Starting phenix.real_space_refine on Tue Nov 19 12:44:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3z_29711/11_2024/8g3z_29711.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3z_29711/11_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_29711/11_2024/8g3z_29711.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3z_29711/11_2024/8g3z_29711.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3z_29711/11_2024/8g3z_29711.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3z_29711/11_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 11.98, per 1000 atoms: 0.61 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: 4.55 Conformation dependent library (CDL) restraints added in 2.3 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: 3.07 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: 7.34 Time building geometry restraints manager: 5.51 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: 1.760 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: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 45.880 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.100 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:11.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.150 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 45 poor density : 467 time to evaluate : 2.297 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: 1.5598 time to fit residues: 875.4076 Evaluate side-chains 344 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 331 time to evaluate : 2.421 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 64 poor density : 346 time to evaluate : 2.338 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: 1.6618 time to fit residues: 704.2240 Evaluate side-chains 358 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 331 time to evaluate : 2.348 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: L 27 GLN F 93 ASN I 27 GLN K 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9048 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19952 Z= 0.250 Angle : 0.605 6.014 27020 Z= 0.325 Chirality : 0.046 0.155 2907 Planarity : 0.004 0.045 3464 Dihedral : 6.521 56.462 2931 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.61 % Favored : 97.23 % Rotamer: Outliers : 3.03 % Allowed : 15.14 % Favored : 81.83 % 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: -1.07 (0.16), residues: 2488 helix: None (None), residues: 0 sheet: -0.61 (0.16), residues: 928 loop : -0.74 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 177 HIS 0.010 0.001 HIS A 101 PHE 0.012 0.002 PHE B 92 TYR 0.019 0.002 TYR K 91 ARG 0.007 0.001 ARG B 295 *********************** REFINEMENT MACRO_CYCLE 3 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 389 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 326 time to evaluate : 2.147 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: H 13 ARG cc_start: 0.9040 (mtp85) cc_final: 0.8453 (mtp85) REVERT: H 38 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.8949 (ptt180) REVERT: L 11 LEU cc_start: 0.8861 (tp) cc_final: 0.8644 (tt) REVERT: L 82 ASP cc_start: 0.8684 (m-30) cc_final: 0.8408 (m-30) REVERT: L 109 ARG cc_start: 0.8617 (ptm160) cc_final: 0.7501 (pmt170) REVERT: E 13 ARG cc_start: 0.9051 (mtp85) cc_final: 0.8537 (mtp85) REVERT: E 84 SER cc_start: 0.9419 (OUTLIER) cc_final: 0.9212 (p) REVERT: F 109 ARG cc_start: 0.8409 (ptm160) cc_final: 0.7357 (pmt170) REVERT: G 13 ARG cc_start: 0.9053 (mtp85) cc_final: 0.8547 (mtp85) REVERT: G 63 LYS cc_start: 0.9437 (tttm) cc_final: 0.9223 (tttt) REVERT: G 98 ARG cc_start: 0.8940 (ttp-110) cc_final: 0.8464 (ttp-110) REVERT: I 93 ASN cc_start: 0.8777 (m110) cc_final: 0.8545 (m-40) REVERT: I 109 ARG cc_start: 0.8595 (ptm160) cc_final: 0.7485 (pmt170) REVERT: J 43 GLN cc_start: 0.7912 (mp10) cc_final: 0.7630 (tt0) REVERT: K 81 GLU cc_start: 0.9048 (pm20) cc_final: 0.8456 (pm20) REVERT: K 104 LYS cc_start: 0.9048 (ttmm) cc_final: 0.8830 (tttt) REVERT: K 109 ARG cc_start: 0.8476 (ptm160) cc_final: 0.7547 (pmt170) REVERT: B 239 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8502 (tmt) REVERT: C 239 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8511 (tmt) REVERT: C 409 TYR cc_start: 0.7941 (OUTLIER) cc_final: 0.5416 (t80) REVERT: D 239 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8571 (tmt) outliers start: 63 outliers final: 25 residues processed: 366 average time/residue: 1.2802 time to fit residues: 516.8813 Evaluate side-chains 334 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 303 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain A residue 135 TYR 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 135 TYR Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 410 SER Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 409 TYR Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 135 TYR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 115 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 222 optimal weight: 5.9990 chunk 235 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 211 optimal weight: 6.9990 chunk 63 optimal weight: 0.5980 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN L 27 GLN E 62 GLN I 27 GLN J 62 GLN K 27 GLN D 151 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9137 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 19952 Z= 0.488 Angle : 0.682 8.128 27020 Z= 0.364 Chirality : 0.048 0.188 2907 Planarity : 0.005 0.040 3464 Dihedral : 6.627 54.742 2929 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.13 % Favored : 97.71 % Rotamer: Outliers : 3.51 % Allowed : 15.53 % Favored : 80.96 % 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: -1.08 (0.16), residues: 2488 helix: None (None), residues: 0 sheet: -0.49 (0.16), residues: 972 loop : -0.84 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 118 HIS 0.011 0.002 HIS A 101 PHE 0.019 0.002 PHE H 104 TYR 0.019 0.002 TYR K 91 ARG 0.007 0.001 ARG G 100 *********************** REFINEMENT MACRO_CYCLE 4 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 380 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 307 time to evaluate : 2.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 ARG cc_start: 0.9030 (mtp85) cc_final: 0.8329 (mtp85) REVERT: H 43 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7725 (tt0) REVERT: H 76 THR cc_start: 0.9414 (p) cc_final: 0.9093 (t) REVERT: L 109 ARG cc_start: 0.8602 (ptm160) cc_final: 0.7370 (pmt170) REVERT: E 3 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7921 (tt0) REVERT: E 13 ARG cc_start: 0.9091 (mtp85) cc_final: 0.8467 (mtp85) REVERT: E 76 THR cc_start: 0.9408 (p) cc_final: 0.9113 (t) REVERT: F 108 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.9031 (ttmm) REVERT: F 109 ARG cc_start: 0.8513 (ptm160) cc_final: 0.7319 (pmt170) REVERT: G 13 ARG cc_start: 0.9091 (mtp85) cc_final: 0.8491 (mtp85) REVERT: G 76 THR cc_start: 0.9398 (p) cc_final: 0.9089 (t) REVERT: I 93 ASN cc_start: 0.8848 (m110) cc_final: 0.8634 (m-40) REVERT: I 109 ARG cc_start: 0.8621 (ptm160) cc_final: 0.7465 (pmt170) REVERT: J 13 ARG cc_start: 0.9078 (mtp85) cc_final: 0.8547 (mtp85) REVERT: J 43 GLN cc_start: 0.8164 (mp10) cc_final: 0.7897 (mp10) REVERT: J 76 THR cc_start: 0.9419 (p) cc_final: 0.9129 (t) REVERT: K 81 GLU cc_start: 0.9064 (pm20) cc_final: 0.8609 (pm20) REVERT: K 82 ASP cc_start: 0.8695 (m-30) cc_final: 0.8313 (m-30) REVERT: K 104 LYS cc_start: 0.9079 (ttmm) cc_final: 0.8862 (tttt) REVERT: K 109 ARG cc_start: 0.8609 (ptm160) cc_final: 0.7481 (pmt170) REVERT: A 239 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8647 (tmt) REVERT: A 292 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.6966 (ttm170) REVERT: B 239 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8609 (tmt) REVERT: B 292 ARG cc_start: 0.9199 (OUTLIER) cc_final: 0.7155 (ttm170) REVERT: C 239 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8608 (tmt) REVERT: D 239 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8596 (tmt) outliers start: 73 outliers final: 32 residues processed: 358 average time/residue: 1.2591 time to fit residues: 496.4641 Evaluate side-chains 333 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 292 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain J residue 87 ARG Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 409 TYR Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 135 TYR 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 456 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 201 optimal weight: 4.9990 chunk 163 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN L 27 GLN E 62 GLN I 27 GLN J 62 GLN K 27 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9074 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19952 Z= 0.215 Angle : 0.577 5.638 27020 Z= 0.308 Chirality : 0.045 0.168 2907 Planarity : 0.004 0.032 3464 Dihedral : 6.171 55.823 2929 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.49 % Favored : 97.35 % Rotamer: Outliers : 2.50 % Allowed : 17.02 % Favored : 80.48 % 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: -1.03 (0.16), residues: 2488 helix: None (None), residues: 0 sheet: -0.55 (0.16), residues: 972 loop : -0.72 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 177 HIS 0.007 0.001 HIS A 101 PHE 0.009 0.001 PHE D 119 TYR 0.017 0.001 TYR K 91 ARG 0.007 0.001 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 5 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 369 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 317 time to evaluate : 2.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 ARG cc_start: 0.9081 (mtp85) cc_final: 0.8414 (mtp85) REVERT: H 76 THR cc_start: 0.9427 (p) cc_final: 0.9128 (t) REVERT: L 82 ASP cc_start: 0.9055 (m-30) cc_final: 0.8616 (m-30) REVERT: L 109 ARG cc_start: 0.8586 (ptm160) cc_final: 0.7457 (pmt170) REVERT: E 43 GLN cc_start: 0.8031 (mp10) cc_final: 0.7828 (tt0) REVERT: E 76 THR cc_start: 0.9413 (p) cc_final: 0.9131 (t) REVERT: E 98 ARG cc_start: 0.8789 (ttt-90) cc_final: 0.8575 (ttt-90) REVERT: F 108 LYS cc_start: 0.9310 (OUTLIER) cc_final: 0.9012 (ttmm) REVERT: F 109 ARG cc_start: 0.8486 (ptm160) cc_final: 0.7320 (pmt170) REVERT: G 13 ARG cc_start: 0.9130 (mtp85) cc_final: 0.8548 (mtp85) REVERT: G 76 THR cc_start: 0.9405 (p) cc_final: 0.9107 (t) REVERT: I 82 ASP cc_start: 0.9124 (m-30) cc_final: 0.8732 (m-30) REVERT: I 93 ASN cc_start: 0.8788 (m110) cc_final: 0.8552 (m-40) REVERT: I 109 ARG cc_start: 0.8580 (ptm160) cc_final: 0.7487 (pmt170) REVERT: J 13 ARG cc_start: 0.9071 (mtp85) cc_final: 0.8513 (mtp85) REVERT: J 43 GLN cc_start: 0.8210 (mp10) cc_final: 0.7939 (mp10) REVERT: J 76 THR cc_start: 0.9412 (p) cc_final: 0.9125 (t) REVERT: K 81 GLU cc_start: 0.9040 (pm20) cc_final: 0.8616 (pm20) REVERT: K 82 ASP cc_start: 0.8648 (m-30) cc_final: 0.8213 (m-30) REVERT: K 109 ARG cc_start: 0.8609 (ptm160) cc_final: 0.7451 (pmt170) REVERT: A 285 LYS cc_start: 0.8829 (mtpp) cc_final: 0.8479 (mttm) REVERT: A 453 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8198 (mt0) REVERT: B 239 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8505 (tmt) REVERT: C 239 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8506 (tmt) REVERT: C 285 LYS cc_start: 0.8994 (mtpp) cc_final: 0.8707 (mttp) REVERT: D 239 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8510 (tmt) REVERT: D 285 LYS cc_start: 0.8992 (mtpp) cc_final: 0.8709 (mttp) REVERT: D 292 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8043 (ttm170) outliers start: 52 outliers final: 25 residues processed: 353 average time/residue: 1.5519 time to fit residues: 601.2379 Evaluate side-chains 335 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 304 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain I residue 7 SER 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 453 GLN Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 275 GLU 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 456 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 9.9990 chunk 212 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 138 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 236 optimal weight: 7.9990 chunk 195 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 123 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN L 27 GLN E 62 GLN I 27 GLN J 62 GLN K 27 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9105 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 19952 Z= 0.326 Angle : 0.598 5.678 27020 Z= 0.319 Chirality : 0.046 0.196 2907 Planarity : 0.004 0.040 3464 Dihedral : 6.140 55.533 2929 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.61 % Favored : 97.23 % Rotamer: Outliers : 2.79 % Allowed : 17.88 % Favored : 79.33 % 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: -0.92 (0.16), residues: 2488 helix: None (None), residues: 0 sheet: -0.44 (0.16), residues: 976 loop : -0.68 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 177 HIS 0.009 0.002 HIS C 101 PHE 0.012 0.002 PHE E 104 TYR 0.017 0.002 TYR K 91 ARG 0.009 0.001 ARG C 295 *********************** REFINEMENT MACRO_CYCLE 6 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 371 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 313 time to evaluate : 2.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 ARG cc_start: 0.9104 (mtp85) cc_final: 0.8435 (mtp85) REVERT: H 76 THR cc_start: 0.9428 (p) cc_final: 0.9135 (t) REVERT: L 109 ARG cc_start: 0.8583 (ptm160) cc_final: 0.7419 (pmt170) REVERT: E 13 ARG cc_start: 0.9106 (mtp85) cc_final: 0.8522 (mtp85) REVERT: E 43 GLN cc_start: 0.8209 (mp10) cc_final: 0.7990 (mp10) REVERT: E 76 THR cc_start: 0.9418 (p) cc_final: 0.9132 (t) REVERT: F 109 ARG cc_start: 0.8517 (ptm160) cc_final: 0.7297 (pmt170) REVERT: G 13 ARG cc_start: 0.9133 (mtp85) cc_final: 0.8505 (mtp85) REVERT: G 76 THR cc_start: 0.9398 (p) cc_final: 0.9111 (t) REVERT: I 81 GLU cc_start: 0.9084 (pm20) cc_final: 0.8543 (pm20) REVERT: I 93 ASN cc_start: 0.8839 (m110) cc_final: 0.8621 (m-40) REVERT: I 109 ARG cc_start: 0.8601 (ptm160) cc_final: 0.7496 (pmt170) REVERT: J 13 ARG cc_start: 0.9070 (mtp85) cc_final: 0.8468 (mtp85) REVERT: J 43 GLN cc_start: 0.8260 (mp10) cc_final: 0.7944 (mp10) REVERT: J 76 THR cc_start: 0.9406 (p) cc_final: 0.9132 (t) REVERT: K 81 GLU cc_start: 0.9053 (pm20) cc_final: 0.8643 (pm20) REVERT: K 82 ASP cc_start: 0.8781 (m-30) cc_final: 0.8378 (m-30) REVERT: K 109 ARG cc_start: 0.8642 (ptm160) cc_final: 0.7396 (pmt170) REVERT: A 239 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8474 (tmt) REVERT: A 285 LYS cc_start: 0.8847 (mtpp) cc_final: 0.8514 (mttm) REVERT: A 453 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8190 (mt0) REVERT: B 153 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8961 (mm) REVERT: B 239 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8458 (tmt) REVERT: B 285 LYS cc_start: 0.9071 (mtpp) cc_final: 0.8764 (mttp) REVERT: C 153 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8957 (mm) REVERT: C 239 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8511 (tmt) REVERT: C 285 LYS cc_start: 0.9006 (mtpp) cc_final: 0.8634 (mttm) REVERT: D 239 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8526 (tmt) REVERT: D 285 LYS cc_start: 0.8986 (mtpp) cc_final: 0.8623 (mttm) outliers start: 58 outliers final: 26 residues processed: 357 average time/residue: 1.7465 time to fit residues: 684.6933 Evaluate side-chains 338 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 305 time to evaluate : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 453 GLN Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 275 GLU 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 456 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 172 optimal weight: 0.2980 chunk 133 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 131 optimal weight: 0.0000 chunk 235 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 62 GLN L 27 GLN E 3 GLN E 62 GLN I 27 GLN J 62 GLN K 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9081 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19952 Z= 0.236 Angle : 0.578 6.546 27020 Z= 0.307 Chirality : 0.045 0.199 2907 Planarity : 0.004 0.054 3464 Dihedral : 5.960 55.782 2928 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.65 % Favored : 97.19 % Rotamer: Outliers : 2.93 % Allowed : 18.22 % Favored : 78.85 % 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: -0.86 (0.16), residues: 2488 helix: None (None), residues: 0 sheet: -0.40 (0.16), residues: 976 loop : -0.64 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 177 HIS 0.008 0.001 HIS A 101 PHE 0.009 0.001 PHE D 119 TYR 0.017 0.001 TYR K 91 ARG 0.012 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 7 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 375 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 314 time to evaluate : 2.193 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: H 13 ARG cc_start: 0.9118 (mtp85) cc_final: 0.8437 (mtp85) REVERT: H 76 THR cc_start: 0.9411 (p) cc_final: 0.9148 (t) REVERT: L 17 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8583 (pm20) REVERT: L 81 GLU cc_start: 0.9091 (pm20) cc_final: 0.8512 (pm20) REVERT: L 109 ARG cc_start: 0.8586 (ptm160) cc_final: 0.7404 (pmt170) REVERT: E 13 ARG cc_start: 0.9111 (mtp85) cc_final: 0.8497 (mtp85) REVERT: E 43 GLN cc_start: 0.8183 (mp10) cc_final: 0.7934 (mp10) REVERT: E 76 THR cc_start: 0.9418 (p) cc_final: 0.9149 (t) REVERT: F 81 GLU cc_start: 0.9082 (pm20) cc_final: 0.8545 (pm20) REVERT: F 108 LYS cc_start: 0.9343 (OUTLIER) cc_final: 0.9035 (ttmm) REVERT: F 109 ARG cc_start: 0.8516 (ptm160) cc_final: 0.7302 (pmt170) REVERT: G 13 ARG cc_start: 0.9137 (mtp85) cc_final: 0.8523 (mtp85) REVERT: G 76 THR cc_start: 0.9401 (p) cc_final: 0.9125 (t) REVERT: I 81 GLU cc_start: 0.9076 (pm20) cc_final: 0.8554 (pm20) REVERT: I 93 ASN cc_start: 0.8785 (m110) cc_final: 0.8555 (m-40) REVERT: I 109 ARG cc_start: 0.8598 (ptm160) cc_final: 0.7490 (pmt170) REVERT: J 13 ARG cc_start: 0.9080 (mtp85) cc_final: 0.8485 (mtp85) REVERT: J 43 GLN cc_start: 0.8271 (mp10) cc_final: 0.7928 (mp10) REVERT: J 76 THR cc_start: 0.9386 (p) cc_final: 0.9127 (t) REVERT: J 89 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8587 (mp0) REVERT: K 81 GLU cc_start: 0.9035 (pm20) cc_final: 0.8640 (pm20) REVERT: K 82 ASP cc_start: 0.8709 (m-30) cc_final: 0.8345 (m-30) REVERT: K 109 ARG cc_start: 0.8650 (ptm160) cc_final: 0.7371 (pmt170) REVERT: A 239 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8457 (tmt) REVERT: A 285 LYS cc_start: 0.8812 (mtpp) cc_final: 0.8500 (mttm) REVERT: B 239 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8500 (tmt) REVERT: B 285 LYS cc_start: 0.9037 (mtpp) cc_final: 0.8675 (mttm) REVERT: C 239 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8478 (tmt) REVERT: C 285 LYS cc_start: 0.8970 (mtpp) cc_final: 0.8630 (mttm) REVERT: D 239 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8486 (tmt) REVERT: D 285 LYS cc_start: 0.8972 (mtpp) cc_final: 0.8618 (mttm) outliers start: 61 outliers final: 31 residues processed: 356 average time/residue: 1.7166 time to fit residues: 672.1038 Evaluate side-chains 342 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 304 time to evaluate : 2.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 409 TYR Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 135 TYR 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 456 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 140 optimal weight: 0.0020 chunk 70 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 184 optimal weight: 3.9990 overall best weight: 2.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 62 GLN L 27 GLN E 3 GLN E 62 GLN G 3 GLN I 27 GLN J 62 GLN K 27 GLN B 134 HIS ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9117 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 19952 Z= 0.364 Angle : 0.614 6.109 27020 Z= 0.327 Chirality : 0.046 0.211 2907 Planarity : 0.004 0.037 3464 Dihedral : 6.075 55.583 2927 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.85 % Favored : 96.99 % Rotamer: Outliers : 3.08 % Allowed : 18.12 % Favored : 78.80 % 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: -0.86 (0.16), residues: 2488 helix: None (None), residues: 0 sheet: -0.36 (0.16), residues: 976 loop : -0.67 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 177 HIS 0.009 0.002 HIS D 101 PHE 0.013 0.002 PHE H 104 TYR 0.017 0.002 TYR K 91 ARG 0.008 0.001 ARG C 295 *********************** REFINEMENT MACRO_CYCLE 8 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 378 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 314 time to evaluate : 2.145 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: H 13 ARG cc_start: 0.9124 (mtp85) cc_final: 0.8403 (mtp85) REVERT: H 76 THR cc_start: 0.9391 (p) cc_final: 0.9146 (t) REVERT: L 17 GLU cc_start: 0.8998 (pt0) cc_final: 0.8602 (pm20) REVERT: L 81 GLU cc_start: 0.9055 (pm20) cc_final: 0.8535 (pm20) REVERT: L 109 ARG cc_start: 0.8614 (ptm160) cc_final: 0.7392 (pmt170) REVERT: E 13 ARG cc_start: 0.9118 (mtp85) cc_final: 0.8498 (mtp85) REVERT: E 43 GLN cc_start: 0.8307 (mp10) cc_final: 0.7997 (mp10) REVERT: E 76 THR cc_start: 0.9411 (p) cc_final: 0.9163 (t) REVERT: F 17 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8654 (pm20) REVERT: F 81 GLU cc_start: 0.9115 (pm20) cc_final: 0.8568 (pm20) REVERT: F 109 ARG cc_start: 0.8553 (ptm160) cc_final: 0.7256 (pmt170) REVERT: G 13 ARG cc_start: 0.9136 (mtp85) cc_final: 0.8491 (mtp85) REVERT: G 76 THR cc_start: 0.9399 (p) cc_final: 0.9144 (t) REVERT: G 89 GLU cc_start: 0.9038 (pm20) cc_final: 0.8686 (mp0) REVERT: I 17 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8716 (pm20) REVERT: I 81 GLU cc_start: 0.9090 (pm20) cc_final: 0.8568 (pm20) REVERT: I 93 ASN cc_start: 0.8835 (m110) cc_final: 0.8595 (m-40) REVERT: I 109 ARG cc_start: 0.8570 (ptm160) cc_final: 0.7404 (pmt170) REVERT: J 13 ARG cc_start: 0.9072 (mtp85) cc_final: 0.8422 (mtp85) REVERT: J 43 GLN cc_start: 0.8299 (mp10) cc_final: 0.7939 (mp10) REVERT: J 76 THR cc_start: 0.9352 (p) cc_final: 0.9104 (t) REVERT: J 89 GLU cc_start: 0.8963 (pm20) cc_final: 0.8629 (mp0) REVERT: K 17 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8678 (pm20) REVERT: K 81 GLU cc_start: 0.9036 (pm20) cc_final: 0.8651 (pm20) REVERT: K 82 ASP cc_start: 0.8719 (m-30) cc_final: 0.8316 (m-30) REVERT: K 109 ARG cc_start: 0.8682 (ptm160) cc_final: 0.7336 (pmt170) REVERT: A 239 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8499 (tmt) REVERT: A 263 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.8728 (ttpt) REVERT: A 285 LYS cc_start: 0.8840 (mtpp) cc_final: 0.8531 (mttm) REVERT: B 239 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8535 (tmt) REVERT: B 285 LYS cc_start: 0.9037 (mtpp) cc_final: 0.8727 (mttp) REVERT: C 239 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8515 (tmt) REVERT: C 285 LYS cc_start: 0.8988 (mtpp) cc_final: 0.8645 (mttm) REVERT: D 239 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8504 (tmt) REVERT: D 285 LYS cc_start: 0.8977 (mtpp) cc_final: 0.8630 (mttm) outliers start: 64 outliers final: 35 residues processed: 359 average time/residue: 1.7051 time to fit residues: 673.5684 Evaluate side-chains 353 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 310 time to evaluate : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 48 MET Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 409 TYR Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 135 TYR 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 456 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 chunk 205 optimal weight: 1.9990 chunk 219 optimal weight: 0.9990 chunk 131 optimal weight: 0.0070 chunk 95 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 chunk 67 optimal weight: 8.9990 chunk 198 optimal weight: 1.9990 chunk 207 optimal weight: 0.6980 chunk 218 optimal weight: 5.9990 overall best weight: 0.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 62 GLN L 27 GLN E 3 GLN E 62 GLN G 3 GLN I 27 GLN J 62 GLN K 27 GLN C 134 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9072 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19952 Z= 0.217 Angle : 0.576 6.784 27020 Z= 0.306 Chirality : 0.045 0.204 2907 Planarity : 0.004 0.057 3464 Dihedral : 5.808 56.092 2926 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.53 % Favored : 97.31 % Rotamer: Outliers : 2.50 % Allowed : 18.94 % Favored : 78.56 % 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: -0.74 (0.17), residues: 2488 helix: None (None), residues: 0 sheet: -0.30 (0.17), residues: 948 loop : -0.56 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 177 HIS 0.007 0.001 HIS B 101 PHE 0.012 0.001 PHE H 29 TYR 0.016 0.001 TYR K 91 ARG 0.014 0.001 ARG I 24 *********************** REFINEMENT MACRO_CYCLE 9 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 365 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 313 time to evaluate : 2.461 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: H 76 THR cc_start: 0.9389 (p) cc_final: 0.9158 (t) REVERT: L 17 GLU cc_start: 0.8998 (pt0) cc_final: 0.8709 (pm20) REVERT: L 109 ARG cc_start: 0.8593 (ptm160) cc_final: 0.7400 (pmt170) REVERT: E 13 ARG cc_start: 0.9126 (mtp85) cc_final: 0.8556 (mtp85) REVERT: E 43 GLN cc_start: 0.8244 (mp10) cc_final: 0.7935 (mp10) REVERT: E 73 ASP cc_start: 0.8421 (t0) cc_final: 0.8077 (t70) REVERT: E 89 GLU cc_start: 0.9008 (pm20) cc_final: 0.8647 (mp0) REVERT: F 17 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8667 (pm20) REVERT: F 81 GLU cc_start: 0.9089 (pm20) cc_final: 0.8510 (pm20) REVERT: F 109 ARG cc_start: 0.8538 (ptm160) cc_final: 0.7180 (pmt170) REVERT: G 12 LYS cc_start: 0.9291 (mmmt) cc_final: 0.8965 (mmtp) REVERT: G 13 ARG cc_start: 0.9141 (mtp85) cc_final: 0.8493 (mtp85) REVERT: G 73 ASP cc_start: 0.8404 (t0) cc_final: 0.8059 (t70) REVERT: G 89 GLU cc_start: 0.9032 (pm20) cc_final: 0.8658 (mp0) REVERT: G 98 ARG cc_start: 0.8782 (ttt-90) cc_final: 0.8542 (ttt-90) REVERT: I 17 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8735 (pm20) REVERT: I 81 GLU cc_start: 0.9069 (pm20) cc_final: 0.8569 (pm20) REVERT: I 104 LYS cc_start: 0.9024 (tttt) cc_final: 0.8816 (tttp) REVERT: I 109 ARG cc_start: 0.8560 (ptm160) cc_final: 0.7412 (pmt170) REVERT: J 13 ARG cc_start: 0.9082 (mtp85) cc_final: 0.8463 (mtp85) REVERT: J 43 GLN cc_start: 0.8267 (mp10) cc_final: 0.7914 (mp10) REVERT: J 73 ASP cc_start: 0.8421 (t0) cc_final: 0.8072 (t0) REVERT: J 89 GLU cc_start: 0.8953 (pm20) cc_final: 0.8598 (mp0) REVERT: K 17 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8634 (pm20) REVERT: K 82 ASP cc_start: 0.8661 (m-30) cc_final: 0.8268 (m-30) REVERT: K 109 ARG cc_start: 0.8651 (ptm160) cc_final: 0.7331 (pmt170) REVERT: A 239 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8472 (tmt) REVERT: A 263 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.8702 (ttpt) REVERT: A 285 LYS cc_start: 0.8713 (mtpp) cc_final: 0.8436 (mttm) REVERT: B 239 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8456 (tmt) REVERT: B 285 LYS cc_start: 0.9006 (mtpp) cc_final: 0.8677 (mttm) REVERT: C 239 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8470 (tmt) REVERT: C 285 LYS cc_start: 0.8951 (mtpp) cc_final: 0.8629 (mttm) REVERT: D 239 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8457 (tmt) REVERT: D 285 LYS cc_start: 0.8944 (mtpp) cc_final: 0.8627 (mttm) REVERT: D 292 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8023 (ttm170) outliers start: 52 outliers final: 28 residues processed: 352 average time/residue: 1.7187 time to fit residues: 666.1771 Evaluate side-chains 345 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 308 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 409 TYR Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 135 TYR 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 456 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 0.8980 chunk 231 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 chunk 243 optimal weight: 0.9980 chunk 223 optimal weight: 0.8980 chunk 193 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 62 GLN L 27 GLN E 3 GLN E 62 GLN F 27 GLN I 27 GLN J 62 GLN K 27 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9075 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19952 Z= 0.241 Angle : 0.582 6.637 27020 Z= 0.309 Chirality : 0.045 0.227 2907 Planarity : 0.004 0.041 3464 Dihedral : 5.750 56.418 2926 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.65 % Favored : 97.19 % Rotamer: Outliers : 1.92 % Allowed : 19.47 % Favored : 78.61 % 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: -0.77 (0.17), residues: 2488 helix: None (None), residues: 0 sheet: -0.35 (0.16), residues: 980 loop : -0.56 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP K 94 HIS 0.008 0.001 HIS B 101 PHE 0.010 0.001 PHE H 29 TYR 0.016 0.001 TYR K 91 ARG 0.012 0.001 ARG C 295 ********************** REFINEMENT MACRO_CYCLE 10 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 350 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 310 time to evaluate : 2.269 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: H 73 ASP cc_start: 0.8394 (t0) cc_final: 0.8012 (t70) REVERT: L 17 GLU cc_start: 0.8965 (pt0) cc_final: 0.8672 (pm20) REVERT: L 48 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8013 (mm) REVERT: L 109 ARG cc_start: 0.8575 (ptm160) cc_final: 0.7365 (pmt170) REVERT: E 13 ARG cc_start: 0.9118 (mtp85) cc_final: 0.8540 (mtp85) REVERT: E 43 GLN cc_start: 0.8242 (mp10) cc_final: 0.7916 (mp10) REVERT: E 73 ASP cc_start: 0.8427 (t0) cc_final: 0.8086 (t70) REVERT: E 89 GLU cc_start: 0.8999 (pm20) cc_final: 0.8619 (mp0) REVERT: F 17 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8703 (pm20) REVERT: F 81 GLU cc_start: 0.9040 (pm20) cc_final: 0.8541 (pm20) REVERT: F 109 ARG cc_start: 0.8533 (ptm160) cc_final: 0.7176 (pmt170) REVERT: G 13 ARG cc_start: 0.9146 (mtp85) cc_final: 0.8556 (mtp85) REVERT: G 73 ASP cc_start: 0.8415 (t0) cc_final: 0.8081 (t70) REVERT: G 89 GLU cc_start: 0.9032 (pm20) cc_final: 0.8650 (mp0) REVERT: I 81 GLU cc_start: 0.9114 (pm20) cc_final: 0.8559 (pm20) REVERT: I 109 ARG cc_start: 0.8539 (ptm160) cc_final: 0.7416 (pmt170) REVERT: J 13 ARG cc_start: 0.9091 (mtp85) cc_final: 0.8486 (mtp85) REVERT: J 43 GLN cc_start: 0.8260 (mp10) cc_final: 0.7924 (mp10) REVERT: J 76 THR cc_start: 0.9351 (p) cc_final: 0.9118 (t) REVERT: J 89 GLU cc_start: 0.8956 (pm20) cc_final: 0.8584 (mp0) REVERT: K 17 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8639 (pm20) REVERT: K 82 ASP cc_start: 0.8667 (m-30) cc_final: 0.8233 (m-30) REVERT: K 109 ARG cc_start: 0.8657 (ptm160) cc_final: 0.7312 (pmt170) REVERT: A 285 LYS cc_start: 0.8709 (mtpp) cc_final: 0.8443 (mttm) REVERT: B 239 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8489 (tmt) REVERT: B 285 LYS cc_start: 0.9012 (mtpp) cc_final: 0.8692 (mttm) REVERT: C 239 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8482 (tmt) REVERT: C 285 LYS cc_start: 0.8956 (mtpp) cc_final: 0.8647 (mttm) REVERT: D 239 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8479 (tmt) REVERT: D 285 LYS cc_start: 0.8947 (mtpp) cc_final: 0.8633 (mttm) REVERT: D 292 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8012 (ttm170) outliers start: 40 outliers final: 27 residues processed: 343 average time/residue: 1.7594 time to fit residues: 663.3507 Evaluate side-chains 340 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 306 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 409 TYR Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 135 TYR 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 456 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 6.9990 chunk 206 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 193 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 199 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 62 GLN L 27 GLN E 3 GLN E 62 GLN F 27 GLN I 27 GLN J 62 GLN K 27 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.066344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.050924 restraints weight = 38251.966| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 2.20 r_work: 0.2583 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2468 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19952 Z= 0.260 Angle : 0.585 6.498 27020 Z= 0.311 Chirality : 0.045 0.222 2907 Planarity : 0.004 0.040 3464 Dihedral : 5.766 56.795 2926 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.61 % Favored : 97.23 % Rotamer: Outliers : 2.02 % Allowed : 19.47 % Favored : 78.51 % 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: -0.78 (0.17), residues: 2488 helix: None (None), residues: 0 sheet: -0.37 (0.16), residues: 980 loop : -0.56 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 94 HIS 0.008 0.001 HIS C 101 PHE 0.010 0.001 PHE J 115 TYR 0.017 0.001 TYR I 91 ARG 0.013 0.001 ARG C 295 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9622.09 seconds wall clock time: 268 minutes 1.19 seconds (16081.19 seconds total)