Starting phenix.real_space_refine (version: dev) on Mon Dec 12 14:17:31 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ty0_26163/12_2022/7ty0_26163.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ty0_26163/12_2022/7ty0_26163.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ty0_26163/12_2022/7ty0_26163.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ty0_26163/12_2022/7ty0_26163.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ty0_26163/12_2022/7ty0_26163.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ty0_26163/12_2022/7ty0_26163.pdb" } resolution = 3.5 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= 0.062 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "J ARG 74": "NH1" <-> "NH2" Residue "J TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 248": "NH1" <-> "NH2" Residue "D TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 393": "OE1" <-> "OE2" Residue "D TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 396": "NH1" <-> "NH2" Residue "C ASP 468": "OD1" <-> "OD2" Residue "C TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 10640 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 458 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 7, 'TRANS': 69} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 63 Chain: "B" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 414 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 62} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "J" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 704 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain breaks: 4 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 55 Chain: "K" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 657 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'TRANS': 98} Chain breaks: 5 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 4, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 61 Chain: "N" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 688 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 97} Chain breaks: 3 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "O" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 621 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 90} Chain breaks: 3 Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "D" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3380 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 153} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 453} Chain breaks: 4 Unresolved non-hydrogen bonds: 423 Unresolved non-hydrogen angles: 540 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 19, 'TYR:plan': 2, 'ASN:plan1': 10, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 17, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 228 Chain: "C" Number of atoms: 3389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3389 Classifications: {'peptide': 488} Incomplete info: {'truncation_to_alanine': 160} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 456} Chain breaks: 3 Unresolved non-hydrogen bonds: 432 Unresolved non-hydrogen angles: 550 Unresolved non-hydrogen dihedrals: 323 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 14, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 16, 'ASP:plan': 17} Unresolved non-hydrogen planarities: 236 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: 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: "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: 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: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "M" 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.27, per 1000 atoms: 0.59 Number of scatterers: 10640 At special positions: 0 Unit cell: (77.7, 144.9, 118.65, 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 66 16.00 O 1876 8.00 N 1854 7.00 C 6844 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS C 146 " distance=2.04 Simple disulfide: pdb=" SG CYS A 158 " - pdb=" SG CYS D 162 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS D 158 " distance=2.03 Simple disulfide: pdb=" SG CYS B 146 " - pdb=" SG CYS D 146 " distance=2.03 Simple disulfide: pdb=" SG CYS B 158 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS C 158 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 98 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 98 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 92 " distance=2.04 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 92 " distance=2.08 Simple disulfide: pdb=" SG CYS D 189 " - pdb=" SG CYS D 601 " distance=2.03 Simple disulfide: pdb=" SG CYS D 216 " - pdb=" SG CYS D 240 " distance=2.04 Simple disulfide: pdb=" SG CYS D 282 " - pdb=" SG CYS D 295 " distance=2.04 Simple disulfide: pdb=" SG CYS D 382 " - pdb=" SG CYS D 395 " distance=2.03 Simple disulfide: pdb=" SG CYS D 387 " - pdb=" SG CYS D 499 " distance=2.02 Simple disulfide: pdb=" SG CYS D 493 " - pdb=" SG CYS D 503 " distance=2.03 Simple disulfide: pdb=" SG CYS D 565 " - pdb=" SG CYS D 574 " distance=2.03 Simple disulfide: pdb=" SG CYS C 189 " - pdb=" SG CYS C 601 " distance=2.03 Simple disulfide: pdb=" SG CYS C 216 " - pdb=" SG CYS C 240 " distance=2.02 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 395 " distance=2.04 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 499 " distance=2.04 Simple disulfide: pdb=" SG CYS C 493 " - pdb=" SG CYS C 503 " distance=2.05 Simple disulfide: pdb=" SG CYS C 565 " - pdb=" SG CYS C 574 " distance=2.04 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG P 1 " - " NAG P 2 " BETA1-6 " NAG I 1 " - " FUC I 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG C 701 " - " ASN C 378 " " NAG C 702 " - " ASN C 481 " " NAG C 703 " - " ASN C 529 " " NAG D 701 " - " ASN D 378 " " NAG D 702 " - " ASN D 159 " " NAG D 703 " - " ASN D 417 " " NAG E 1 " - " ASN A 159 " " NAG F 1 " - " ASN B 159 " " NAG G 1 " - " ASN D 306 " " NAG H 1 " - " ASN D 481 " " NAG I 1 " - " ASN D 529 " " NAG L 1 " - " ASN C 306 " " NAG M 1 " - " ASN C 417 " " NAG P 1 " - " ASN C 159 " Time building additional restraints: 4.30 Conformation dependent library (CDL) restraints added in 1.6 seconds 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2824 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 28 sheets defined 19.4% alpha, 40.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 96 through 104 Processing helix chain 'A' and resid 105 through 118 removed outlier: 4.098A pdb=" N LEU A 111 " --> pdb=" O PRO A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 146 Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'B' and resid 97 through 104 Processing helix chain 'B' and resid 105 through 118 Processing helix chain 'B' and resid 118 through 146 Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 53 through 57 Processing helix chain 'J' and resid 89 through 93 Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 53 through 57 Processing helix chain 'K' and resid 76 through 78 No H-bonds generated for 'chain 'K' and resid 76 through 78' Processing helix chain 'N' and resid 30 through 34 Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'O' and resid 83 through 87 removed outlier: 3.773A pdb=" N ILE O 87 " --> pdb=" O GLU O 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 104 Processing helix chain 'D' and resid 105 through 118 Processing helix chain 'D' and resid 118 through 146 Processing helix chain 'D' and resid 204 through 207 Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 306 through 310 Processing helix chain 'D' and resid 327 through 330 Processing helix chain 'D' and resid 393 through 398 Processing helix chain 'C' and resid 98 through 104 Processing helix chain 'C' and resid 105 through 118 Processing helix chain 'C' and resid 118 through 146 Processing helix chain 'C' and resid 204 through 207 Processing helix chain 'C' and resid 275 through 277 No H-bonds generated for 'chain 'C' and resid 275 through 277' Processing helix chain 'C' and resid 373 through 375 No H-bonds generated for 'chain 'C' and resid 373 through 375' Processing helix chain 'C' and resid 378 through 382 Processing helix chain 'C' and resid 393 through 398 Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 161 Processing sheet with id=AA2, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA3, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'J' and resid 60 through 61 removed outlier: 6.591A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N MET J 34 " --> pdb=" O GLU J 50 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TRP J 33 " --> pdb=" O VAL J 101 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N CYS J 98 " --> pdb=" O TRP J 109 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N TRP J 109 " --> pdb=" O CYS J 98 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG J 100 " --> pdb=" O ALA J 107 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 60 through 61 removed outlier: 6.591A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N MET J 34 " --> pdb=" O GLU J 50 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TRP J 33 " --> pdb=" O VAL J 101 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'K' and resid 10 through 11 removed outlier: 3.936A pdb=" N TRP K 33 " --> pdb=" O VAL K 101 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N MET K 34 " --> pdb=" O GLU K 50 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLU K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.854A pdb=" N CYS K 98 " --> pdb=" O TRP K 109 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TRP K 109 " --> pdb=" O CYS K 98 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG K 100 " --> pdb=" O ALA K 107 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.004A pdb=" N GLN N 41 " --> pdb=" O LEU N 50 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU N 50 " --> pdb=" O GLN N 41 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'O' and resid 4 through 5 Processing sheet with id=AB3, first strand: chain 'O' and resid 30 through 31 Processing sheet with id=AB4, first strand: chain 'O' and resid 49 through 52 removed outlier: 5.532A pdb=" N LEU O 50 " --> pdb=" O GLN O 41 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLN O 41 " --> pdb=" O LEU O 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 49 through 52 removed outlier: 5.532A pdb=" N LEU O 50 " --> pdb=" O GLN O 41 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLN O 41 " --> pdb=" O LEU O 50 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 178 through 180 removed outlier: 5.040A pdb=" N LYS D 560 " --> pdb=" O GLU D 579 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 216 through 225 removed outlier: 6.404A pdb=" N SER D 232 " --> pdb=" O PRO D 220 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU D 222 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA D 230 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N MET D 224 " --> pdb=" O TYR D 228 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TYR D 228 " --> pdb=" O MET D 224 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N PHE D 229 " --> pdb=" O VAL D 252 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL D 252 " --> pdb=" O PHE D 229 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TYR D 231 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE D 250 " --> pdb=" O TYR D 231 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N HIS D 233 " --> pdb=" O ARG D 248 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ARG D 248 " --> pdb=" O HIS D 233 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLU D 235 " --> pdb=" O LYS D 246 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL D 244 " --> pdb=" O ILE D 237 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLU D 254 " --> pdb=" O MET D 267 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N MET D 267 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU D 256 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N LEU D 265 " --> pdb=" O LEU D 256 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 279 through 287 removed outlier: 5.618A pdb=" N HIS D 281 " --> pdb=" O ALA D 296 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA D 296 " --> pdb=" O HIS D 281 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 340 through 341 removed outlier: 3.577A pdb=" N LYS D 347 " --> pdb=" O PHE D 369 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 340 through 341 Processing sheet with id=AC2, first strand: chain 'D' and resid 442 through 447 removed outlier: 4.124A pdb=" N LYS D 465 " --> pdb=" O GLN D 455 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP D 468 " --> pdb=" O ASN D 478 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL D 476 " --> pdb=" O LEU D 470 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 512 through 515 removed outlier: 6.820A pdb=" N ILE D 520 " --> pdb=" O ILE D 514 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR D 547 " --> pdb=" O VAL D 539 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS D 541 " --> pdb=" O ILE D 545 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ILE D 545 " --> pdb=" O LYS D 541 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 178 through 179 removed outlier: 6.652A pdb=" N ALA C 558 " --> pdb=" O TYR C 581 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N TYR C 581 " --> pdb=" O ALA C 558 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LYS C 560 " --> pdb=" O GLU C 579 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 215 through 225 removed outlier: 6.485A pdb=" N SER C 232 " --> pdb=" O PRO C 220 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU C 222 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA C 230 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N MET C 224 " --> pdb=" O TYR C 228 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR C 228 " --> pdb=" O MET C 224 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE C 229 " --> pdb=" O VAL C 252 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL C 252 " --> pdb=" O PHE C 229 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR C 231 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE C 250 " --> pdb=" O TYR C 231 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N HIS C 233 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ARG C 248 " --> pdb=" O HIS C 233 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLU C 235 " --> pdb=" O LYS C 246 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL C 244 " --> pdb=" O ILE C 237 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLU C 254 " --> pdb=" O MET C 267 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N MET C 267 " --> pdb=" O GLU C 254 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU C 256 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N LEU C 265 " --> pdb=" O LEU C 256 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 279 through 287 removed outlier: 5.608A pdb=" N HIS C 281 " --> pdb=" O ALA C 296 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA C 296 " --> pdb=" O HIS C 281 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 340 through 341 Processing sheet with id=AC8, first strand: chain 'C' and resid 340 through 341 Processing sheet with id=AC9, first strand: chain 'C' and resid 442 through 447 removed outlier: 4.354A pdb=" N LYS C 465 " --> pdb=" O GLN C 455 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP C 468 " --> pdb=" O ASN C 478 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL C 476 " --> pdb=" O LEU C 470 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 512 through 515 removed outlier: 6.740A pdb=" N ILE C 520 " --> pdb=" O ILE C 514 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR C 547 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS C 541 " --> pdb=" O ILE C 545 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ILE C 545 " --> pdb=" O LYS C 541 " (cutoff:3.500A) 582 hydrogen bonds defined for protein. 1518 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.10 Time building geometry restraints manager: 4.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 2705 1.33 - 1.46: 3326 1.46 - 1.60: 4758 1.60 - 1.73: 2 1.73 - 1.87: 84 Bond restraints: 10875 Sorted by residual: bond pdb=" C3 NAG D 702 " pdb=" C4 NAG D 702 " ideal model delta sigma weight residual 1.523 1.566 -0.043 1.00e-02 1.00e+04 1.89e+01 bond pdb=" C5 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.435 1.482 -0.047 1.10e-02 8.26e+03 1.81e+01 bond pdb=" C5 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.435 1.481 -0.046 1.10e-02 8.26e+03 1.73e+01 bond pdb=" C1 NAG C 703 " pdb=" C2 NAG C 703 " ideal model delta sigma weight residual 1.526 1.608 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C5 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.435 1.480 -0.045 1.10e-02 8.26e+03 1.67e+01 ... (remaining 10870 not shown) Histogram of bond angle deviations from ideal: 97.26 - 104.64: 275 104.64 - 112.01: 5069 112.01 - 119.39: 3554 119.39 - 126.76: 5876 126.76 - 134.14: 109 Bond angle restraints: 14883 Sorted by residual: angle pdb=" CG1 VAL C 209 " pdb=" CB VAL C 209 " pdb=" CG2 VAL C 209 " ideal model delta sigma weight residual 110.80 130.94 -20.14 2.20e+00 2.07e-01 8.38e+01 angle pdb=" C CYS C 493 " pdb=" N PRO C 494 " pdb=" CA PRO C 494 " ideal model delta sigma weight residual 120.03 128.47 -8.44 9.90e-01 1.02e+00 7.27e+01 angle pdb=" C ASN C 275 " pdb=" N PRO C 276 " pdb=" CA PRO C 276 " ideal model delta sigma weight residual 119.56 127.28 -7.72 1.02e+00 9.61e-01 5.73e+01 angle pdb=" C GLY A 106 " pdb=" N PRO A 107 " pdb=" CA PRO A 107 " ideal model delta sigma weight residual 119.56 127.03 -7.47 1.02e+00 9.61e-01 5.36e+01 angle pdb=" C LYS D 322 " pdb=" N PRO D 323 " pdb=" CA PRO D 323 " ideal model delta sigma weight residual 120.03 127.21 -7.18 9.90e-01 1.02e+00 5.25e+01 ... (remaining 14878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 6193 17.95 - 35.89: 125 35.89 - 53.84: 42 53.84 - 71.78: 5 71.78 - 89.73: 5 Dihedral angle restraints: 6370 sinusoidal: 1989 harmonic: 4381 Sorted by residual: dihedral pdb=" CB CYS A 146 " pdb=" SG CYS A 146 " pdb=" SG CYS C 146 " pdb=" CB CYS C 146 " ideal model delta sinusoidal sigma weight residual 93.00 166.68 -73.68 1 1.00e+01 1.00e-02 6.90e+01 dihedral pdb=" CB CYS B 146 " pdb=" SG CYS B 146 " pdb=" SG CYS D 146 " pdb=" CB CYS D 146 " ideal model delta sinusoidal sigma weight residual 93.00 142.53 -49.53 1 1.00e+01 1.00e-02 3.37e+01 dihedral pdb=" CB CYS O 23 " pdb=" SG CYS O 23 " pdb=" SG CYS O 92 " pdb=" CB CYS O 92 " ideal model delta sinusoidal sigma weight residual 93.00 48.46 44.54 1 1.00e+01 1.00e-02 2.76e+01 ... (remaining 6367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.293: 1747 0.293 - 0.586: 26 0.586 - 0.879: 1 0.879 - 1.173: 1 1.173 - 1.466: 1 Chirality restraints: 1776 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.33e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.07e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.17e+01 ... (remaining 1773 not shown) Planarity restraints: 1922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 529 " 0.124 2.00e-02 2.50e+03 2.39e-01 7.15e+02 pdb=" CG ASN C 529 " -0.069 2.00e-02 2.50e+03 pdb=" OD1 ASN C 529 " 0.102 2.00e-02 2.50e+03 pdb=" ND2 ASN C 529 " -0.427 2.00e-02 2.50e+03 pdb=" C1 NAG C 703 " 0.270 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 159 " -0.112 2.00e-02 2.50e+03 1.83e-01 4.19e+02 pdb=" CG ASN C 159 " 0.068 2.00e-02 2.50e+03 pdb=" OD1 ASN C 159 " -0.082 2.00e-02 2.50e+03 pdb=" ND2 ASN C 159 " 0.324 2.00e-02 2.50e+03 pdb=" C1 NAG P 1 " -0.198 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 481 " -0.039 2.00e-02 2.50e+03 4.67e-02 2.72e+01 pdb=" CG ASN D 481 " 0.002 2.00e-02 2.50e+03 pdb=" OD1 ASN D 481 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN D 481 " 0.075 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " -0.058 2.00e-02 2.50e+03 ... (remaining 1919 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 4224 2.91 - 3.41: 9120 3.41 - 3.91: 17275 3.91 - 4.40: 19318 4.40 - 4.90: 32191 Nonbonded interactions: 82128 Sorted by model distance: nonbonded pdb=" O ARG D 435 " pdb=" NZ LYS D 465 " model vdw 2.417 2.520 nonbonded pdb=" N SER C 440 " pdb=" O SER C 440 " model vdw 2.447 2.496 nonbonded pdb=" OE1 GLN C 455 " pdb=" NZ LYS C 465 " model vdw 2.467 2.520 nonbonded pdb=" N PHE D 458 " pdb=" N SER D 459 " model vdw 2.525 2.560 nonbonded pdb=" O VAL C 182 " pdb=" N LEU C 184 " model vdw 2.533 2.520 ... (remaining 82123 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 96 through 105 and (name N or name CA or name C or name O \ or name CB )) or resid 106 through 131 or (resid 132 and (name N or name CA or \ name C or name O or name CB )) or resid 133 through 141 or (resid 142 through 14 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 145 through \ 163)) selection = (chain 'B' and (resid 96 through 112 or (resid 113 through 119 and (name N or na \ me CA or name C or name O or name CB )) or resid 120 through 152 or (resid 153 t \ hrough 157 and (name N or name CA or name C or name O or name CB )) or resid 158 \ through 163)) } ncs_group { reference = (chain 'C' and (resid 97 through 113 or (resid 114 through 117 and (name N or na \ me CA or name C or name O or name CB )) or resid 118 or (resid 119 and (name N o \ r name CA or name C or name O or name CB )) or resid 120 through 131 or (resid 1 \ 32 and (name N or name CA or name C or name O or name CB )) or resid 133 through \ 153 or (resid 154 through 157 and (name N or name CA or name C or name O or nam \ e CB )) or resid 158 through 205 or (resid 206 and (name N or name CA or name C \ or name O or name CB )) or resid 207 through 208 or (resid 209 through 210 and ( \ name N or name CA or name C or name O or name CB )) or resid 211 or (resid 212 t \ hrough 213 and (name N or name CA or name C or name O or name CB )) or resid 214 \ through 237 or resid 240 through 253 or (resid 254 and (name N or name CA or na \ me C or name O or name CB )) or resid 255 through 278 or (resid 279 and (name N \ or name CA or name C or name O or name CB )) or resid 280 through 284 or (resid \ 285 and (name N or name CA or name C or name O or name CB )) or resid 286 throug \ h 339 or (resid 340 through 342 and (name N or name CA or name C or name O or na \ me CB )) or resid 343 or (resid 344 and (name N or name CA or name C or name O o \ r name CB )) or resid 345 through 356 or (resid 357 and (name N or name CA or na \ me C or name O or name CB )) or resid 358 through 378 or (resid 379 through 381 \ and (name N or name CA or name C or name O or name CB )) or resid 382 through 42 \ 4 or (resid 425 and (name N or name CA or name C or name O or name CB )) or resi \ d 426 through 467 or (resid 468 and (name N or name CA or name C or name O or na \ me CB )) or resid 469 through 477 or (resid 478 and (name N or name CA or name C \ or name O or name CB )) or resid 479 through 508 or (resid 509 and (name N or n \ ame CA or name C or name O or name CB )) or resid 510 through 520 or (resid 521 \ through 522 and (name N or name CA or name C or name O or name CB )) or resid 52 \ 3 through 526 or (resid 527 through 528 and (name N or name CA or name C or name \ O or name CB )) or resid 529 through 532 or (resid 533 and (name N or name CA o \ r name C or name O or name CB )) or resid 534 through 569 or (resid 570 and (nam \ e N or name CA or name C or name O or name CB )) or resid 571 through 577 or (re \ sid 578 and (name N or name CA or name C or name O or name CB )) or resid 579 or \ (resid 580 through 582 and (name N or name CA or name C or name O or name CB )) \ or resid 587 through 602 or resid 701 through 703)) selection = (chain 'D' and (resid 97 through 133 or (resid 134 through 137 and (name N or na \ me CA or name C or name O or name CB )) or resid 138 through 179 or (resid 180 a \ nd (name N or name CA or name C or name O or name CB )) or resid 181 through 186 \ or (resid 187 through 188 and (name N or name CA or name C or name O or name CB \ )) or resid 189 or (resid 190 through 191 and (name N or name CA or name C or n \ ame O or name CB )) or resid 192 through 194 or (resid 195 through 196 and (name \ N or name CA or name C or name O or name CB )) or resid 197 through 202 or (res \ id 203 and (name N or name CA or name C or name O or name CB )) or resid 204 thr \ ough 263 or (resid 264 and (name N or name CA or name C or name O or name CB )) \ or resid 265 through 286 or (resid 287 through 289 and (name N or name CA or nam \ e C or name O or name CB )) or resid 290 through 312 or (resid 313 and (name N o \ r name CA or name C or name O or name CB )) or resid 314 through 371 or (resid 3 \ 72 through 374 and (name N or name CA or name C or name O or name CB )) or resid \ 375 or (resid 376 and (name N or name CA or name C or name O or name CB )) or r \ esid 377 through 383 or (resid 384 through 386 and (name N or name CA or name C \ or name O or name CB )) or resid 387 through 397 or (resid 398 and (name N or na \ me CA or name C or name O or name CB )) or resid 399 through 401 or (resid 402 a \ nd (name N or name CA or name C or name O or name CB )) or resid 403 through 410 \ or (resid 411 and (name N or name CA or name C or name O or name CB )) or resid \ 412 through 419 or resid 424 through 433 or (resid 434 and (name N or name CA o \ r name C or name O or name CB )) or resid 435 through 446 or (resid 447 and (nam \ e N or name CA or name C or name O or name CB )) or resid 448 through 456 or (re \ sid 457 and (name N or name CA or name C or name O or name CB )) or resid 458 th \ rough 461 or (resid 462 and (name N or name CA or name C or name O or name CB )) \ or resid 463 through 490 or resid 492 through 496 or (resid 497 through 498 and \ (name N or name CA or name C or name O or name CB )) or resid 499 through 504 o \ r (resid 505 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 06 through 519 or (resid 520 through 522 and (name N or name CA or name C or nam \ e O or name CB )) or resid 523 through 529 or (resid 530 through 533 and (name N \ or name CA or name C or name O or name CB )) or resid 534 through 541 or (resid \ 542 through 544 and (name N or name CA or name C or name O or name CB )) or res \ id 545 through 560 or (resid 561 and (name N or name CA or name C or name O or n \ ame CB )) or resid 562 through 568 or (resid 569 through 570 and (name N or name \ CA or name C or name O or name CB )) or resid 571 through 602 or resid 701 thro \ ugh 703)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'M' selection = chain 'P' } ncs_group { reference = (chain 'I' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) } ncs_group { reference = (chain 'J' and (resid 2 through 9 or resid 15 or (resid 18 through 21 and (name \ N or name CA or name C or name O or name CB )) or resid 22 through 29 or (resid \ 30 and (name N or name CA or name C or name O or name CB )) or resid 31 through \ 34 or (resid 35 and (name N or name CA or name C or name O or name CB )) or resi \ d 36 through 37 or (resid 38 and (name N or name CA or name C or name O or name \ CB )) or resid 39 through 62 or (resid 69 through 73 and (name N or name CA or n \ ame C or name O or name CB )) or resid 74 through 84 or (resid 85 through 86 and \ (name N or name CA or name C or name O or name CB )) or (resid 92 through 95 an \ d (name N or name CA or name C or name O or name CB )) or resid 96 through 100 o \ r (resid 101 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 02 or (resid 103 through 104 and (name N or name CA or name C or name O or name \ CB )) or resid 105 through 116)) selection = (chain 'K' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 10 or resid 18 through 39 or (resid 45 through 46 \ and (name N or name CA or name C or name O or name CB )) or resid 47 through 62 \ or resid 69 through 75 or resid 78 through 82 or (resid 83 through 93 and (name \ N or name CA or name C or name O or name CB )) or resid 94 through 116)) } ncs_group { reference = (chain 'N' and (resid 2 through 6 or resid 17 through 23 or (resid 24 through 31 \ and (name N or name CA or name C or name O or name CB )) or resid 32 through 44 \ or (resid 46 and (name N or name CA or name C or name O or name CB )) or resid \ 47 through 51 or (resid 52 and (name N or name CA or name C or name O or name CB \ )) or resid 53 through 60 or resid 62 through 64 or (resid 65 and (name N or na \ me CA or name C or name O or name CB )) or resid 66 through 77 or (resid 78 thro \ ugh 80 and (name N or name CA or name C or name O or name CB )) or resid 81 thro \ ugh 85 or (resid 86 through 89 and (name N or name CA or name C or name O or nam \ e CB )) or resid 90 through 110)) selection = (chain 'O' and ((resid 2 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 through 29 or (resid 30 through 31 and (name N or name CA \ or name C or name O or name CB )) or resid 32 through 42 or (resid 43 and (name \ N or name CA or name C or name O or name CB )) or resid 44 through 103 or resid \ 106 through 110)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 6844 2.51 5 N 1854 2.21 5 O 1876 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 7.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 21.040 Check model and map are aligned: 0.160 Convert atoms to be neutral: 0.090 Process input model: 31.600 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 0.083 10875 Z= 0.841 Angle : 1.484 20.144 14883 Z= 1.016 Chirality : 0.102 1.466 1776 Planarity : 0.006 0.026 1908 Dihedral : 8.956 89.727 3474 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.12 % Favored : 97.74 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 8.05 % 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: 0.78 (0.21), residues: 1462 helix: 1.59 (0.37), residues: 194 sheet: 0.93 (0.23), residues: 475 loop : 0.06 (0.21), residues: 793 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 219 time to evaluate : 1.301 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 222 average time/residue: 0.2264 time to fit residues: 70.8359 Evaluate side-chains 126 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 1.313 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0962 time to fit residues: 1.8991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 75 optimal weight: 0.0870 chunk 59 optimal weight: 0.2980 chunk 115 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 chunk 133 optimal weight: 0.6980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 57 ASN N 80 HIS D 187 ASN D 406 HIS D 518 ASN D 564 ASN ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN C 559 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 10875 Z= 0.217 Angle : 0.643 9.605 14883 Z= 0.346 Chirality : 0.056 0.863 1776 Planarity : 0.005 0.050 1908 Dihedral : 4.992 18.458 1747 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer Outliers : 3.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % 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: 0.83 (0.21), residues: 1462 helix: 3.14 (0.37), residues: 193 sheet: 0.61 (0.22), residues: 494 loop : -0.10 (0.21), residues: 775 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 136 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 150 average time/residue: 0.2096 time to fit residues: 48.1317 Evaluate side-chains 123 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 1.232 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 2 residues processed: 13 average time/residue: 0.1148 time to fit residues: 4.3151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN B 133 GLN ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 HIS ** C 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.113 10875 Z= 0.366 Angle : 0.644 8.804 14883 Z= 0.345 Chirality : 0.052 0.660 1776 Planarity : 0.005 0.055 1908 Dihedral : 4.949 18.224 1747 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 3.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % 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: 0.47 (0.22), residues: 1462 helix: 3.26 (0.38), residues: 193 sheet: 0.28 (0.22), residues: 487 loop : -0.39 (0.21), residues: 782 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 126 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 10 residues processed: 149 average time/residue: 0.2023 time to fit residues: 45.0580 Evaluate side-chains 122 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 1.284 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.1121 time to fit residues: 3.6437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 63 optimal weight: 0.2980 chunk 89 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 127 optimal weight: 0.1980 chunk 38 optimal weight: 5.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 518 ASN C 186 ASN C 518 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 10875 Z= 0.199 Angle : 0.549 6.795 14883 Z= 0.291 Chirality : 0.051 0.602 1776 Planarity : 0.004 0.057 1908 Dihedral : 4.673 23.164 1747 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % 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: 0.47 (0.22), residues: 1462 helix: 3.56 (0.38), residues: 192 sheet: 0.23 (0.22), residues: 497 loop : -0.44 (0.21), residues: 773 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 119 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 4 residues processed: 129 average time/residue: 0.2079 time to fit residues: 40.2858 Evaluate side-chains 113 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 109 time to evaluate : 1.519 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.0822 time to fit residues: 2.2541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 4.9990 chunk 80 optimal weight: 0.2980 chunk 2 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 72 optimal weight: 0.0010 chunk 127 optimal weight: 0.0270 chunk 35 optimal weight: 2.9990 overall best weight: 0.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 94 GLN C 186 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 10875 Z= 0.148 Angle : 0.509 5.757 14883 Z= 0.268 Chirality : 0.048 0.562 1776 Planarity : 0.004 0.057 1908 Dihedral : 4.437 18.625 1747 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % 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: 0.50 (0.22), residues: 1462 helix: 3.66 (0.39), residues: 192 sheet: 0.28 (0.22), residues: 495 loop : -0.46 (0.21), residues: 775 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 132 average time/residue: 0.2061 time to fit residues: 40.5925 Evaluate side-chains 117 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 108 time to evaluate : 1.310 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.1034 time to fit residues: 3.2506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 137 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 ASN D 518 ASN C 455 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.145 10875 Z= 0.458 Angle : 0.658 9.323 14883 Z= 0.349 Chirality : 0.054 0.603 1776 Planarity : 0.005 0.062 1908 Dihedral : 5.001 22.886 1747 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % 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: 0.19 (0.22), residues: 1462 helix: 3.25 (0.37), residues: 193 sheet: 0.13 (0.23), residues: 484 loop : -0.67 (0.21), residues: 785 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 112 average time/residue: 0.2046 time to fit residues: 34.7555 Evaluate side-chains 101 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 1.319 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.1342 time to fit residues: 3.1954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 141 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 10875 Z= 0.211 Angle : 0.537 6.715 14883 Z= 0.283 Chirality : 0.049 0.542 1776 Planarity : 0.004 0.058 1908 Dihedral : 4.636 19.651 1747 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % 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: 0.24 (0.22), residues: 1462 helix: 3.11 (0.38), residues: 200 sheet: 0.28 (0.23), residues: 481 loop : -0.71 (0.22), residues: 781 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 108 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 113 average time/residue: 0.2070 time to fit residues: 35.2806 Evaluate side-chains 103 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 100 time to evaluate : 1.350 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.0977 time to fit residues: 2.2800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 20.0000 chunk 84 optimal weight: 0.5980 chunk 42 optimal weight: 10.0000 chunk 27 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 111 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 518 ASN C 559 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 10875 Z= 0.222 Angle : 0.524 6.543 14883 Z= 0.276 Chirality : 0.048 0.526 1776 Planarity : 0.004 0.059 1908 Dihedral : 4.534 18.174 1747 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % 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: 0.29 (0.22), residues: 1462 helix: 3.38 (0.38), residues: 194 sheet: 0.31 (0.23), residues: 486 loop : -0.72 (0.22), residues: 782 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 114 average time/residue: 0.2050 time to fit residues: 35.6370 Evaluate side-chains 103 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 1.282 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 5 average time/residue: 0.1261 time to fit residues: 3.1111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 0.9990 chunk 132 optimal weight: 0.5980 chunk 135 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 131 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 478 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 10875 Z= 0.195 Angle : 0.525 7.070 14883 Z= 0.278 Chirality : 0.048 0.504 1776 Planarity : 0.004 0.058 1908 Dihedral : 4.467 20.154 1747 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % 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: 0.29 (0.22), residues: 1462 helix: 3.44 (0.39), residues: 194 sheet: 0.31 (0.23), residues: 487 loop : -0.73 (0.22), residues: 781 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 118 average time/residue: 0.2192 time to fit residues: 38.3684 Evaluate side-chains 109 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 1.317 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 7 average time/residue: 0.1168 time to fit residues: 3.0738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 97 optimal weight: 0.0980 chunk 146 optimal weight: 0.0030 chunk 134 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 518 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 10875 Z= 0.166 Angle : 0.504 5.976 14883 Z= 0.264 Chirality : 0.047 0.485 1776 Planarity : 0.004 0.059 1908 Dihedral : 4.381 18.113 1747 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % 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: 0.36 (0.22), residues: 1462 helix: 3.48 (0.39), residues: 194 sheet: 0.37 (0.23), residues: 490 loop : -0.69 (0.22), residues: 778 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 108 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 112 average time/residue: 0.2059 time to fit residues: 35.3068 Evaluate side-chains 110 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 104 time to evaluate : 1.279 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.1126 time to fit residues: 2.8989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 102 optimal weight: 0.4980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 6 GLN ** D 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.153398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.125420 restraints weight = 15372.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.124059 restraints weight = 14812.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.125350 restraints weight = 13470.374| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.089 10875 Z= 0.306 Angle : 0.569 7.399 14883 Z= 0.302 Chirality : 0.050 0.667 1776 Planarity : 0.005 0.060 1908 Dihedral : 4.608 21.262 1747 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % 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: 0.20 (0.22), residues: 1462 helix: 3.31 (0.39), residues: 194 sheet: 0.32 (0.23), residues: 494 loop : -0.84 (0.21), residues: 774 =============================================================================== Job complete usr+sys time: 2203.92 seconds wall clock time: 40 minutes 43.20 seconds (2443.20 seconds total)