Starting phenix.real_space_refine on Tue Oct 15 02:03:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3z_29711/10_2024/8g3z_29711.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3z_29711/10_2024/8g3z_29711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3z_29711/10_2024/8g3z_29711.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3z_29711/10_2024/8g3z_29711.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3z_29711/10_2024/8g3z_29711.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3z_29711/10_2024/8g3z_29711.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.023 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: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 144 5.16 5 C 12244 2.51 5 N 3360 2.21 5 O 3732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 19485 Number of models: 1 Model: "" Number of chains: 16 Chain: "H" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 986 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "L" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 834 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "E" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 986 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "F" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 834 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "G" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 986 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "I" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 834 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "J" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 986 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "K" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 834 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3022 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 370} Chain: "B" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3022 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 370} Chain: "C" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3022 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 370} Chain: "D" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3022 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 370} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 12.37, per 1000 atoms: 0.63 Number of scatterers: 19485 At special positions: 0 Unit cell: (170.56, 168.92, 94.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 5 19.99 S 144 16.00 O 3732 8.00 N 3360 7.00 C 12244 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.01 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.01 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.00 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.05 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 420 " distance=2.05 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 127 " distance=2.04 Simple disulfide: pdb=" SG CYS A 182 " - pdb=" SG CYS A 229 " distance=2.04 Simple disulfide: pdb=" SG CYS A 231 " - pdb=" SG CYS A 236 " distance=2.04 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.04 Simple disulfide: pdb=" SG CYS A 424 " - pdb=" SG CYS A 447 " distance=2.05 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 420 " distance=2.04 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 127 " distance=2.04 Simple disulfide: pdb=" SG CYS B 182 " - pdb=" SG CYS B 229 " distance=2.05 Simple disulfide: pdb=" SG CYS B 231 " - pdb=" SG CYS B 236 " distance=2.04 Simple disulfide: pdb=" SG CYS B 277 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 424 " - pdb=" SG CYS B 447 " distance=2.04 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 420 " distance=2.04 Simple disulfide: pdb=" SG CYS C 122 " - pdb=" SG CYS C 127 " distance=2.04 Simple disulfide: pdb=" SG CYS C 182 " - pdb=" SG CYS C 229 " distance=2.04 Simple disulfide: pdb=" SG CYS C 231 " - pdb=" SG CYS C 236 " distance=2.05 Simple disulfide: pdb=" SG CYS C 277 " - pdb=" SG CYS C 291 " distance=2.03 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 337 " distance=2.04 Simple disulfide: pdb=" SG CYS C 424 " - pdb=" SG CYS C 447 " distance=2.04 Simple disulfide: pdb=" SG CYS D 87 " - pdb=" SG CYS D 420 " distance=2.04 Simple disulfide: pdb=" SG CYS D 122 " - pdb=" SG CYS D 127 " distance=2.04 Simple disulfide: pdb=" SG CYS D 182 " - pdb=" SG CYS D 229 " distance=2.04 Simple disulfide: pdb=" SG CYS D 231 " - pdb=" SG CYS D 236 " distance=2.03 Simple disulfide: pdb=" SG CYS D 277 " - pdb=" SG CYS D 291 " distance=2.03 Simple disulfide: pdb=" SG CYS D 279 " - pdb=" SG CYS D 289 " distance=2.03 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 337 " distance=2.04 Simple disulfide: pdb=" SG CYS D 424 " - pdb=" SG CYS D 447 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 503 " - " ASN A 144 " " NAG B 502 " - " ASN B 284 " " NAG B 503 " - " ASN B 144 " " NAG C 502 " - " ASN C 284 " " NAG C 503 " - " ASN C 144 " " NAG D 502 " - " ASN D 284 " " NAG D 503 " - " ASN D 144 " Time building additional restraints: 4.23 Conformation dependent library (CDL) restraints added in 2.7 seconds 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4512 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 49 sheets defined 3.0% alpha, 40.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.80 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.551A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.552A pdb=" N PHE F 83 " --> pdb=" O SER F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.553A pdb=" N PHE I 83 " --> pdb=" O SER I 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'A' and resid 99 through 104 Processing helix chain 'A' and resid 196 through 199 Processing helix chain 'B' and resid 99 through 104 Processing helix chain 'C' and resid 99 through 104 Processing helix chain 'C' and resid 196 through 199 Processing helix chain 'D' and resid 99 through 104 Processing helix chain 'D' and resid 196 through 199 Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.529A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.522A pdb=" N ASN H 117 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.992A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.572A pdb=" N ILE E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLY E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.522A pdb=" N ASN E 117 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 104 through 105 Processing sheet with id=AB2, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.515A pdb=" N GLU F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.888A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AB5, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.530A pdb=" N ILE G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLY G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.523A pdb=" N ASN G 117 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 104 through 105 Processing sheet with id=AB8, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.953A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AC2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.551A pdb=" N ILE J 34 " --> pdb=" O GLY J 50 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLY J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.512A pdb=" N ASN J 117 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 104 through 105 Processing sheet with id=AC5, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.522A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 92 through 98 removed outlier: 5.376A pdb=" N LYS A 94 " --> pdb=" O CYS A 447 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N CYS A 447 " --> pdb=" O LYS A 94 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 113 through 122 removed outlier: 4.715A pdb=" N LEU A 113 " --> pdb=" O ALA A 136 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ALA A 136 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ILE A 115 " --> pdb=" O HIS A 134 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N HIS A 134 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLU A 117 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU A 132 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU A 156 " --> pdb=" O HIS A 173 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 178 through 183 removed outlier: 6.714A pdb=" N LEU A 202 " --> pdb=" O THR A 213 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THR A 213 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE A 204 " --> pdb=" O THR A 211 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 230 through 232 removed outlier: 3.587A pdb=" N LYS A 263 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG A 257 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ILE A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 267 through 269 removed outlier: 6.189A pdb=" N THR A 268 " --> pdb=" O ILE A 314 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N LEU A 316 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ARG A 292 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLU A 276 " --> pdb=" O ARG A 292 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 352 through 357 removed outlier: 3.580A pdb=" N LYS A 360 " --> pdb=" O MET A 357 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N MET A 375 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL A 401 " --> pdb=" O MET A 375 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N MET A 377 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL A 399 " --> pdb=" O MET A 377 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU A 379 " --> pdb=" O SER A 397 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 92 through 98 removed outlier: 5.374A pdb=" N LYS B 94 " --> pdb=" O CYS B 447 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N CYS B 447 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR B 409 " --> pdb=" O GLU B 428 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL B 430 " --> pdb=" O GLY B 407 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLY B 407 " --> pdb=" O VAL B 430 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 113 through 122 removed outlier: 4.725A pdb=" N LEU B 113 " --> pdb=" O ALA B 136 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ALA B 136 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE B 115 " --> pdb=" O HIS B 134 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N HIS B 134 " --> pdb=" O ILE B 115 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLU B 117 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU B 132 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU B 156 " --> pdb=" O HIS B 173 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 178 through 183 removed outlier: 6.698A pdb=" N LEU B 202 " --> pdb=" O THR B 213 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR B 213 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE B 204 " --> pdb=" O THR B 211 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 230 through 232 removed outlier: 3.594A pdb=" N LYS B 263 " --> pdb=" O LYS B 255 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG B 257 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ILE B 261 " --> pdb=" O ARG B 257 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 267 through 269 removed outlier: 6.134A pdb=" N THR B 268 " --> pdb=" O ILE B 314 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ARG B 292 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLU B 276 " --> pdb=" O ARG B 292 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 352 through 357 removed outlier: 3.577A pdb=" N LYS B 360 " --> pdb=" O MET B 357 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N MET B 377 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N VAL B 399 " --> pdb=" O MET B 377 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU B 379 " --> pdb=" O SER B 397 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 92 through 98 removed outlier: 5.372A pdb=" N LYS C 94 " --> pdb=" O CYS C 447 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N CYS C 447 " --> pdb=" O LYS C 94 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 113 through 122 removed outlier: 4.731A pdb=" N LEU C 113 " --> pdb=" O ALA C 136 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ALA C 136 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ILE C 115 " --> pdb=" O HIS C 134 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N HIS C 134 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N GLU C 117 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU C 132 " --> pdb=" O GLU C 117 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU C 156 " --> pdb=" O HIS C 173 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 178 through 183 removed outlier: 6.700A pdb=" N LEU C 202 " --> pdb=" O THR C 213 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR C 213 " --> pdb=" O LEU C 202 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE C 204 " --> pdb=" O THR C 211 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 230 through 232 removed outlier: 3.590A pdb=" N LYS C 263 " --> pdb=" O LYS C 255 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ARG C 257 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ILE C 261 " --> pdb=" O ARG C 257 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 267 through 269 removed outlier: 6.147A pdb=" N THR C 268 " --> pdb=" O ILE C 314 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N LEU C 316 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR C 286 " --> pdb=" O ALA C 282 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ARG C 292 " --> pdb=" O GLU C 276 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N GLU C 276 " --> pdb=" O ARG C 292 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 352 through 357 removed outlier: 3.580A pdb=" N LYS C 360 " --> pdb=" O MET C 357 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N MET C 375 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N VAL C 401 " --> pdb=" O MET C 375 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N MET C 377 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N VAL C 399 " --> pdb=" O MET C 377 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU C 379 " --> pdb=" O SER C 397 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 430 through 431 Processing sheet with id=AE8, first strand: chain 'D' and resid 92 through 98 removed outlier: 5.376A pdb=" N LYS D 94 " --> pdb=" O CYS D 447 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N CYS D 447 " --> pdb=" O LYS D 94 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 113 through 122 removed outlier: 4.731A pdb=" N LEU D 113 " --> pdb=" O ALA D 136 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ALA D 136 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ILE D 115 " --> pdb=" O HIS D 134 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N HIS D 134 " --> pdb=" O ILE D 115 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N GLU D 117 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU D 132 " --> pdb=" O GLU D 117 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU D 156 " --> pdb=" O HIS D 173 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 178 through 183 removed outlier: 6.705A pdb=" N LEU D 202 " --> pdb=" O THR D 213 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N THR D 213 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE D 204 " --> pdb=" O THR D 211 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 230 through 232 removed outlier: 3.587A pdb=" N LYS D 263 " --> pdb=" O LYS D 255 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ARG D 257 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ILE D 261 " --> pdb=" O ARG D 257 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 267 through 269 removed outlier: 6.151A pdb=" N THR D 268 " --> pdb=" O ILE D 314 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N LEU D 316 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR D 286 " --> pdb=" O ALA D 282 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ARG D 292 " --> pdb=" O GLU D 276 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N GLU D 276 " --> pdb=" O ARG D 292 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 352 through 357 removed outlier: 3.582A pdb=" N LYS D 360 " --> pdb=" O MET D 357 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N MET D 375 " --> pdb=" O VAL D 401 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N VAL D 401 " --> pdb=" O MET D 375 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N MET D 377 " --> pdb=" O VAL D 399 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N VAL D 399 " --> pdb=" O MET D 377 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU D 379 " --> pdb=" O SER D 397 " (cutoff:3.500A) 678 hydrogen bonds defined for protein. 1650 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: 7.62 Time building geometry restraints manager: 5.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 3169 1.31 - 1.44: 5590 1.44 - 1.57: 10989 1.57 - 1.71: 0 1.71 - 1.84: 204 Bond restraints: 19952 Sorted by residual: bond pdb=" N GLU D 117 " pdb=" CA GLU D 117 " ideal model delta sigma weight residual 1.460 1.498 -0.038 7.10e-03 1.98e+04 2.79e+01 bond pdb=" C PHE K 83 " pdb=" O PHE K 83 " ideal model delta sigma weight residual 1.235 1.292 -0.057 1.15e-02 7.56e+03 2.42e+01 bond pdb=" N GLU A 117 " pdb=" CA GLU A 117 " ideal model delta sigma weight residual 1.460 1.495 -0.035 7.10e-03 1.98e+04 2.40e+01 bond pdb=" C ILE L 48 " pdb=" O ILE L 48 " ideal model delta sigma weight residual 1.236 1.186 0.051 1.04e-02 9.25e+03 2.36e+01 bond pdb=" C PRO B 406 " pdb=" O PRO B 406 " ideal model delta sigma weight residual 1.235 1.173 0.062 1.30e-02 5.92e+03 2.29e+01 ... (remaining 19947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 24171 2.59 - 5.18: 2641 5.18 - 7.77: 186 7.77 - 10.37: 12 10.37 - 12.96: 10 Bond angle restraints: 27020 Sorted by residual: angle pdb=" CA ILE D 120 " pdb=" CB ILE D 120 " pdb=" CG1 ILE D 120 " ideal model delta sigma weight residual 110.40 121.76 -11.36 1.70e+00 3.46e-01 4.46e+01 angle pdb=" CA ASP J 107 " pdb=" CB ASP J 107 " pdb=" CG ASP J 107 " ideal model delta sigma weight residual 112.60 118.82 -6.22 1.00e+00 1.00e+00 3.87e+01 angle pdb=" CB GLU J 89 " pdb=" CG GLU J 89 " pdb=" CD GLU J 89 " ideal model delta sigma weight residual 112.60 122.99 -10.39 1.70e+00 3.46e-01 3.74e+01 angle pdb=" C THR C 368 " pdb=" CA THR C 368 " pdb=" CB THR C 368 " ideal model delta sigma weight residual 109.65 119.64 -9.99 1.71e+00 3.42e-01 3.41e+01 angle pdb=" C ILE I 107 " pdb=" CA ILE I 107 " pdb=" CB ILE I 107 " ideal model delta sigma weight residual 111.23 117.41 -6.18 1.08e+00 8.57e-01 3.28e+01 ... (remaining 27015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 10924 17.93 - 35.87: 811 35.87 - 53.80: 201 53.80 - 71.73: 45 71.73 - 89.67: 15 Dihedral angle restraints: 11996 sinusoidal: 4872 harmonic: 7124 Sorted by residual: dihedral pdb=" CA ALA B 441 " pdb=" C ALA B 441 " pdb=" N ALA B 442 " pdb=" CA ALA B 442 " ideal model delta harmonic sigma weight residual 180.00 142.19 37.81 0 5.00e+00 4.00e-02 5.72e+01 dihedral pdb=" CA ALA A 441 " pdb=" C ALA A 441 " pdb=" N ALA A 442 " pdb=" CA ALA A 442 " ideal model delta harmonic sigma weight residual 180.00 142.31 37.69 0 5.00e+00 4.00e-02 5.68e+01 dihedral pdb=" CA ALA D 441 " pdb=" C ALA D 441 " pdb=" N ALA D 442 " pdb=" CA ALA D 442 " ideal model delta harmonic sigma weight residual 180.00 142.45 37.55 0 5.00e+00 4.00e-02 5.64e+01 ... (remaining 11993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 2528 0.140 - 0.280: 372 0.280 - 0.420: 6 0.420 - 0.560: 0 0.560 - 0.701: 1 Chirality restraints: 2907 Sorted by residual: chirality pdb=" CB ILE D 120 " pdb=" CA ILE D 120 " pdb=" CG1 ILE D 120 " pdb=" CG2 ILE D 120 " both_signs ideal model delta sigma weight residual False 2.64 1.94 0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" CA ASN B 199 " pdb=" N ASN B 199 " pdb=" C ASN B 199 " pdb=" CB ASN B 199 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA ASP C 184 " pdb=" N ASP C 184 " pdb=" C ASP C 184 " pdb=" CB ASP C 184 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 2904 not shown) Planarity restraints: 3471 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 503 " -0.114 2.00e-02 2.50e+03 9.42e-02 1.11e+02 pdb=" C7 NAG D 503 " 0.054 2.00e-02 2.50e+03 pdb=" C8 NAG D 503 " -0.092 2.00e-02 2.50e+03 pdb=" N2 NAG D 503 " 0.141 2.00e-02 2.50e+03 pdb=" O7 NAG D 503 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 503 " -0.099 2.00e-02 2.50e+03 8.18e-02 8.37e+01 pdb=" C7 NAG A 503 " 0.048 2.00e-02 2.50e+03 pdb=" C8 NAG A 503 " -0.081 2.00e-02 2.50e+03 pdb=" N2 NAG A 503 " 0.122 2.00e-02 2.50e+03 pdb=" O7 NAG A 503 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 503 " -0.089 2.00e-02 2.50e+03 7.37e-02 6.79e+01 pdb=" C7 NAG B 503 " 0.044 2.00e-02 2.50e+03 pdb=" C8 NAG B 503 " -0.073 2.00e-02 2.50e+03 pdb=" N2 NAG B 503 " 0.109 2.00e-02 2.50e+03 pdb=" O7 NAG B 503 " 0.009 2.00e-02 2.50e+03 ... (remaining 3468 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 6941 2.89 - 3.39: 17440 3.39 - 3.89: 36680 3.89 - 4.40: 42530 4.40 - 4.90: 71053 Nonbonded interactions: 174644 Sorted by model distance: nonbonded pdb=" O GLU B 168 " pdb=" NZ LYS C 163 " model vdw 2.386 3.120 nonbonded pdb=" O ASP C 293 " pdb="CA CA C 501 " model vdw 2.449 2.510 nonbonded pdb=" O ASP A 293 " pdb="CA CA A 501 " model vdw 2.463 2.510 nonbonded pdb=" O ASP D 293 " pdb="CA CA D 501 " model vdw 2.467 2.510 nonbonded pdb=" OE2 GLU B 276 " pdb=" OH TYR B 409 " model vdw 2.469 3.040 ... (remaining 174639 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 77 through 466 or resid 501 through 503)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.610 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: 0.050 Extract box with map and model: 0.820 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 46.190 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.140 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:14.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 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 0.101 19952 Z= 0.886 Angle : 1.656 12.957 27020 Z= 1.084 Chirality : 0.093 0.701 2907 Planarity : 0.010 0.094 3464 Dihedral : 14.361 89.667 7364 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.70 % Favored : 95.10 % Rotamer: Outliers : 2.16 % Allowed : 6.49 % Favored : 91.35 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.34 (0.14), residues: 2488 helix: None (None), residues: 0 sheet: -1.45 (0.16), residues: 820 loop : -1.67 (0.13), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.010 TRP J 47 HIS 0.043 0.006 HIS D 129 PHE 0.031 0.007 PHE E 64 TYR 0.081 0.011 TYR C 409 ARG 0.050 0.005 ARG D 257 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 467 time to evaluate : 2.666 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: L 61 ARG cc_start: 0.8633 (mtm-85) cc_final: 0.8314 (mtm-85) REVERT: L 82 ASP cc_start: 0.8602 (m-30) cc_final: 0.8065 (m-30) REVERT: L 93 ASN cc_start: 0.8789 (m110) cc_final: 0.8550 (m110) REVERT: L 109 ARG cc_start: 0.8374 (ptm160) cc_final: 0.7505 (pmt170) REVERT: F 92 ASN cc_start: 0.8669 (t0) cc_final: 0.8460 (m-40) REVERT: F 109 ARG cc_start: 0.8170 (ptm160) cc_final: 0.7303 (pmt170) REVERT: G 43 GLN cc_start: 0.7936 (mm-40) cc_final: 0.7726 (tt0) REVERT: I 61 ARG cc_start: 0.8632 (mtm-85) cc_final: 0.7903 (mtm-85) REVERT: I 82 ASP cc_start: 0.8641 (m-30) cc_final: 0.8007 (m-30) REVERT: I 93 ASN cc_start: 0.8781 (m110) cc_final: 0.8545 (m-40) REVERT: I 109 ARG cc_start: 0.8417 (ptm160) cc_final: 0.7454 (pmt170) REVERT: J 43 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7718 (tt0) REVERT: K 14 SER cc_start: 0.9197 (OUTLIER) cc_final: 0.8973 (m) REVERT: K 109 ARG cc_start: 0.8325 (ptm160) cc_final: 0.7620 (pmt170) REVERT: A 285 LYS cc_start: 0.8681 (ttpp) cc_final: 0.8428 (ttmm) REVERT: A 369 MET cc_start: 0.9003 (mmp) cc_final: 0.8795 (mmm) REVERT: C 409 TYR cc_start: 0.7791 (OUTLIER) cc_final: 0.7109 (t80) outliers start: 45 outliers final: 11 residues processed: 506 average time/residue: 1.5724 time to fit residues: 883.6445 Evaluate side-chains 344 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 331 time to evaluate : 2.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain C residue 409 TYR Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 456 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 0.9980 chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 191 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 142 optimal weight: 0.9980 chunk 221 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN L 92 ASN F 27 GLN G 117 ASN I 27 GLN I 37 GLN I 92 ASN K 27 GLN K 92 ASN A 134 HIS A 306 ASN C 169 ASN ** D 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19952 Z= 0.216 Angle : 0.660 6.931 27020 Z= 0.358 Chirality : 0.047 0.188 2907 Planarity : 0.004 0.036 3464 Dihedral : 7.426 58.767 2940 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.25 % Favored : 97.59 % Rotamer: Outliers : 3.08 % Allowed : 12.88 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -1.50 (0.15), residues: 2488 helix: None (None), residues: 0 sheet: -0.99 (0.15), residues: 976 loop : -0.96 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 177 HIS 0.008 0.002 HIS A 101 PHE 0.011 0.002 PHE K 83 TYR 0.023 0.002 TYR K 91 ARG 0.007 0.001 ARG B 295 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 346 time to evaluate : 2.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 63 LYS cc_start: 0.9335 (ptmm) cc_final: 0.9114 (ptmt) REVERT: L 11 LEU cc_start: 0.8906 (tp) cc_final: 0.8621 (tt) REVERT: L 61 ARG cc_start: 0.8721 (mtm-85) cc_final: 0.8407 (mtm-85) REVERT: L 93 ASN cc_start: 0.8780 (m110) cc_final: 0.8543 (m-40) REVERT: L 109 ARG cc_start: 0.8501 (ptm160) cc_final: 0.7477 (pmt170) REVERT: E 13 ARG cc_start: 0.8941 (mtp85) cc_final: 0.8440 (mtp85) REVERT: E 84 SER cc_start: 0.9400 (OUTLIER) cc_final: 0.9176 (p) REVERT: F 108 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.8967 (ttmm) REVERT: F 109 ARG cc_start: 0.8356 (ptm160) cc_final: 0.7381 (pmt170) REVERT: G 13 ARG cc_start: 0.8910 (mtp85) cc_final: 0.8407 (mtp85) REVERT: G 46 GLU cc_start: 0.8692 (tt0) cc_final: 0.8472 (tt0) REVERT: G 63 LYS cc_start: 0.9439 (tttm) cc_final: 0.9208 (tttt) REVERT: G 98 ARG cc_start: 0.8813 (ttp-110) cc_final: 0.8583 (ttp-110) REVERT: I 82 ASP cc_start: 0.8755 (m-30) cc_final: 0.8407 (m-30) REVERT: I 93 ASN cc_start: 0.8789 (m110) cc_final: 0.8586 (m-40) REVERT: I 109 ARG cc_start: 0.8544 (ptm160) cc_final: 0.7535 (pmt170) REVERT: J 13 ARG cc_start: 0.8899 (mtp85) cc_final: 0.8456 (mtp85) REVERT: K 61 ARG cc_start: 0.8786 (mtm-85) cc_final: 0.8538 (mtm-85) REVERT: K 82 ASP cc_start: 0.8411 (m-30) cc_final: 0.8136 (m-30) REVERT: K 104 LYS cc_start: 0.9079 (ttmm) cc_final: 0.8796 (tttt) REVERT: K 109 ARG cc_start: 0.8398 (ptm160) cc_final: 0.7647 (pmt170) REVERT: A 292 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.7287 (ttm170) REVERT: C 409 TYR cc_start: 0.7813 (OUTLIER) cc_final: 0.5777 (t80) REVERT: D 239 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8669 (tmt) outliers start: 64 outliers final: 22 residues processed: 383 average time/residue: 1.6619 time to fit residues: 702.2913 Evaluate side-chains 358 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 331 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 410 SER Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 409 TYR Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 456 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 184 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 61 optimal weight: 0.0670 chunk 221 optimal weight: 4.9990 chunk 239 optimal weight: 6.9990 chunk 197 optimal weight: 4.9990 chunk 220 optimal weight: 0.5980 chunk 75 optimal weight: 10.0000 chunk 178 optimal weight: 2.9990 overall best weight: 1.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: