441 HIS ** d5189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d5301 GLN m5032 GLN N 69 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 42522 Z= 0.300 Angle : 0.792 14.753 58759 Z= 0.353 Chirality : 0.044 0.336 5783 Planarity : 0.005 0.064 7335 Dihedral : 17.927 169.485 6770 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.88 % Favored : 95.02 % Rotamer Outliers : 3.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.12), residues: 4240 helix: 0.17 (0.10), residues: 2382 sheet: -1.53 (1.02), residues: 24 loop : -1.43 (0.14), residues: 1834 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 3493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 716 time to evaluate : 4.770 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 125 outliers final: 69 residues processed: 788 average time/residue: 0.5015 time to fit residues: 673.8586 Evaluate side-chains 710 residues out of total 3493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 641 time to evaluate : 4.177 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 0 residues processed: 69 average time/residue: 0.3736 time to fit residues: 54.7650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 373 optimal weight: 10.0000 chunk 283 optimal weight: 10.0000 chunk 195 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 chunk 180 optimal weight: 0.9980 chunk 253 optimal weight: 8.9990 chunk 378 optimal weight: 4.9990 chunk 401 optimal weight: 1.9990 chunk 197 optimal weight: 0.6980 chunk 359 optimal weight: 0.0070 chunk 108 optimal weight: 2.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS Z 6 GLN a5130 GLN ** b5281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d5189 HIS e5074 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 42522 Z= 0.198 Angle : 0.731 13.166 58759 Z= 0.324 Chirality : 0.042 0.285 5783 Planarity : 0.005 0.065 7335 Dihedral : 17.214 164.907 6770 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.50 % Favored : 95.40 % Rotamer Outliers : 2.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.12), residues: 4240 helix: 0.54 (0.10), residues: 2366 sheet: -1.82 (0.89), residues: 29 loop : -1.35 (0.14), residues: 1845 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 3493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 737 time to evaluate : 4.322 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 38 residues processed: 776 average time/residue: 0.5026 time to fit residues: 668.4968 Evaluate side-chains 698 residues out of total 3493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 660 time to evaluate : 3.982 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.3918 time to fit residues: 32.7564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 334 optimal weight: 0.7980 chunk 227 optimal weight: 6.9990 chunk 5 optimal weight: 0.0020 chunk 298 optimal weight: 0.9990 chunk 165 optimal weight: 6.9990 chunk 342 optimal weight: 0.7980 chunk 277 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 204 optimal weight: 5.9990 chunk 360 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 overall best weight: 1.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS D 189 HIS D 224 GLN E 74 GLN L 13 ASN ** b5053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b5281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d5334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k5040 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 42522 Z= 0.225 Angle : 0.731 13.460 58759 Z= 0.324 Chirality : 0.043 0.353 5783 Planarity : 0.005 0.133 7335 Dihedral : 16.669 158.718 6770 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.83 % Favored : 95.07 % Rotamer Outliers : 2.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.12), residues: 4240 helix: 0.63 (0.10), residues: 2377 sheet: -1.71 (0.88), residues: 29 loop : -1.26 (0.14), residues: 1834 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 3493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 702 time to evaluate : 4.560 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 48 residues processed: 742 average time/residue: 0.5273 time to fit residues: 674.2680 Evaluate side-chains 687 residues out of total 3493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 639 time to evaluate : 4.030 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.4104 time to fit residues: 41.5047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 134 optimal weight: 0.9990 chunk 361 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 235 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 401 optimal weight: 3.9990 chunk 333 optimal weight: 7.9990 chunk 185 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 210 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 ASN ** d5334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z5058 ASN n 91 GLN n 119 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 42522 Z= 0.184 Angle : 0.712 14.490 58759 Z= 0.316 Chirality : 0.042 0.375 5783 Planarity : 0.007 0.415 7335 Dihedral : 16.180 149.693 6770 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.65 % Favored : 95.26 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.13), residues: 4240 helix: 0.75 (0.10), residues: 2387 sheet: -1.60 (0.89), residues: 29 loop : -1.24 (0.14), residues: 1824 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 3493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 715 time to evaluate : 4.228 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 41 residues processed: 749 average time/residue: 0.5239 time to fit residues: 673.0956 Evaluate side-chains 684 residues out of total 3493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 643 time to evaluate : 4.212 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.3906 time to fit residues: 35.5169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 387 optimal weight: 30.0000 chunk 45 optimal weight: 7.9990 chunk 228 optimal weight: 6.9990 chunk 293 optimal weight: 0.8980 chunk 227 optimal weight: 1.9990 chunk 338 optimal weight: 3.9990 chunk 224 optimal weight: 0.6980 chunk 399 optimal weight: 0.9980 chunk 250 optimal weight: 0.9990 chunk 243 optimal weight: 0.7980 chunk 184 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN D 224 GLN E 74 GLN L 13 ASN ** a5315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b5053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b5317 ASN ** d5292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d5334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z5058 ASN n 91 GLN n 119 GLN ** N 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 42522 Z= 0.184 Angle : 0.700 13.105 58759 Z= 0.310 Chirality : 0.042 0.400 5783 Planarity : 0.005 0.073 7335 Dihedral : 15.734 136.843 6770 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.60 % Favored : 95.31 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.13), residues: 4240 helix: 0.87 (0.10), residues: 2388 sheet: -1.01 (1.01), residues: 24 loop : -1.21 (0.14), residues: 1828 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 3493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 684 time to evaluate : 4.233 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 27 residues processed: 711 average time/residue: 0.5060 time to fit residues: 615.9400 Evaluate side-chains 668 residues out of total 3493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 641 time to evaluate : 4.246 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.4155 time to fit residues: 26.9400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.35 > 50: distance: 6 - 14: 15.194 distance: 14 - 15: 12.209 distance: 14 - 20: 6.997 distance: 15 - 16: 16.413 distance: 15 - 18: 12.070 distance: 16 - 17: 17.990 distance: 16 - 21: 23.872 distance: 18 - 19: 14.687 distance: 19 - 20: 9.110 distance: 21 - 22: 14.973 distance: 21 - 27: 31.604 distance: 22 - 23: 22.407 distance: 22 - 25: 34.279 distance: 23 - 24: 8.236 distance: 23 - 28: 36.645 distance: 25 - 26: 8.476 distance: 26 - 27: 23.907 distance: 28 - 29: 34.272 distance: 29 - 30: 13.895 distance: 29 - 32: 5.659 distance: 30 - 31: 11.335 distance: 30 - 37: 15.753 distance: 31 - 62: 13.289 distance: 32 - 33: 34.450 distance: 33 - 34: 24.394 distance: 34 - 35: 20.603 distance: 34 - 36: 12.103 distance: 37 - 38: 8.077 distance: 38 - 39: 7.397 distance: 38 - 41: 15.233 distance: 39 - 40: 8.836 distance: 39 - 42: 20.251 distance: 40 - 71: 11.543 distance: 42 - 43: 9.158 distance: 43 - 44: 12.745 distance: 43 - 46: 9.836 distance: 44 - 45: 14.412 distance: 44 - 50: 7.964 distance: 45 - 76: 8.810 distance: 46 - 47: 17.986 distance: 47 - 48: 13.803 distance: 47 - 49: 10.927 distance: 50 - 51: 19.263 distance: 51 - 52: 14.323 distance: 51 - 54: 11.741 distance: 52 - 62: 10.643 distance: 54 - 55: 10.192 distance: 55 - 56: 6.265 distance: 55 - 57: 9.537 distance: 56 - 58: 14.708 distance: 57 - 59: 15.361 distance: 58 - 60: 8.025 distance: 59 - 60: 4.354 distance: 60 - 61: 20.896 distance: 62 - 63: 10.179 distance: 63 - 64: 7.171 distance: 63 - 66: 13.427 distance: 64 - 65: 12.105 distance: 64 - 71: 8.419 distance: 66 - 67: 14.477 distance: 67 - 68: 4.274 distance: 68 - 69: 21.860 distance: 69 - 70: 15.426 distance: 71 - 72: 12.953 distance: 72 - 73: 5.374 distance: 72 - 75: 17.914 distance: 73 - 74: 15.218 distance: 73 - 76: 9.883 distance: 76 - 77: 6.316 distance: 77 - 78: 18.837 distance: 77 - 80: 23.210 distance: 78 - 79: 10.557 distance: 78 - 84: 16.726 distance: 81 - 82: 18.990 distance: 81 - 83: 20.610 distance: 84 - 85: 11.296 distance: 85 - 86: 8.287 distance: 85 - 88: 8.866 distance: 86 - 87: 9.455 distance: 86 - 95: 17.110 distance: 88 - 89: 15.130 distance: 89 - 90: 16.176 distance: 90 - 91: 13.020 distance: 91 - 92: 7.774 distance: 92 - 93: 7.024 distance: 92 - 94: 7.089