Starting phenix.real_space_refine (version: 1.21rc1) on Tue May 16 13:38:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7q_12753/05_2023/7o7q_12753.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7q_12753/05_2023/7o7q_12753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7q_12753/05_2023/7o7q_12753.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7q_12753/05_2023/7o7q_12753.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7q_12753/05_2023/7o7q_12753.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7q_12753/05_2023/7o7q_12753.pdb" } resolution = 3.6 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= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 172 5.16 5 C 25734 2.51 5 N 6746 2.21 5 O 7878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 82": "OD1" <-> "OD2" Residue "A PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 184": "OE1" <-> "OE2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A ASP 282": "OD1" <-> "OD2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 519": "OD1" <-> "OD2" Residue "A ASP 533": "OD1" <-> "OD2" Residue "A GLU 612": "OE1" <-> "OE2" Residue "A PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 636": "OD1" <-> "OD2" Residue "A ARG 645": "NH1" <-> "NH2" Residue "A TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 672": "OD1" <-> "OD2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 737": "OE1" <-> "OE2" Residue "A GLU 753": "OE1" <-> "OE2" Residue "A PHE 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 795": "OE1" <-> "OE2" Residue "A TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 842": "OE1" <-> "OE2" Residue "A GLU 878": "OE1" <-> "OE2" Residue "A GLU 908": "OE1" <-> "OE2" Residue "A ASP 953": "OD1" <-> "OD2" Residue "A ASP 988": "OD1" <-> "OD2" Residue "A GLU 999": "OE1" <-> "OE2" Residue "A TYR 1025": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1030": "OE1" <-> "OE2" Residue "A TYR 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1137": "OE1" <-> "OE2" Residue "A TYR 1197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1198": "OE1" <-> "OE2" Residue "A TYR 1216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1227": "OD1" <-> "OD2" Residue "A TYR 1264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1311": "OE1" <-> "OE2" Residue "A TYR 1312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1337": "OE1" <-> "OE2" Residue "A PHE 1339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 56": "OE1" <-> "OE2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 160": "OE1" <-> "OE2" Residue "B ASP 169": "OD1" <-> "OD2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 243": "OE1" <-> "OE2" Residue "B GLU 244": "OE1" <-> "OE2" Residue "B TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 274": "OD1" <-> "OD2" Residue "B TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "B TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 323": "OE1" <-> "OE2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "B PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 533": "OD1" <-> "OD2" Residue "B ASP 554": "OD1" <-> "OD2" Residue "B ASP 601": "OD1" <-> "OD2" Residue "B GLU 612": "OE1" <-> "OE2" Residue "B PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 636": "OD1" <-> "OD2" Residue "B ARG 645": "NH1" <-> "NH2" Residue "B TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 753": "OE1" <-> "OE2" Residue "B ASP 760": "OD1" <-> "OD2" Residue "B PHE 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 795": "OE1" <-> "OE2" Residue "B TYR 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 842": "OE1" <-> "OE2" Residue "B PHE 870": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 886": "OE1" <-> "OE2" Residue "B GLU 911": "OE1" <-> "OE2" Residue "B GLU 930": "OE1" <-> "OE2" Residue "B GLU 941": "OE1" <-> "OE2" Residue "B ASP 953": "OD1" <-> "OD2" Residue "B GLU 992": "OE1" <-> "OE2" Residue "B TYR 1025": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1030": "OE1" <-> "OE2" Residue "B TYR 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1097": "OD1" <-> "OD2" Residue "B GLU 1137": "OE1" <-> "OE2" Residue "B TYR 1197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1227": "OD1" <-> "OD2" Residue "B TYR 1264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 82": "OD1" <-> "OD2" Residue "C PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 184": "OE1" <-> "OE2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 216": "OE1" <-> "OE2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C ASP 282": "OD1" <-> "OD2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "C TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 323": "OE1" <-> "OE2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "C PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 519": "OD1" <-> "OD2" Residue "C ASP 533": "OD1" <-> "OD2" Residue "C GLU 612": "OE1" <-> "OE2" Residue "C PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 636": "OD1" <-> "OD2" Residue "C ARG 645": "NH1" <-> "NH2" Residue "C TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 672": "OD1" <-> "OD2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 737": "OE1" <-> "OE2" Residue "C GLU 753": "OE1" <-> "OE2" Residue "C PHE 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 795": "OE1" <-> "OE2" Residue "C TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 842": "OE1" <-> "OE2" Residue "C GLU 878": "OE1" <-> "OE2" Residue "C GLU 908": "OE1" <-> "OE2" Residue "C ASP 953": "OD1" <-> "OD2" Residue "C ASP 988": "OD1" <-> "OD2" Residue "C GLU 999": "OE1" <-> "OE2" Residue "C TYR 1025": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1030": "OE1" <-> "OE2" Residue "C TYR 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1137": "OE1" <-> "OE2" Residue "C TYR 1197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1198": "OE1" <-> "OE2" Residue "C TYR 1216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1227": "OD1" <-> "OD2" Residue "C TYR 1264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1311": "OE1" <-> "OE2" Residue "C TYR 1312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1337": "OE1" <-> "OE2" Residue "C PHE 1339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D GLU 78": "OE1" <-> "OE2" Residue "D PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "D ASP 169": "OD1" <-> "OD2" Residue "D PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D GLU 244": "OE1" <-> "OE2" Residue "D TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 274": "OD1" <-> "OD2" Residue "D TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 313": "NH1" <-> "NH2" Residue "D TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 323": "OE1" <-> "OE2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "D PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 533": "OD1" <-> "OD2" Residue "D ASP 554": "OD1" <-> "OD2" Residue "D ASP 601": "OD1" <-> "OD2" Residue "D GLU 612": "OE1" <-> "OE2" Residue "D PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 636": "OD1" <-> "OD2" Residue "D ARG 645": "NH1" <-> "NH2" Residue "D TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 753": "OE1" <-> "OE2" Residue "D ASP 760": "OD1" <-> "OD2" Residue "D PHE 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 795": "OE1" <-> "OE2" Residue "D TYR 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 842": "OE1" <-> "OE2" Residue "D PHE 870": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 886": "OE1" <-> "OE2" Residue "D GLU 908": "OE1" <-> "OE2" Residue "D GLU 911": "OE1" <-> "OE2" Residue "D GLU 930": "OE1" <-> "OE2" Residue "D GLU 941": "OE1" <-> "OE2" Residue "D ASP 953": "OD1" <-> "OD2" Residue "D GLU 992": "OE1" <-> "OE2" Residue "D TYR 1025": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1030": "OE1" <-> "OE2" Residue "D TYR 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1097": "OD1" <-> "OD2" Residue "D GLU 1137": "OE1" <-> "OE2" Residue "D TYR 1197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1227": "OD1" <-> "OD2" Residue "D TYR 1264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1312": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 40530 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 10023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1285, 10023 Classifications: {'peptide': 1285} Link IDs: {'PTRANS': 67, 'TRANS': 1217} Chain breaks: 1 Chain: "B" Number of atoms: 9968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1278, 9968 Classifications: {'peptide': 1278} Link IDs: {'PTRANS': 66, 'TRANS': 1211} Chain breaks: 1 Chain: "C" Number of atoms: 10023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1285, 10023 Classifications: {'peptide': 1285} Link IDs: {'PTRANS': 67, 'TRANS': 1217} Chain breaks: 1 Chain: "D" Number of atoms: 9968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1278, 9968 Classifications: {'peptide': 1278} Link IDs: {'PTRANS': 66, 'TRANS': 1211} Chain breaks: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 20.57, per 1000 atoms: 0.51 Number of scatterers: 40530 At special positions: 0 Unit cell: (214.635, 149.721, 158.097, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 172 16.00 O 7878 8.00 N 6746 7.00 C 25734 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 86 " distance=2.03 Simple disulfide: pdb=" SG CYS A 251 " - pdb=" SG CYS A 299 " distance=2.02 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 287 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS B 431 " distance=2.02 Simple disulfide: pdb=" SG CYS A 431 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 563 " distance=2.03 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS A 771 " distance=2.03 Simple disulfide: pdb=" SG CYS A 642 " - pdb=" SG CYS A 689 " distance=2.03 Simple disulfide: pdb=" SG CYS A 821 " - pdb=" SG CYS A 849 " distance=2.03 Simple disulfide: pdb=" SG CYS A 847 " - pdb=" SG CYS A 883 " distance=2.03 Simple disulfide: pdb=" SG CYS A 921 " - pdb=" SG CYS A1321 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1127 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 86 " distance=2.03 Simple disulfide: pdb=" SG CYS B 251 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 269 " - pdb=" SG CYS B 287 " distance=2.03 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 563 " distance=2.03 Simple disulfide: pdb=" SG CYS B 595 " - pdb=" SG CYS B 771 " distance=2.03 Simple disulfide: pdb=" SG CYS B 642 " - pdb=" SG CYS B 689 " distance=2.03 Simple disulfide: pdb=" SG CYS B 821 " - pdb=" SG CYS B 849 " distance=2.04 Simple disulfide: pdb=" SG CYS B 847 " - pdb=" SG CYS B 883 " distance=2.03 Simple disulfide: pdb=" SG CYS B 921 " - pdb=" SG CYS B1321 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 86 " distance=2.03 Simple disulfide: pdb=" SG CYS C 251 " - pdb=" SG CYS C 299 " distance=2.02 Simple disulfide: pdb=" SG CYS C 269 " - pdb=" SG CYS C 287 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS D 431 " distance=2.02 Simple disulfide: pdb=" SG CYS C 431 " - pdb=" SG CYS D 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 470 " - pdb=" SG CYS C 563 " distance=2.03 Simple disulfide: pdb=" SG CYS C 595 " - pdb=" SG CYS C 771 " distance=2.03 Simple disulfide: pdb=" SG CYS C 642 " - pdb=" SG CYS C 689 " distance=2.03 Simple disulfide: pdb=" SG CYS C 821 " - pdb=" SG CYS C 849 " distance=2.03 Simple disulfide: pdb=" SG CYS C 847 " - pdb=" SG CYS C 883 " distance=2.03 Simple disulfide: pdb=" SG CYS C 921 " - pdb=" SG CYS C1321 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1127 " distance=2.03 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 86 " distance=2.03 Simple disulfide: pdb=" SG CYS D 251 " - pdb=" SG CYS D 299 " distance=2.03 Simple disulfide: pdb=" SG CYS D 269 " - pdb=" SG CYS D 287 " distance=2.03 Simple disulfide: pdb=" SG CYS D 470 " - pdb=" SG CYS D 563 " distance=2.03 Simple disulfide: pdb=" SG CYS D 595 " - pdb=" SG CYS D 771 " distance=2.03 Simple disulfide: pdb=" SG CYS D 642 " - pdb=" SG CYS D 689 " distance=2.03 Simple disulfide: pdb=" SG CYS D 821 " - pdb=" SG CYS D 849 " distance=2.04 Simple disulfide: pdb=" SG CYS D 847 " - pdb=" SG CYS D 883 " distance=2.03 Simple disulfide: pdb=" SG CYS D 921 " - pdb=" SG CYS D1321 " distance=2.03 Simple disulfide: pdb=" SG CYS D1079 " - pdb=" SG CYS D1127 " distance=2.03 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=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG A2001 " - " ASN A 55 " " NAG A2002 " - " ASN A 70 " " NAG A2003 " - " ASN A 247 " " NAG A2004 " - " ASN A 396 " " NAG A2005 " - " ASN A 410 " " NAG B2001 " - " ASN B 55 " " NAG B2002 " - " ASN B 70 " " NAG B2003 " - " ASN B 247 " " NAG B2004 " - " ASN B 396 " " NAG B2005 " - " ASN B 410 " " NAG C2001 " - " ASN C 55 " " NAG C2002 " - " ASN C 70 " " NAG C2003 " - " ASN C 247 " " NAG C2004 " - " ASN C 396 " " NAG C2005 " - " ASN C 410 " " NAG D2001 " - " ASN D 55 " " NAG D2002 " - " ASN D 70 " " NAG D2003 " - " ASN D 247 " " NAG D2004 " - " ASN D 396 " " NAG D2005 " - " ASN D 410 " " NAG E 1 " - " ASN A 869 " " NAG F 1 " - " ASN A 991 " " NAG G 1 " - " ASN B 869 " " NAG H 1 " - " ASN B 991 " " NAG I 1 " - " ASN C 869 " " NAG J 1 " - " ASN C 991 " " NAG K 1 " - " ASN D 869 " " NAG L 1 " - " ASN D 991 " Time building additional restraints: 17.78 Conformation dependent library (CDL) restraints added in 6.4 seconds 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9600 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 0 sheets defined 16.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 602 through 607 Processing helix chain 'A' and resid 615 through 621 Processing helix chain 'A' and resid 666 through 673 Processing helix chain 'A' and resid 953 through 965 removed outlier: 5.227A pdb=" N SER A 957 " --> pdb=" O ASP A 953 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA A 958 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N MET A 959 " --> pdb=" O LEU A 955 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLN A 960 " --> pdb=" O GLY A 956 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN A 961 " --> pdb=" O SER A 957 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 993 Proline residue: A 982 - end of helix removed outlier: 3.806A pdb=" N TYR A 985 " --> pdb=" O ALA A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1017 Processing helix chain 'A' and resid 1039 through 1055 Processing helix chain 'A' and resid 1060 through 1073 Processing helix chain 'A' and resid 1098 through 1111 Processing helix chain 'A' and resid 1119 through 1137 Processing helix chain 'A' and resid 1144 through 1157 Processing helix chain 'A' and resid 1160 through 1172 Processing helix chain 'A' and resid 1225 through 1241 Processing helix chain 'A' and resid 1251 through 1268 Processing helix chain 'A' and resid 1294 through 1297 No H-bonds generated for 'chain 'A' and resid 1294 through 1297' Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 602 through 607 Processing helix chain 'B' and resid 615 through 621 Processing helix chain 'B' and resid 666 through 673 Processing helix chain 'B' and resid 953 through 965 removed outlier: 5.227A pdb=" N SER B 957 " --> pdb=" O ASP B 953 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA B 958 " --> pdb=" O ILE B 954 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N MET B 959 " --> pdb=" O LEU B 955 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLN B 960 " --> pdb=" O GLY B 956 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN B 961 " --> pdb=" O SER B 957 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 993 Proline residue: B 982 - end of helix removed outlier: 3.811A pdb=" N TYR B 985 " --> pdb=" O ALA B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1017 Processing helix chain 'B' and resid 1039 through 1055 Processing helix chain 'B' and resid 1060 through 1073 Processing helix chain 'B' and resid 1098 through 1111 Processing helix chain 'B' and resid 1119 through 1137 Processing helix chain 'B' and resid 1144 through 1157 Processing helix chain 'B' and resid 1160 through 1172 Processing helix chain 'B' and resid 1225 through 1241 Processing helix chain 'B' and resid 1251 through 1268 Processing helix chain 'B' and resid 1294 through 1297 No H-bonds generated for 'chain 'B' and resid 1294 through 1297' Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 602 through 607 Processing helix chain 'C' and resid 615 through 621 Processing helix chain 'C' and resid 666 through 673 Processing helix chain 'C' and resid 953 through 965 removed outlier: 5.227A pdb=" N SER C 957 " --> pdb=" O ASP C 953 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA C 958 " --> pdb=" O ILE C 954 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N MET C 959 " --> pdb=" O LEU C 955 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLN C 960 " --> pdb=" O GLY C 956 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN C 961 " --> pdb=" O SER C 957 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 993 Proline residue: C 982 - end of helix removed outlier: 3.806A pdb=" N TYR C 985 " --> pdb=" O ALA C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 998 through 1017 Processing helix chain 'C' and resid 1039 through 1055 Processing helix chain 'C' and resid 1060 through 1073 Processing helix chain 'C' and resid 1098 through 1111 Processing helix chain 'C' and resid 1119 through 1137 Processing helix chain 'C' and resid 1144 through 1157 Processing helix chain 'C' and resid 1160 through 1172 Processing helix chain 'C' and resid 1225 through 1241 Processing helix chain 'C' and resid 1251 through 1268 Processing helix chain 'C' and resid 1294 through 1297 No H-bonds generated for 'chain 'C' and resid 1294 through 1297' Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 602 through 607 Processing helix chain 'D' and resid 615 through 621 Processing helix chain 'D' and resid 666 through 673 Processing helix chain 'D' and resid 953 through 965 removed outlier: 5.228A pdb=" N SER D 957 " --> pdb=" O ASP D 953 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA D 958 " --> pdb=" O ILE D 954 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N MET D 959 " --> pdb=" O LEU D 955 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLN D 960 " --> pdb=" O GLY D 956 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN D 961 " --> pdb=" O SER D 957 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR D 962 " --> pdb=" O ALA D 958 " (cutoff:3.500A) Processing helix chain 'D' and resid 973 through 993 Proline residue: D 982 - end of helix removed outlier: 3.811A pdb=" N TYR D 985 " --> pdb=" O ALA D 981 " (cutoff:3.500A) Processing helix chain 'D' and resid 998 through 1017 Processing helix chain 'D' and resid 1039 through 1055 Processing helix chain 'D' and resid 1060 through 1073 Processing helix chain 'D' and resid 1098 through 1111 Processing helix chain 'D' and resid 1119 through 1137 Processing helix chain 'D' and resid 1144 through 1157 Processing helix chain 'D' and resid 1160 through 1172 Processing helix chain 'D' and resid 1225 through 1241 Processing helix chain 'D' and resid 1251 through 1268 Processing helix chain 'D' and resid 1294 through 1297 No H-bonds generated for 'chain 'D' and resid 1294 through 1297' 540 hydrogen bonds defined for protein. 1620 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: 7.95 Time building geometry restraints manager: 19.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 6721 1.26 - 1.41: 9881 1.41 - 1.55: 24495 1.55 - 1.70: 71 1.70 - 1.84: 252 Bond restraints: 41420 Sorted by residual: bond pdb=" C SER D 949 " pdb=" N VAL D 950 " ideal model delta sigma weight residual 1.330 1.117 0.213 1.42e-02 4.96e+03 2.25e+02 bond pdb=" C SER C 949 " pdb=" N VAL C 950 " ideal model delta sigma weight residual 1.330 1.172 0.159 1.97e-02 2.58e+03 6.48e+01 bond pdb=" C GLN C 168 " pdb=" N ASP C 169 " ideal model delta sigma weight residual 1.329 1.466 -0.138 1.86e-02 2.89e+03 5.47e+01 bond pdb=" C GLN A 168 " pdb=" N ASP A 169 " ideal model delta sigma weight residual 1.329 1.466 -0.137 1.86e-02 2.89e+03 5.44e+01 bond pdb=" C GLY B 629 " pdb=" N PHE B 630 " ideal model delta sigma weight residual 1.331 1.241 0.089 1.48e-02 4.57e+03 3.64e+01 ... (remaining 41415 not shown) Histogram of bond angle deviations from ideal: 97.32 - 105.39: 1204 105.39 - 113.47: 22591 113.47 - 121.54: 21611 121.54 - 129.62: 10486 129.62 - 137.69: 378 Bond angle restraints: 56270 Sorted by residual: angle pdb=" N MET A 464 " pdb=" CA MET A 464 " pdb=" C MET A 464 " ideal model delta sigma weight residual 110.65 99.13 11.52 1.26e+00 6.30e-01 8.35e+01 angle pdb=" N MET C 464 " pdb=" CA MET C 464 " pdb=" C MET C 464 " ideal model delta sigma weight residual 110.65 99.13 11.52 1.26e+00 6.30e-01 8.35e+01 angle pdb=" N ASN B 154 " pdb=" CA ASN B 154 " pdb=" C ASN B 154 " ideal model delta sigma weight residual 110.48 97.32 13.16 1.48e+00 4.57e-01 7.91e+01 angle pdb=" N ASN D 154 " pdb=" CA ASN D 154 " pdb=" C ASN D 154 " ideal model delta sigma weight residual 110.48 97.37 13.11 1.48e+00 4.57e-01 7.84e+01 angle pdb=" N MET D 464 " pdb=" CA MET D 464 " pdb=" C MET D 464 " ideal model delta sigma weight residual 110.65 99.92 10.73 1.26e+00 6.30e-01 7.25e+01 ... (remaining 56265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 22139 18.04 - 36.07: 2060 36.07 - 54.11: 405 54.11 - 72.15: 98 72.15 - 90.18: 28 Dihedral angle restraints: 24730 sinusoidal: 9816 harmonic: 14914 Sorted by residual: dihedral pdb=" CB CYS D1079 " pdb=" SG CYS D1079 " pdb=" SG CYS D1127 " pdb=" CB CYS D1127 " ideal model delta sinusoidal sigma weight residual 93.00 175.59 -82.59 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS B1079 " pdb=" SG CYS B1079 " pdb=" SG CYS B1127 " pdb=" CB CYS B1127 " ideal model delta sinusoidal sigma weight residual 93.00 175.59 -82.59 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS A 431 " pdb=" SG CYS A 431 " pdb=" SG CYS B 278 " pdb=" CB CYS B 278 " ideal model delta sinusoidal sigma weight residual 93.00 152.91 -59.91 1 1.00e+01 1.00e-02 4.79e+01 ... (remaining 24727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.308: 6479 0.308 - 0.617: 31 0.617 - 0.925: 0 0.925 - 1.234: 0 1.234 - 1.542: 4 Chirality restraints: 6514 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.76 0.36 2.00e-02 2.50e+03 3.16e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.42e+02 chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.32e+02 ... (remaining 6511 not shown) Planarity restraints: 7230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " -0.175 2.00e-02 2.50e+03 1.48e-01 2.74e+02 pdb=" C7 NAG L 1 " 0.037 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " 0.040 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " 0.238 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " -0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " -0.162 2.00e-02 2.50e+03 1.37e-01 2.34e+02 pdb=" C7 NAG H 1 " 0.034 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " 0.039 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " 0.219 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " -0.129 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.163 2.00e-02 2.50e+03 1.35e-01 2.28e+02 pdb=" C7 NAG E 2 " 0.045 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.120 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.218 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " 0.021 2.00e-02 2.50e+03 ... (remaining 7227 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 245 2.39 - 3.02: 26835 3.02 - 3.65: 62657 3.65 - 4.27: 89987 4.27 - 4.90: 143593 Nonbonded interactions: 323317 Sorted by model distance: nonbonded pdb=" O GLY C 952 " pdb=" NH1 ARG C1297 " model vdw 1.769 2.520 nonbonded pdb=" SD MET C 959 " pdb=" NE2 GLN C 995 " model vdw 1.802 2.880 nonbonded pdb=" OG1 THR A 656 " pdb=" O PRO D 657 " model vdw 1.867 2.440 nonbonded pdb=" SD MET A 959 " pdb=" NE2 GLN A 995 " model vdw 1.874 2.880 nonbonded pdb=" O PRO B 657 " pdb=" OG1 THR C 656 " model vdw 1.878 2.440 ... (remaining 323312 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 26 through 1337 or resid 2001 through 2005)) selection = chain 'B' selection = (chain 'C' and (resid 26 through 1337 or resid 2001 through 2005)) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 9.730 Check model and map are aligned: 0.630 Set scattering table: 0.350 Process input model: 93.540 Find NCS groups from input model: 3.370 Set up NCS constraints: 0.330 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 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 : 0.010 0.297 41420 Z= 0.640 Angle : 1.538 17.084 56270 Z= 0.891 Chirality : 0.081 1.542 6514 Planarity : 0.009 0.148 7202 Dihedral : 14.433 90.182 14998 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 1.45 % Allowed : 14.50 % Favored : 84.05 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -4.14 (0.10), residues: 5110 helix: -0.89 (0.15), residues: 856 sheet: -2.05 (0.10), residues: 1858 loop : -4.12 (0.10), residues: 2396 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 851 time to evaluate : 5.215 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: 28 outliers final: 20 residues processed: 869 average time/residue: 0.5054 time to fit residues: 731.2517 Evaluate side-chains 564 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 544 time to evaluate : 4.652 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 2 residues processed: 20 average time/residue: 0.3635 time to fit residues: 19.9235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 430 optimal weight: 1.9990 chunk 386 optimal weight: 9.9990 chunk 214 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 260 optimal weight: 9.9990 chunk 206 optimal weight: 30.0000 chunk 399 optimal weight: 0.9990 chunk 154 optimal weight: 9.9990 chunk 243 optimal weight: 0.8980 chunk 297 optimal weight: 4.9990 chunk 463 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 GLN A 208 GLN A 217 HIS A 851 ASN ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 ASN ** A 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN A1035 ASN ** A1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 GLN B 132 GLN B 413 ASN B 424 ASN B 479 HIS B 511 HIS B 693 GLN ** B 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1020 HIS ** B1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1038 ASN B1089 ASN C 132 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 HIS C 851 ASN ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 938 ASN ** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 983 ASN ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN D 132 GLN D 413 ASN D 424 ASN D 479 HIS D 511 HIS ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN ** D 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1020 HIS ** D1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1038 ASN D1089 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 41420 Z= 0.262 Angle : 0.881 13.736 56270 Z= 0.433 Chirality : 0.052 0.553 6514 Planarity : 0.006 0.069 7202 Dihedral : 5.369 33.324 5470 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.71 % Favored : 90.02 % Rotamer Outliers : 2.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.12 (0.11), residues: 5110 helix: 0.29 (0.17), residues: 882 sheet: -1.63 (0.11), residues: 1882 loop : -3.45 (0.11), residues: 2346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 670 time to evaluate : 4.911 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 128 outliers final: 70 residues processed: 751 average time/residue: 0.4882 time to fit residues: 622.8203 Evaluate side-chains 615 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 545 time to evaluate : 5.184 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 0 residues processed: 70 average time/residue: 0.3863 time to fit residues: 57.7566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 257 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 385 optimal weight: 7.9990 chunk 315 optimal weight: 9.9990 chunk 127 optimal weight: 7.9990 chunk 463 optimal weight: 0.8980 chunk 501 optimal weight: 0.5980 chunk 413 optimal weight: 9.9990 chunk 460 optimal weight: 9.9990 chunk 158 optimal weight: 8.9990 chunk 372 optimal weight: 8.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 GLN A 460 HIS A 851 ASN ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 964 ASN ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1009 ASN ** A1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN ** B 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 994 GLN B1035 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 GLN C 303 GLN C 460 HIS ** C 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 851 ASN ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 964 ASN ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1009 ASN D 302 GLN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 GLN D1013 GLN ** D1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.076 41420 Z= 0.350 Angle : 0.852 12.947 56270 Z= 0.425 Chirality : 0.050 0.348 6514 Planarity : 0.006 0.072 7202 Dihedral : 5.404 32.900 5470 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.12 % Favored : 88.65 % Rotamer Outliers : 3.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.74 (0.11), residues: 5110 helix: 0.64 (0.17), residues: 856 sheet: -1.31 (0.11), residues: 1804 loop : -3.21 (0.11), residues: 2450 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 588 time to evaluate : 5.098 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: 142 outliers final: 45 residues processed: 704 average time/residue: 0.4648 time to fit residues: 566.9956 Evaluate side-chains 556 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 511 time to evaluate : 4.662 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.3523 time to fit residues: 37.0154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 458 optimal weight: 20.0000 chunk 348 optimal weight: 10.0000 chunk 240 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 chunk 311 optimal weight: 0.8980 chunk 465 optimal weight: 0.9990 chunk 492 optimal weight: 1.9990 chunk 243 optimal weight: 4.9990 chunk 441 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 HIS A 466 HIS A 851 ASN ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN B 85 HIS ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 HIS C 466 HIS C 851 ASN ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 983 ASN C1252 GLN D 85 HIS D1035 ASN ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 41420 Z= 0.236 Angle : 0.805 15.049 56270 Z= 0.386 Chirality : 0.050 0.426 6514 Planarity : 0.005 0.065 7202 Dihedral : 5.308 35.116 5470 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.67 % Favored : 90.10 % Rotamer Outliers : 2.86 % 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: -2.44 (0.11), residues: 5110 helix: 0.95 (0.18), residues: 856 sheet: -1.13 (0.12), residues: 1774 loop : -3.03 (0.11), residues: 2480 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 582 time to evaluate : 5.295 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: 128 outliers final: 55 residues processed: 679 average time/residue: 0.4856 time to fit residues: 571.5764 Evaluate side-chains 585 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 530 time to evaluate : 5.044 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 0 residues processed: 55 average time/residue: 0.4032 time to fit residues: 47.3756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 410 optimal weight: 3.9990 chunk 279 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 367 optimal weight: 7.9990 chunk 203 optimal weight: 4.9990 chunk 420 optimal weight: 0.3980 chunk 340 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 251 optimal weight: 4.9990 chunk 442 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 ASN A 303 GLN A 460 HIS A 511 HIS ** A 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 ASN ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 GLN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN B 691 GLN ** B 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 964 ASN B1013 GLN ** B1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN C 303 GLN C 460 HIS ** C 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 851 ASN ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1179 ASN ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 GLN D1013 GLN ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 41420 Z= 0.304 Angle : 0.806 14.754 56270 Z= 0.391 Chirality : 0.049 0.325 6514 Planarity : 0.005 0.060 7202 Dihedral : 5.405 31.649 5470 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.15 % Favored : 88.65 % Rotamer Outliers : 2.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.40 (0.11), residues: 5110 helix: 0.92 (0.18), residues: 850 sheet: -1.07 (0.12), residues: 1752 loop : -2.99 (0.11), residues: 2508 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 574 time to evaluate : 5.116 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 outliers start: 131 outliers final: 66 residues processed: 678 average time/residue: 0.4765 time to fit residues: 556.9093 Evaluate side-chains 583 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 517 time to evaluate : 4.899 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 0 residues processed: 66 average time/residue: 0.3820 time to fit residues: 53.7012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 165 optimal weight: 5.9990 chunk 443 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 289 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 chunk 493 optimal weight: 6.9990 chunk 409 optimal weight: 9.9990 chunk 228 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 163 optimal weight: 0.9980 chunk 259 optimal weight: 7.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 HIS A 851 ASN ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1187 GLN A1252 GLN B 132 GLN ** B 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 GLN B1072 GLN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 HIS ** C 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 851 ASN ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN ** D 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1072 GLN ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.077 41420 Z= 0.408 Angle : 0.866 14.327 56270 Z= 0.427 Chirality : 0.051 0.359 6514 Planarity : 0.006 0.061 7202 Dihedral : 5.791 31.558 5470 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 22.98 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.70 % Favored : 88.08 % Rotamer Outliers : 2.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.66 (0.11), residues: 5110 helix: 0.58 (0.17), residues: 842 sheet: -1.28 (0.12), residues: 1744 loop : -3.04 (0.11), residues: 2524 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 521 time to evaluate : 5.184 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 outliers start: 132 outliers final: 71 residues processed: 619 average time/residue: 0.4773 time to fit residues: 514.2954 Evaluate side-chains 552 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 481 time to evaluate : 4.909 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 2 residues processed: 71 average time/residue: 0.3665 time to fit residues: 55.9204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 475 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 281 optimal weight: 10.0000 chunk 360 optimal weight: 0.9980 chunk 279 optimal weight: 3.9990 chunk 415 optimal weight: 8.9990 chunk 275 optimal weight: 6.9990 chunk 491 optimal weight: 9.9990 chunk 307 optimal weight: 0.0770 chunk 299 optimal weight: 3.9990 chunk 226 optimal weight: 0.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 GLN ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 HIS A1252 GLN A1325 GLN ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 GLN ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 HIS ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 ASN ** D 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1072 GLN ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 41420 Z= 0.213 Angle : 0.790 14.754 56270 Z= 0.375 Chirality : 0.049 0.375 6514 Planarity : 0.005 0.060 7202 Dihedral : 5.342 28.407 5470 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.90 % Favored : 89.90 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.32 (0.11), residues: 5110 helix: 0.94 (0.18), residues: 836 sheet: -1.03 (0.12), residues: 1708 loop : -2.85 (0.12), residues: 2566 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 581 time to evaluate : 5.087 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: 56 outliers final: 33 residues processed: 626 average time/residue: 0.4717 time to fit residues: 512.5580 Evaluate side-chains 552 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 519 time to evaluate : 4.742 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 2 residues processed: 33 average time/residue: 0.3938 time to fit residues: 30.5142 ------------------------------------------------------------------------------- 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: 61.2714 > 50: distance: 119 - 123: 16.489 distance: 123 - 124: 10.262 distance: 124 - 125: 13.401 distance: 124 - 127: 31.141 distance: 125 - 126: 32.938 distance: 125 - 130: 17.573 distance: 127 - 128: 43.209 distance: 127 - 129: 15.675 distance: 130 - 131: 15.333 distance: 131 - 132: 4.703 distance: 131 - 134: 11.476 distance: 132 - 133: 14.150 distance: 132 - 139: 25.710 distance: 134 - 135: 11.303 distance: 135 - 136: 10.797 distance: 136 - 137: 13.280 distance: 136 - 138: 8.881 distance: 139 - 140: 19.536 distance: 140 - 141: 12.700 distance: 140 - 143: 9.564 distance: 141 - 142: 11.054 distance: 141 - 150: 12.535 distance: 143 - 144: 7.800 distance: 144 - 145: 4.718 distance: 144 - 146: 11.539 distance: 145 - 147: 9.197 distance: 146 - 148: 12.657 distance: 147 - 149: 15.741 distance: 148 - 149: 18.391 distance: 150 - 151: 13.630 distance: 151 - 152: 3.836 distance: 151 - 154: 7.113 distance: 152 - 153: 10.610 distance: 152 - 156: 8.532 distance: 154 - 155: 12.021 distance: 156 - 157: 7.716 distance: 157 - 158: 3.363 distance: 158 - 159: 14.291 distance: 158 - 164: 7.809 distance: 160 - 161: 7.892 distance: 160 - 162: 15.729 distance: 161 - 163: 7.124 distance: 164 - 165: 6.850 distance: 165 - 166: 9.618 distance: 165 - 168: 3.795 distance: 166 - 167: 7.815 distance: 166 - 172: 17.040 distance: 168 - 169: 13.799 distance: 169 - 170: 11.421 distance: 169 - 171: 10.471 distance: 171 - 217: 8.256 distance: 172 - 173: 9.350 distance: 173 - 174: 5.292 distance: 173 - 176: 7.578 distance: 174 - 175: 6.066 distance: 174 - 179: 5.054 distance: 176 - 177: 16.400 distance: 176 - 178: 26.614 distance: 179 - 180: 8.334 distance: 180 - 181: 13.625 distance: 180 - 183: 11.654 distance: 181 - 182: 9.352 distance: 181 - 186: 20.671 distance: 183 - 184: 30.935 distance: 183 - 185: 33.824 distance: 186 - 187: 20.721 distance: 187 - 188: 6.871 distance: 187 - 190: 19.960 distance: 188 - 189: 26.317 distance: 188 - 194: 28.013 distance: 190 - 191: 19.779 distance: 191 - 192: 13.050 distance: 194 - 195: 5.872 distance: 195 - 196: 10.043 distance: 195 - 198: 16.920 distance: 196 - 197: 26.602 distance: 196 - 201: 23.384 distance: 198 - 199: 47.148 distance: 198 - 200: 50.352