Starting phenix.real_space_refine on Wed Jul 24 18:27:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd4_37124/07_2024/8kd4_37124_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd4_37124/07_2024/8kd4_37124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd4_37124/07_2024/8kd4_37124.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd4_37124/07_2024/8kd4_37124.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd4_37124/07_2024/8kd4_37124_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd4_37124/07_2024/8kd4_37124_neut.cif" } resolution = 2.93 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= 0.011 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 328 5.49 5 S 91 5.16 5 C 16152 2.51 5 N 4810 2.21 5 O 5682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 234": "OD1" <-> "OD2" Residue "D ASP 242": "OD1" <-> "OD2" Residue "D ASP 251": "OD1" <-> "OD2" Residue "D GLU 255": "OE1" <-> "OE2" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 307": "OD1" <-> "OD2" Residue "D PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 376": "OD1" <-> "OD2" Residue "D ASP 378": "OD1" <-> "OD2" Residue "D ASP 384": "OD1" <-> "OD2" Residue "D TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 237": "OE1" <-> "OE2" Residue "F GLU 280": "OE1" <-> "OE2" Residue "F TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 302": "OE1" <-> "OE2" Residue "F GLU 308": "OE1" <-> "OE2" Residue "F GLU 360": "OE1" <-> "OE2" Residue "F GLU 372": "OE1" <-> "OE2" Residue "O TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 133": "OE1" <-> "OE2" Residue "P GLU 52": "OE1" <-> "OE2" Residue "P TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 56": "OE1" <-> "OE2" Residue "Q TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 32": "OE1" <-> "OE2" Residue "R TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 48": "OD1" <-> "OD2" Residue "R GLU 68": "OE1" <-> "OE2" Residue "R GLU 73": "OE1" <-> "OE2" Residue "R GLU 90": "OE1" <-> "OE2" Residue "R GLU 110": "OE1" <-> "OE2" Residue "S GLU 94": "OE1" <-> "OE2" Residue "S GLU 105": "OE1" <-> "OE2" Residue "S ASP 106": "OD1" <-> "OD2" Residue "S GLU 133": "OE1" <-> "OE2" Residue "T GLU 52": "OE1" <-> "OE2" Residue "U ASP 90": "OD1" <-> "OD2" Residue "U GLU 91": "OE1" <-> "OE2" Residue "V TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 73": "OE1" <-> "OE2" Residue "V GLU 90": "OE1" <-> "OE2" Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "A GLU 118": "OE1" <-> "OE2" Residue "A TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 201": "OD1" <-> "OD2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 223": "OD1" <-> "OD2" Residue "A ASP 243": "OD1" <-> "OD2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "A TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "A TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 345": "OE1" <-> "OE2" Residue "A ASP 407": "OD1" <-> "OD2" Residue "B GLU 664": "OE1" <-> "OE2" Residue "B GLU 665": "OE1" <-> "OE2" Residue "B TYR 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 811": "OE1" <-> "OE2" Residue "B GLU 813": "OE1" <-> "OE2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "B GLU 951": "OE1" <-> "OE2" Residue "B ASP 958": "OD1" <-> "OD2" Residue "B PHE 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1012": "OD1" <-> "OD2" Residue "B PHE 1022": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1026": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1027": "OE1" <-> "OE2" Residue "B PHE 1136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1166": "OE1" <-> "OE2" Residue "B ASP 1183": "OD1" <-> "OD2" Residue "B GLU 1193": "OE1" <-> "OE2" Residue "B GLU 1264": "OE1" <-> "OE2" Residue "B PHE 1269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1306": "OD1" <-> "OD2" Residue "E ASP 261": "OD1" <-> "OD2" Residue "E PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 305": "OE1" <-> "OE2" Residue "E PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 374": "OD1" <-> "OD2" Residue "E ASP 377": "OD1" <-> "OD2" Residue "E ASP 383": "OD1" <-> "OD2" Residue "E TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 404": "OD1" <-> "OD2" Residue "E TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 507": "OE1" <-> "OE2" Residue "E GLU 544": "OE1" <-> "OE2" Residue "G GLU 323": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 27064 Number of models: 1 Model: "" Number of chains: 17 Chain: "D" Number of atoms: 1883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1883 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 8, 'TRANS': 222} Chain breaks: 2 Chain: "F" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1639 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain breaks: 2 Chain: "O" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "P" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "Q" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "R" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 730 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "S" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "U" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "V" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 715 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "X" Number of atoms: 3384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3384 Classifications: {'DNA': 164} Link IDs: {'rna3p': 163} Chain: "Y" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3340 Classifications: {'DNA': 164} Link IDs: {'rna3p': 163} Chain: "A" Number of atoms: 3073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3073 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 15, 'TRANS': 372} Chain breaks: 1 Chain: "B" Number of atoms: 4545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4545 Classifications: {'peptide': 542} Link IDs: {'PTRANS': 12, 'TRANS': 529} Chain breaks: 2 Chain: "E" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2611 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 18, 'TRANS': 298} Chain breaks: 3 Chain: "G" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 598 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.73, per 1000 atoms: 0.62 Number of scatterers: 27064 At special positions: 0 Unit cell: (138.45, 161.88, 186.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 91 16.00 P 328 15.00 O 5682 8.00 N 4810 7.00 C 16152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 303 " - pdb=" SG CYS E 306 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.33 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 188 " 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4742 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 17 sheets defined 58.2% alpha, 3.5% beta 140 base pairs and 275 stacking pairs defined. Time for finding SS restraints: 11.73 Creating SS restraints... Processing helix chain 'D' and resid 98 through 113 Processing helix chain 'D' and resid 225 through 241 Processing helix chain 'D' and resid 253 through 269 Processing helix chain 'D' and resid 273 through 293 removed outlier: 4.419A pdb=" N GLN D 277 " --> pdb=" O GLY D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 317 removed outlier: 4.456A pdb=" N GLN D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 309 " --> pdb=" O GLN D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 327 through 344 removed outlier: 4.027A pdb=" N LEU D 331 " --> pdb=" O GLY D 327 " (cutoff:3.500A) Proline residue: D 339 - end of helix Processing helix chain 'D' and resid 348 through 369 Processing helix chain 'D' and resid 391 through 399 Processing helix chain 'F' and resid 98 through 112 removed outlier: 3.995A pdb=" N GLU F 102 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 239 removed outlier: 4.034A pdb=" N VAL F 233 " --> pdb=" O LYS F 229 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU F 237 " --> pdb=" O VAL F 233 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR F 238 " --> pdb=" O ASP F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 260 removed outlier: 4.370A pdb=" N VAL F 257 " --> pdb=" O THR F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 265 removed outlier: 3.574A pdb=" N VAL F 265 " --> pdb=" O TYR F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 290 removed outlier: 4.500A pdb=" N TYR F 281 " --> pdb=" O GLN F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 314 Processing helix chain 'F' and resid 328 through 343 removed outlier: 4.186A pdb=" N LEU F 332 " --> pdb=" O ALA F 328 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ARG F 333 " --> pdb=" O ILE F 329 " (cutoff:3.500A) Proline residue: F 339 - end of helix removed outlier: 3.735A pdb=" N SER F 343 " --> pdb=" O PRO F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 348 through 367 removed outlier: 3.957A pdb=" N CYS F 352 " --> pdb=" O ASP F 348 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 55 Processing helix chain 'O' and resid 63 through 76 removed outlier: 3.544A pdb=" N LEU O 70 " --> pdb=" O PRO O 66 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 114 Processing helix chain 'O' and resid 120 through 132 Processing helix chain 'P' and resid 25 through 29 removed outlier: 3.705A pdb=" N ILE P 29 " --> pdb=" O ILE P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 41 Processing helix chain 'P' and resid 49 through 76 removed outlier: 4.025A pdb=" N ARG P 67 " --> pdb=" O GLU P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 92 Processing helix chain 'Q' and resid 16 through 21 Processing helix chain 'Q' and resid 26 through 37 Processing helix chain 'Q' and resid 45 through 73 removed outlier: 4.344A pdb=" N VAL Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 90 Processing helix chain 'Q' and resid 90 through 97 Processing helix chain 'R' and resid 34 through 46 removed outlier: 3.687A pdb=" N TYR R 39 " --> pdb=" O ALA R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 81 Processing helix chain 'R' and resid 87 through 99 removed outlier: 3.542A pdb=" N ILE R 91 " --> pdb=" O THR R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 120 Processing helix chain 'S' and resid 44 through 56 removed outlier: 3.628A pdb=" N LYS S 56 " --> pdb=" O ARG S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 79 removed outlier: 3.619A pdb=" N ASP S 77 " --> pdb=" O GLU S 73 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE S 78 " --> pdb=" O ILE S 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 85 through 114 Processing helix chain 'S' and resid 120 through 132 Processing helix chain 'T' and resid 25 through 29 removed outlier: 3.807A pdb=" N ILE T 29 " --> pdb=" O ILE T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 30 through 41 Processing helix chain 'T' and resid 49 through 76 removed outlier: 3.824A pdb=" N ARG T 67 " --> pdb=" O GLU T 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 82 through 92 Processing helix chain 'U' and resid 16 through 21 Processing helix chain 'U' and resid 26 through 37 Processing helix chain 'U' and resid 45 through 73 removed outlier: 4.039A pdb=" N VAL U 49 " --> pdb=" O ALA U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 90 removed outlier: 3.524A pdb=" N ASP U 90 " --> pdb=" O ALA U 86 " (cutoff:3.500A) Processing helix chain 'U' and resid 90 through 97 Processing helix chain 'V' and resid 34 through 46 removed outlier: 3.527A pdb=" N VAL V 38 " --> pdb=" O TYR V 34 " (cutoff:3.500A) Processing helix chain 'V' and resid 52 through 81 removed outlier: 3.716A pdb=" N ASN V 81 " --> pdb=" O LEU V 77 " (cutoff:3.500A) Processing helix chain 'V' and resid 87 through 99 Processing helix chain 'V' and resid 101 through 119 removed outlier: 4.067A pdb=" N LYS V 105 " --> pdb=" O GLY V 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 removed outlier: 4.202A pdb=" N TYR A 32 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 55 removed outlier: 4.306A pdb=" N ARG A 46 " --> pdb=" O PRO A 42 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET A 47 " --> pdb=" O HIS A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 61 removed outlier: 4.018A pdb=" N LYS A 59 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 60 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET A 61 " --> pdb=" O TYR A 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 56 through 61' Processing helix chain 'A' and resid 79 through 89 Processing helix chain 'A' and resid 90 through 94 removed outlier: 3.502A pdb=" N ASN A 93 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 94 " --> pdb=" O PRO A 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 90 through 94' Processing helix chain 'A' and resid 98 through 104 removed outlier: 3.548A pdb=" N VAL A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 137 Processing helix chain 'A' and resid 164 through 175 removed outlier: 3.689A pdb=" N LEU A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 removed outlier: 3.736A pdb=" N GLU A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 243 through 262 Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 287 through 300 removed outlier: 3.866A pdb=" N CYS A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL A 295 " --> pdb=" O HIS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 330 removed outlier: 3.751A pdb=" N ARG A 320 " --> pdb=" O ARG A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 347 removed outlier: 3.529A pdb=" N TYR A 346 " --> pdb=" O TYR A 343 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR A 347 " --> pdb=" O TYR A 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 343 through 347' Processing helix chain 'A' and resid 365 through 381 Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'B' and resid 665 through 677 removed outlier: 4.601A pdb=" N PHE B 669 " --> pdb=" O GLU B 665 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLU B 670 " --> pdb=" O VAL B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 694 Processing helix chain 'B' and resid 698 through 710 removed outlier: 3.711A pdb=" N PHE B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 725 Processing helix chain 'B' and resid 771 through 778 Processing helix chain 'B' and resid 785 through 791 removed outlier: 3.945A pdb=" N ALA B 789 " --> pdb=" O HIS B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 840 removed outlier: 3.604A pdb=" N ASP B 818 " --> pdb=" O ARG B 814 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN B 840 " --> pdb=" O ASN B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 848 removed outlier: 3.896A pdb=" N ASN B 848 " --> pdb=" O ASN B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 871 Processing helix chain 'B' and resid 872 through 886 removed outlier: 3.884A pdb=" N PHE B 877 " --> pdb=" O LYS B 873 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU B 878 " --> pdb=" O GLU B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 929 removed outlier: 3.923A pdb=" N LYS B 914 " --> pdb=" O ARG B 910 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL B 915 " --> pdb=" O GLU B 911 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N PHE B 925 " --> pdb=" O GLN B 921 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS B 926 " --> pdb=" O LYS B 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 934 through 943 removed outlier: 4.290A pdb=" N LYS B 940 " --> pdb=" O LYS B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 944 through 967 removed outlier: 3.606A pdb=" N ILE B 955 " --> pdb=" O GLU B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 997 removed outlier: 4.199A pdb=" N TYR B 986 " --> pdb=" O LYS B 982 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR B 997 " --> pdb=" O ASP B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1022 removed outlier: 4.059A pdb=" N ILE B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE B1022 " --> pdb=" O ILE B1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1164 removed outlier: 4.039A pdb=" N MET B1164 " --> pdb=" O GLU B1160 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1174 removed outlier: 3.877A pdb=" N LYS B1170 " --> pdb=" O GLU B1166 " (cutoff:3.500A) Processing helix chain 'B' and resid 1178 through 1185 Processing helix chain 'B' and resid 1202 through 1216 Processing helix chain 'B' and resid 1221 through 1230 Processing helix chain 'B' and resid 1236 through 1240 removed outlier: 3.849A pdb=" N LEU B1239 " --> pdb=" O ALA B1236 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR B1240 " --> pdb=" O PHE B1237 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1236 through 1240' Processing helix chain 'B' and resid 1241 through 1259 removed outlier: 3.596A pdb=" N THR B1255 " --> pdb=" O LYS B1251 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU B1256 " --> pdb=" O HIS B1252 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N MET B1257 " --> pdb=" O ALA B1253 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B1258 " --> pdb=" O HIS B1254 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP B1259 " --> pdb=" O THR B1255 " (cutoff:3.500A) Processing helix chain 'B' and resid 1259 through 1273 Processing helix chain 'B' and resid 1282 through 1294 removed outlier: 3.518A pdb=" N TYR B1286 " --> pdb=" O ASP B1282 " (cutoff:3.500A) Processing helix chain 'B' and resid 1307 through 1309 No H-bonds generated for 'chain 'B' and resid 1307 through 1309' Processing helix chain 'E' and resid 292 through 296 removed outlier: 3.855A pdb=" N LEU E 296 " --> pdb=" O PRO E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 308 Processing helix chain 'E' and resid 321 through 330 removed outlier: 3.734A pdb=" N ILE E 327 " --> pdb=" O GLU E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 345 removed outlier: 4.479A pdb=" N LYS E 338 " --> pdb=" O LYS E 334 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU E 339 " --> pdb=" O ILE E 335 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASP E 344 " --> pdb=" O LEU E 340 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER E 345 " --> pdb=" O PHE E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 360 removed outlier: 4.162A pdb=" N THR E 360 " --> pdb=" O TYR E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 387 Processing helix chain 'E' and resid 402 through 407 removed outlier: 3.503A pdb=" N THR E 405 " --> pdb=" O ASN E 402 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE E 407 " --> pdb=" O ASP E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 434 Processing helix chain 'E' and resid 543 through 559 Processing helix chain 'G' and resid 322 through 326 removed outlier: 3.597A pdb=" N ASN G 325 " --> pdb=" O ILE G 322 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 342 removed outlier: 3.995A pdb=" N PHE G 341 " --> pdb=" O ALA G 337 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASN G 342 " --> pdb=" O LYS G 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 337 through 342' Processing helix chain 'G' and resid 541 through 569 Processing sheet with id=AA1, first strand: chain 'D' and resid 244 through 246 Processing sheet with id=AA2, first strand: chain 'O' and resid 83 through 84 removed outlier: 6.704A pdb=" N ARG O 83 " --> pdb=" O VAL P 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'O' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'P' and resid 96 through 98 removed outlier: 6.076A pdb=" N THR P 96 " --> pdb=" O THR U 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'Q' and resid 42 through 43 removed outlier: 7.339A pdb=" N ARG Q 42 " --> pdb=" O ILE R 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'Q' and resid 77 through 78 Processing sheet with id=AA7, first strand: chain 'Q' and resid 100 through 102 Processing sheet with id=AA8, first strand: chain 'S' and resid 83 through 84 removed outlier: 6.826A pdb=" N ARG S 83 " --> pdb=" O VAL T 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'S' and resid 118 through 119 Processing sheet with id=AB1, first strand: chain 'U' and resid 42 through 43 removed outlier: 7.010A pdb=" N ARG U 42 " --> pdb=" O ILE V 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'U' and resid 77 through 78 Processing sheet with id=AB3, first strand: chain 'A' and resid 62 through 64 removed outlier: 5.900A pdb=" N VAL A 21 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N TYR A 64 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N TYR A 23 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA A 22 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA A 142 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N GLY A 309 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ASN A 144 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N GLY A 311 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL A 267 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL A 308 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU A 269 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLY A 310 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N CYS A 271 " --> pdb=" O GLY A 310 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL A 180 " --> pdb=" O MET A 204 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N CYS A 206 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N TYR A 182 " --> pdb=" O CYS A 206 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N PHE A 208 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ASP A 184 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N LYS A 210 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N VAL A 234 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N THR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL A 236 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER A 207 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU A 238 " --> pdb=" O SER A 207 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N HIS A 209 " --> pdb=" O LEU A 238 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 977 through 978 removed outlier: 3.946A pdb=" N PHE B 977 " --> pdb=" O VAL B1312 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL B1312 " --> pdb=" O PHE B 977 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 272 through 274 Processing sheet with id=AB6, first strand: chain 'E' and resid 365 through 366 Processing sheet with id=AB7, first strand: chain 'E' and resid 437 through 438 Processing sheet with id=AB8, first strand: chain 'E' and resid 521 through 522 removed outlier: 5.602A pdb=" N GLN E 521 " --> pdb=" O ILE E 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 983 hydrogen bonds defined for protein. 2895 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 368 hydrogen bonds 736 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 275 stacking parallelities Total time for adding SS restraints: 18.57 Time building geometry restraints manager: 14.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6715 1.34 - 1.46: 7613 1.46 - 1.58: 13159 1.58 - 1.70: 654 1.70 - 1.82: 144 Bond restraints: 28285 Sorted by residual: bond pdb=" CB PRO D 319 " pdb=" CG PRO D 319 " ideal model delta sigma weight residual 1.492 1.708 -0.216 5.00e-02 4.00e+02 1.86e+01 bond pdb=" CA SER A 408 " pdb=" C SER A 408 " ideal model delta sigma weight residual 1.529 1.478 0.051 1.40e-02 5.10e+03 1.32e+01 bond pdb=" CG PRO D 319 " pdb=" CD PRO D 319 " ideal model delta sigma weight residual 1.503 1.402 0.101 3.40e-02 8.65e+02 8.76e+00 bond pdb=" N PRO D 319 " pdb=" CD PRO D 319 " ideal model delta sigma weight residual 1.473 1.513 -0.040 1.40e-02 5.10e+03 8.00e+00 bond pdb=" C ASN B1004 " pdb=" N PRO B1005 " ideal model delta sigma weight residual 1.336 1.370 -0.035 1.23e-02 6.61e+03 7.94e+00 ... (remaining 28280 not shown) Histogram of bond angle deviations from ideal: 93.25 - 102.11: 354 102.11 - 110.98: 11619 110.98 - 119.84: 14733 119.84 - 128.71: 12500 128.71 - 137.57: 373 Bond angle restraints: 39579 Sorted by residual: angle pdb=" CA PRO D 319 " pdb=" N PRO D 319 " pdb=" CD PRO D 319 " ideal model delta sigma weight residual 112.00 96.38 15.62 1.40e+00 5.10e-01 1.24e+02 angle pdb=" N PRO D 319 " pdb=" CD PRO D 319 " pdb=" CG PRO D 319 " ideal model delta sigma weight residual 103.20 93.25 9.95 1.50e+00 4.44e-01 4.40e+01 angle pdb=" CA MET D 107 " pdb=" CB MET D 107 " pdb=" CG MET D 107 " ideal model delta sigma weight residual 114.10 125.58 -11.48 2.00e+00 2.50e-01 3.29e+01 angle pdb=" CA GLU E 507 " pdb=" CB GLU E 507 " pdb=" CG GLU E 507 " ideal model delta sigma weight residual 114.10 124.92 -10.82 2.00e+00 2.50e-01 2.93e+01 angle pdb=" CA LEU F 297 " pdb=" CB LEU F 297 " pdb=" CG LEU F 297 " ideal model delta sigma weight residual 116.30 133.36 -17.06 3.50e+00 8.16e-02 2.38e+01 ... (remaining 39574 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 14091 35.18 - 70.36: 2029 70.36 - 105.54: 47 105.54 - 140.72: 2 140.72 - 175.89: 1 Dihedral angle restraints: 16170 sinusoidal: 8831 harmonic: 7339 Sorted by residual: dihedral pdb=" CA LEU B1184 " pdb=" C LEU B1184 " pdb=" N ASP B1185 " pdb=" CA ASP B1185 " ideal model delta harmonic sigma weight residual 180.00 155.66 24.34 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA GLU B1220 " pdb=" C GLU B1220 " pdb=" N HIS B1221 " pdb=" CA HIS B1221 " ideal model delta harmonic sigma weight residual -180.00 -159.26 -20.74 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA MET D 347 " pdb=" C MET D 347 " pdb=" N ASP D 348 " pdb=" CA ASP D 348 " ideal model delta harmonic sigma weight residual -180.00 -159.66 -20.34 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 16167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 4131 0.086 - 0.173: 228 0.173 - 0.259: 6 0.259 - 0.345: 4 0.345 - 0.432: 1 Chirality restraints: 4370 Sorted by residual: chirality pdb=" CG LEU B 825 " pdb=" CB LEU B 825 " pdb=" CD1 LEU B 825 " pdb=" CD2 LEU B 825 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.66e+00 chirality pdb=" CA PRO D 319 " pdb=" N PRO D 319 " pdb=" C PRO D 319 " pdb=" CB PRO D 319 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB VAL F 364 " pdb=" CA VAL F 364 " pdb=" CG1 VAL F 364 " pdb=" CG2 VAL F 364 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.29 2.00e-01 2.50e+01 2.18e+00 ... (remaining 4367 not shown) Planarity restraints: 3885 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 318 " 0.059 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO D 319 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO D 319 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 319 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 775 " 0.018 2.00e-02 2.50e+03 1.94e-02 9.37e+00 pdb=" CG TRP B 775 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP B 775 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP B 775 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 775 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 775 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 775 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 775 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 775 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 775 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 492 " 0.015 2.00e-02 2.50e+03 1.76e-02 7.75e+00 pdb=" CG TRP E 492 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP E 492 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP E 492 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 492 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 492 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 492 " 0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 492 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 492 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 492 " -0.001 2.00e-02 2.50e+03 ... (remaining 3882 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 236 2.60 - 3.17: 21330 3.17 - 3.75: 48536 3.75 - 4.32: 62990 4.32 - 4.90: 95594 Nonbonded interactions: 228686 Sorted by model distance: nonbonded pdb=" CD2 LEU B 883 " pdb=" OG1 THR B 890 " model vdw 2.023 3.460 nonbonded pdb=" CB HIS A 188 " pdb="ZN ZN A 501 " model vdw 2.036 2.104 nonbonded pdb=" CB ALA A 36 " pdb=" CD2 LEU E 48 " model vdw 2.122 3.880 nonbonded pdb=" OG SER A 123 " pdb=" OD2 ASP A 165 " model vdw 2.222 2.440 nonbonded pdb=" OG SER D 392 " pdb=" OE1 GLU A 156 " model vdw 2.227 2.440 ... (remaining 228681 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'D' and (resid 11 through 24 or resid 80 through 112 or resid 222 through \ 373)) selection = chain 'F' } ncs_group { reference = (chain 'O' and resid 37 through 133) selection = (chain 'S' and resid 37 through 133) } ncs_group { reference = chain 'P' selection = chain 'T' } ncs_group { reference = chain 'Q' selection = chain 'U' } ncs_group { reference = (chain 'R' and resid 29 through 119) selection = chain 'V' } 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: 12.090 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: 0.030 Extract box with map and model: 1.170 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 97.080 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 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 : 0.004 0.216 28285 Z= 0.228 Angle : 0.809 17.062 39579 Z= 0.429 Chirality : 0.042 0.432 4370 Planarity : 0.005 0.095 3885 Dihedral : 24.504 175.895 11425 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.99 % Favored : 94.97 % Rotamer: Outliers : 0.59 % Allowed : 32.67 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.15), residues: 2447 helix: -0.45 (0.13), residues: 1312 sheet: 0.18 (0.64), residues: 85 loop : -1.70 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 775 HIS 0.011 0.001 HIS B 785 PHE 0.020 0.001 PHE B 708 TYR 0.038 0.002 TYR A 176 ARG 0.021 0.001 ARG B 799 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 354 time to evaluate : 2.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 323 ILE cc_start: 0.8233 (pt) cc_final: 0.7910 (pt) REVERT: D 349 LEU cc_start: 0.8262 (mm) cc_final: 0.8057 (tp) REVERT: F 95 ASP cc_start: 0.3396 (p0) cc_final: 0.2587 (t70) REVERT: F 233 VAL cc_start: 0.2420 (t) cc_final: 0.2121 (m) REVERT: F 234 ASP cc_start: 0.5247 (t70) cc_final: 0.4881 (m-30) REVERT: F 296 MET cc_start: 0.3920 (mmm) cc_final: 0.3703 (mpp) REVERT: U 74 LYS cc_start: 0.7930 (mptp) cc_final: 0.7626 (mptt) REVERT: U 90 ASP cc_start: 0.7919 (t0) cc_final: 0.7697 (t0) REVERT: U 95 LYS cc_start: 0.7882 (ttpt) cc_final: 0.7458 (tttt) REVERT: A 316 ARG cc_start: 0.7054 (mtm110) cc_final: 0.6845 (ttp-110) REVERT: B 670 GLU cc_start: 0.7535 (mp0) cc_final: 0.7122 (pt0) REVERT: B 684 GLU cc_start: 0.8307 (tp30) cc_final: 0.8009 (tp30) REVERT: B 799 ARG cc_start: 0.7430 (mmm160) cc_final: 0.7116 (mtt-85) REVERT: B 813 GLU cc_start: 0.7398 (mt-10) cc_final: 0.6522 (mm-30) REVERT: B 907 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7867 (pmm-80) REVERT: E 545 ASN cc_start: 0.7508 (t0) cc_final: 0.7273 (t0) REVERT: G 560 MET cc_start: 0.8508 (mpt) cc_final: 0.7893 (ptp) REVERT: G 565 LYS cc_start: 0.6179 (mptt) cc_final: 0.5907 (tptp) outliers start: 13 outliers final: 8 residues processed: 361 average time/residue: 1.2850 time to fit residues: 548.7008 Evaluate side-chains 319 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 310 time to evaluate : 2.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 817 TYR Chi-restraints excluded: chain B residue 886 HIS Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 907 ARG Chi-restraints excluded: chain B residue 1306 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 213 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 247 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 358 GLN F 267 GLN F 350 GLN S 108 ASN U 38 ASN ** V 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 64 ASN ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1150 HIS E 314 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 28285 Z= 0.292 Angle : 0.622 14.818 39579 Z= 0.336 Chirality : 0.039 0.222 4370 Planarity : 0.004 0.056 3885 Dihedral : 26.635 178.211 6328 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 5.81 % Allowed : 26.27 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.16), residues: 2447 helix: 0.37 (0.14), residues: 1356 sheet: 0.71 (0.62), residues: 86 loop : -1.51 (0.18), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 775 HIS 0.010 0.001 HIS B 785 PHE 0.026 0.002 PHE G 551 TYR 0.041 0.002 TYR P 88 ARG 0.010 0.001 ARG R 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 375 time to evaluate : 2.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 278 LEU cc_start: 0.8249 (tp) cc_final: 0.7986 (tp) REVERT: D 323 ILE cc_start: 0.8417 (pt) cc_final: 0.8163 (pt) REVERT: D 341 LEU cc_start: 0.6008 (OUTLIER) cc_final: 0.5717 (pp) REVERT: F 95 ASP cc_start: 0.3196 (p0) cc_final: 0.2540 (t70) REVERT: F 233 VAL cc_start: 0.2753 (t) cc_final: 0.2472 (m) REVERT: F 234 ASP cc_start: 0.5476 (t70) cc_final: 0.4835 (m-30) REVERT: F 256 MET cc_start: 0.1696 (OUTLIER) cc_final: 0.1209 (pp-130) REVERT: F 371 ASP cc_start: 0.4972 (OUTLIER) cc_final: 0.4530 (t70) REVERT: O 59 GLU cc_start: 0.7408 (pm20) cc_final: 0.6918 (pm20) REVERT: R 39 TYR cc_start: 0.7868 (t80) cc_final: 0.7353 (t80) REVERT: R 46 HIS cc_start: 0.8077 (OUTLIER) cc_final: 0.7364 (m170) REVERT: R 110 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7677 (mm-30) REVERT: R 113 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8026 (ptpp) REVERT: T 91 LYS cc_start: 0.8742 (ttmt) cc_final: 0.8494 (tttt) REVERT: U 36 LYS cc_start: 0.8254 (ptmt) cc_final: 0.7858 (ptmm) REVERT: U 95 LYS cc_start: 0.8799 (ttpt) cc_final: 0.8500 (ttmm) REVERT: V 105 LYS cc_start: 0.8339 (mtpt) cc_final: 0.7779 (mttp) REVERT: A 47 MET cc_start: 0.7005 (ptt) cc_final: 0.6783 (ptt) REVERT: A 88 ARG cc_start: 0.8033 (mtm110) cc_final: 0.7526 (mtm180) REVERT: A 263 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.8024 (mt0) REVERT: A 365 THR cc_start: 0.8680 (p) cc_final: 0.8302 (p) REVERT: B 670 GLU cc_start: 0.7598 (mp0) cc_final: 0.7310 (pt0) REVERT: B 813 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7611 (mt-10) REVERT: B 817 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.7698 (m-80) REVERT: B 825 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8846 (mm) REVERT: B 910 ARG cc_start: 0.7869 (ttm110) cc_final: 0.7558 (tmt170) REVERT: B 918 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7909 (mp0) REVERT: B 1136 PHE cc_start: 0.5066 (OUTLIER) cc_final: 0.4638 (m-10) REVERT: B 1187 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7116 (mm) REVERT: B 1222 GLN cc_start: 0.7888 (pt0) cc_final: 0.7628 (pm20) REVERT: B 1257 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7453 (mtm) REVERT: E 271 SER cc_start: 0.7600 (OUTLIER) cc_final: 0.7338 (m) REVERT: E 369 ARG cc_start: 0.7464 (pmm-80) cc_final: 0.7088 (mtm110) REVERT: E 371 GLN cc_start: 0.7763 (pm20) cc_final: 0.7465 (pm20) REVERT: E 375 GLU cc_start: 0.8803 (pm20) cc_final: 0.8522 (pm20) REVERT: E 512 ILE cc_start: 0.6342 (OUTLIER) cc_final: 0.5671 (pt) REVERT: E 549 TYR cc_start: 0.8369 (OUTLIER) cc_final: 0.7905 (t80) outliers start: 129 outliers final: 39 residues processed: 447 average time/residue: 1.3482 time to fit residues: 703.0189 Evaluate side-chains 377 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 321 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 371 ASP Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 25 ASN Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain R residue 44 GLN Chi-restraints excluded: chain R residue 46 HIS Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain R residue 113 LYS Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain V residue 44 GLN Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 817 TYR Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1136 PHE Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain B residue 1278 THR Chi-restraints excluded: chain B residue 1289 GLN Chi-restraints excluded: chain B residue 1317 ILE Chi-restraints excluded: chain B residue 1323 THR Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 343 ILE Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 512 ILE Chi-restraints excluded: chain E residue 543 ASP Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain G residue 335 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 268 optimal weight: 0.0970 chunk 221 optimal weight: 9.9990 chunk 246 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 199 optimal weight: 9.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 HIS O 68 GLN O 76 GLN O 108 ASN S 76 GLN S 85 GLN S 125 GLN U 38 ASN ** V 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 GLN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN A 419 GLN ** B 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1150 HIS E 314 ASN ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 410 ASN ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 28285 Z= 0.397 Angle : 0.694 12.927 39579 Z= 0.376 Chirality : 0.043 0.216 4370 Planarity : 0.005 0.052 3885 Dihedral : 27.124 179.644 6315 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 6.67 % Allowed : 25.46 % Favored : 67.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.16), residues: 2447 helix: 0.41 (0.14), residues: 1354 sheet: -0.06 (0.57), residues: 90 loop : -1.35 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 775 HIS 0.010 0.002 HIS R 46 PHE 0.018 0.002 PHE A 24 TYR 0.036 0.002 TYR B1145 ARG 0.012 0.001 ARG B 799 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 359 time to evaluate : 2.625 Fit side-chains revert: symmetry clash REVERT: D 275 GLN cc_start: 0.6778 (mm-40) cc_final: 0.6338 (mp10) REVERT: D 277 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7488 (tt0) REVERT: D 358 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7999 (mp10) REVERT: F 24 GLU cc_start: 0.4930 (mt-10) cc_final: 0.4639 (mm-30) REVERT: F 95 ASP cc_start: 0.2997 (p0) cc_final: 0.2407 (t70) REVERT: F 270 GLU cc_start: 0.0622 (OUTLIER) cc_final: -0.0337 (pm20) REVERT: P 77 LYS cc_start: 0.8894 (mmtt) cc_final: 0.8665 (mmtp) REVERT: Q 36 LYS cc_start: 0.8379 (ptmt) cc_final: 0.8175 (mmtm) REVERT: Q 90 ASP cc_start: 0.8460 (t70) cc_final: 0.8186 (t0) REVERT: S 73 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8141 (tt0) REVERT: S 131 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8540 (mtt180) REVERT: T 25 ASN cc_start: 0.8795 (m-40) cc_final: 0.8404 (m110) REVERT: T 91 LYS cc_start: 0.8825 (ttmt) cc_final: 0.8459 (tttt) REVERT: U 36 LYS cc_start: 0.8323 (ptmt) cc_final: 0.8097 (mmmt) REVERT: U 56 GLU cc_start: 0.8552 (tt0) cc_final: 0.8283 (tt0) REVERT: V 68 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7222 (mt-10) REVERT: V 105 LYS cc_start: 0.8423 (mtpt) cc_final: 0.7905 (mttp) REVERT: A 47 MET cc_start: 0.7887 (ptt) cc_final: 0.7475 (ptp) REVERT: A 88 ARG cc_start: 0.8245 (mtm110) cc_final: 0.7842 (mtm180) REVERT: A 189 HIS cc_start: 0.7257 (OUTLIER) cc_final: 0.6599 (p90) REVERT: A 240 ASP cc_start: 0.8782 (m-30) cc_final: 0.8533 (m-30) REVERT: A 261 TRP cc_start: 0.7012 (m-90) cc_final: 0.6651 (m-90) REVERT: A 373 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.6886 (mpp) REVERT: B 670 GLU cc_start: 0.7737 (mp0) cc_final: 0.6889 (mp0) REVERT: B 817 TYR cc_start: 0.8237 (OUTLIER) cc_final: 0.7943 (m-80) REVERT: B 825 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8808 (mm) REVERT: B 828 ILE cc_start: 0.7346 (OUTLIER) cc_final: 0.6899 (mm) REVERT: B 910 ARG cc_start: 0.7973 (ttm110) cc_final: 0.7660 (tmt170) REVERT: B 918 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8206 (mp0) REVERT: B 982 LYS cc_start: 0.7606 (mtmt) cc_final: 0.6993 (mtmm) REVERT: B 1016 TYR cc_start: 0.7955 (OUTLIER) cc_final: 0.7530 (t80) REVERT: B 1136 PHE cc_start: 0.5819 (OUTLIER) cc_final: 0.5189 (m-10) REVERT: B 1160 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.6944 (mp0) REVERT: B 1187 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7197 (mm) REVERT: B 1317 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7996 (mt) REVERT: E 262 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7420 (t80) REVERT: E 282 PHE cc_start: 0.7026 (m-80) cc_final: 0.6733 (m-80) REVERT: E 355 ASN cc_start: 0.8548 (m-40) cc_final: 0.7995 (m-40) REVERT: E 359 GLU cc_start: 0.7784 (pp20) cc_final: 0.7382 (pm20) REVERT: E 369 ARG cc_start: 0.7904 (pmm-80) cc_final: 0.7630 (mtm-85) REVERT: E 375 GLU cc_start: 0.8837 (pm20) cc_final: 0.8558 (pm20) REVERT: E 413 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8066 (mppt) REVERT: E 512 ILE cc_start: 0.7609 (OUTLIER) cc_final: 0.6924 (pt) REVERT: E 549 TYR cc_start: 0.8309 (OUTLIER) cc_final: 0.7835 (t80) REVERT: E 556 TYR cc_start: 0.8322 (m-10) cc_final: 0.7822 (m-10) outliers start: 148 outliers final: 41 residues processed: 458 average time/residue: 1.4203 time to fit residues: 751.3120 Evaluate side-chains 364 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 303 time to evaluate : 2.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 358 GLN Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain R residue 32 GLU Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 46 HIS Chi-restraints excluded: chain S residue 45 THR Chi-restraints excluded: chain S residue 73 GLU Chi-restraints excluded: chain S residue 131 ARG Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 115 LEU Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain B residue 817 TYR Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1016 TYR Chi-restraints excluded: chain B residue 1136 PHE Chi-restraints excluded: chain B residue 1160 GLU Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1189 SER Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1278 THR Chi-restraints excluded: chain B residue 1317 ILE Chi-restraints excluded: chain B residue 1323 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 262 PHE Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 365 LYS Chi-restraints excluded: chain E residue 404 ASP Chi-restraints excluded: chain E residue 413 LYS Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 512 ILE Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 539 ILE Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain E residue 549 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 245 optimal weight: 0.0030 chunk 186 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 249 optimal weight: 0.8980 chunk 263 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 236 optimal weight: 7.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 GLN V 46 HIS ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1221 HIS B1222 GLN E 410 ASN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28285 Z= 0.205 Angle : 0.582 12.230 39579 Z= 0.318 Chirality : 0.037 0.208 4370 Planarity : 0.004 0.052 3885 Dihedral : 26.923 177.004 6312 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.69 % Allowed : 28.62 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.17), residues: 2447 helix: 0.87 (0.14), residues: 1358 sheet: -0.39 (0.56), residues: 90 loop : -1.23 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 775 HIS 0.006 0.001 HIS B 815 PHE 0.017 0.001 PHE B1147 TYR 0.027 0.002 TYR F 281 ARG 0.012 0.000 ARG B 799 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 346 time to evaluate : 2.625 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: D 81 TYR cc_start: 0.5286 (OUTLIER) cc_final: 0.4324 (m-80) REVERT: D 354 LEU cc_start: 0.8515 (tm) cc_final: 0.8225 (pp) REVERT: F 24 GLU cc_start: 0.5070 (mt-10) cc_final: 0.4752 (mm-30) REVERT: F 95 ASP cc_start: 0.2949 (p0) cc_final: 0.2363 (t70) REVERT: F 256 MET cc_start: 0.1196 (OUTLIER) cc_final: 0.0913 (pp-130) REVERT: Q 36 LYS cc_start: 0.8323 (ptmt) cc_final: 0.8091 (mmtm) REVERT: Q 90 ASP cc_start: 0.8487 (t70) cc_final: 0.8207 (t0) REVERT: R 110 GLU cc_start: 0.8181 (tp30) cc_final: 0.7959 (mm-30) REVERT: S 73 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7974 (tt0) REVERT: S 129 ARG cc_start: 0.8009 (tpt-90) cc_final: 0.7770 (tpt90) REVERT: S 131 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8331 (mtt180) REVERT: T 25 ASN cc_start: 0.8752 (m-40) cc_final: 0.8025 (m-40) REVERT: T 91 LYS cc_start: 0.8778 (ttmt) cc_final: 0.8436 (tttt) REVERT: U 36 LYS cc_start: 0.8266 (ptmt) cc_final: 0.8032 (mmmt) REVERT: U 56 GLU cc_start: 0.8509 (tt0) cc_final: 0.8235 (tt0) REVERT: V 68 GLU cc_start: 0.7375 (mt-10) cc_final: 0.7157 (mt-10) REVERT: V 105 LYS cc_start: 0.8334 (mtpt) cc_final: 0.7855 (mttp) REVERT: A 88 ARG cc_start: 0.8209 (mtm110) cc_final: 0.7736 (mtm180) REVERT: A 189 HIS cc_start: 0.6802 (OUTLIER) cc_final: 0.5979 (p90) REVERT: A 240 ASP cc_start: 0.8730 (m-30) cc_final: 0.8505 (m-30) REVERT: A 325 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7598 (mm-30) REVERT: B 670 GLU cc_start: 0.7723 (mp0) cc_final: 0.6831 (mp0) REVERT: B 684 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7746 (mm-30) REVERT: B 825 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8824 (mm) REVERT: B 826 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7953 (mmm160) REVERT: B 910 ARG cc_start: 0.8011 (ttm110) cc_final: 0.7735 (tmt170) REVERT: B 918 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: B 970 LYS cc_start: 0.5638 (OUTLIER) cc_final: 0.5317 (pmmt) REVERT: B 982 LYS cc_start: 0.7387 (mttt) cc_final: 0.6923 (mtmm) REVERT: B 1016 TYR cc_start: 0.7961 (OUTLIER) cc_final: 0.7612 (t80) REVERT: B 1136 PHE cc_start: 0.5652 (OUTLIER) cc_final: 0.4966 (m-10) REVERT: B 1160 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.6763 (mp0) REVERT: B 1289 GLN cc_start: 0.7319 (tm-30) cc_final: 0.7016 (pt0) REVERT: B 1317 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7689 (mt) REVERT: E 262 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.7338 (t80) REVERT: E 282 PHE cc_start: 0.7021 (m-80) cc_final: 0.6588 (m-80) REVERT: E 355 ASN cc_start: 0.8546 (m-40) cc_final: 0.8340 (m-40) REVERT: E 359 GLU cc_start: 0.7611 (pp20) cc_final: 0.7322 (pp20) REVERT: E 369 ARG cc_start: 0.7890 (pmm-80) cc_final: 0.7676 (mtm-85) REVERT: E 375 GLU cc_start: 0.8817 (pm20) cc_final: 0.8510 (pm20) REVERT: E 413 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8080 (mppt) REVERT: E 542 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7792 (tt) REVERT: E 556 TYR cc_start: 0.8334 (m-10) cc_final: 0.7865 (m-10) outliers start: 104 outliers final: 36 residues processed: 416 average time/residue: 1.4552 time to fit residues: 699.1972 Evaluate side-chains 352 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 300 time to evaluate : 2.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 TYR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 73 GLU Chi-restraints excluded: chain S residue 131 ARG Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 826 ARG Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 970 LYS Chi-restraints excluded: chain B residue 1016 TYR Chi-restraints excluded: chain B residue 1136 PHE Chi-restraints excluded: chain B residue 1160 GLU Chi-restraints excluded: chain B residue 1193 GLU Chi-restraints excluded: chain B residue 1278 THR Chi-restraints excluded: chain B residue 1317 ILE Chi-restraints excluded: chain B residue 1323 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 262 PHE Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 365 LYS Chi-restraints excluded: chain E residue 404 ASP Chi-restraints excluded: chain E residue 413 LYS Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 539 ILE Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 547 ILE Chi-restraints excluded: chain G residue 335 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 219 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 chunk 196 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 225 optimal weight: 0.7980 chunk 182 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 134 optimal weight: 1.9990 chunk 236 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 HIS ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 76 GLN U 38 ASN ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 28285 Z= 0.270 Angle : 0.603 12.388 39579 Z= 0.327 Chirality : 0.038 0.211 4370 Planarity : 0.004 0.055 3885 Dihedral : 26.950 178.507 6310 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 5.23 % Allowed : 28.12 % Favored : 66.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.17), residues: 2447 helix: 0.89 (0.14), residues: 1365 sheet: -0.64 (0.55), residues: 90 loop : -1.14 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 261 HIS 0.007 0.001 HIS B1254 PHE 0.019 0.002 PHE G 551 TYR 0.017 0.002 TYR F 281 ARG 0.014 0.001 ARG B 799 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 324 time to evaluate : 2.854 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: D 275 GLN cc_start: 0.6762 (mm110) cc_final: 0.6091 (mt0) REVERT: F 24 GLU cc_start: 0.5050 (mt-10) cc_final: 0.4644 (mm-30) REVERT: F 95 ASP cc_start: 0.2859 (p0) cc_final: 0.2337 (t70) REVERT: F 256 MET cc_start: 0.1581 (OUTLIER) cc_final: 0.1174 (pp-130) REVERT: F 270 GLU cc_start: 0.0656 (OUTLIER) cc_final: -0.0254 (pm20) REVERT: Q 36 LYS cc_start: 0.8328 (ptmt) cc_final: 0.8082 (mmtm) REVERT: Q 90 ASP cc_start: 0.8473 (t70) cc_final: 0.8194 (t0) REVERT: R 90 GLU cc_start: 0.8294 (mp0) cc_final: 0.7721 (mp0) REVERT: S 73 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7956 (tt0) REVERT: S 129 ARG cc_start: 0.8052 (tpt-90) cc_final: 0.7814 (tpt90) REVERT: S 131 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8286 (mtt180) REVERT: T 25 ASN cc_start: 0.8778 (m-40) cc_final: 0.8040 (m-40) REVERT: T 91 LYS cc_start: 0.8799 (ttmt) cc_final: 0.8461 (tttt) REVERT: U 36 LYS cc_start: 0.8295 (ptmt) cc_final: 0.8070 (mmmt) REVERT: U 56 GLU cc_start: 0.8513 (tt0) cc_final: 0.8272 (tt0) REVERT: V 68 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7108 (mt-10) REVERT: V 105 LYS cc_start: 0.8380 (mtpt) cc_final: 0.7892 (mttp) REVERT: A 60 LYS cc_start: 0.6737 (mttm) cc_final: 0.6214 (ptpt) REVERT: A 88 ARG cc_start: 0.8237 (mtm110) cc_final: 0.7764 (mtm180) REVERT: A 189 HIS cc_start: 0.7148 (OUTLIER) cc_final: 0.6365 (p90) REVERT: A 240 ASP cc_start: 0.8745 (m-30) cc_final: 0.8497 (m-30) REVERT: A 373 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.6622 (mpp) REVERT: B 670 GLU cc_start: 0.7773 (mp0) cc_final: 0.6895 (mp0) REVERT: B 684 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7700 (mm-30) REVERT: B 812 GLU cc_start: 0.7803 (tp30) cc_final: 0.7401 (tp30) REVERT: B 825 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8900 (mm) REVERT: B 826 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7955 (mmm160) REVERT: B 910 ARG cc_start: 0.8002 (ttm110) cc_final: 0.7711 (tmt170) REVERT: B 918 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8175 (mp0) REVERT: B 982 LYS cc_start: 0.7413 (mttt) cc_final: 0.6918 (mtmm) REVERT: B 1016 TYR cc_start: 0.8002 (OUTLIER) cc_final: 0.7702 (t80) REVERT: B 1136 PHE cc_start: 0.5735 (OUTLIER) cc_final: 0.5097 (m-10) REVERT: B 1160 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.6899 (mp0) REVERT: E 262 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7343 (t80) REVERT: E 282 PHE cc_start: 0.7034 (m-80) cc_final: 0.6596 (m-80) REVERT: E 359 GLU cc_start: 0.7657 (pp20) cc_final: 0.7108 (pp20) REVERT: E 369 ARG cc_start: 0.8025 (pmm-80) cc_final: 0.7752 (mtm-85) REVERT: E 375 GLU cc_start: 0.8830 (pm20) cc_final: 0.8528 (pm20) REVERT: E 388 ASN cc_start: 0.4683 (OUTLIER) cc_final: 0.4360 (m-40) REVERT: E 413 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8100 (mppt) REVERT: E 549 TYR cc_start: 0.8301 (OUTLIER) cc_final: 0.7841 (t80) REVERT: E 556 TYR cc_start: 0.8434 (m-10) cc_final: 0.7952 (m-10) outliers start: 116 outliers final: 47 residues processed: 398 average time/residue: 1.4293 time to fit residues: 661.2137 Evaluate side-chains 369 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 306 time to evaluate : 2.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain F residue 81 TYR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 105 LYS Chi-restraints excluded: chain R residue 113 LYS Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 73 GLU Chi-restraints excluded: chain S residue 131 ARG Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 826 ARG Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 1016 TYR Chi-restraints excluded: chain B residue 1136 PHE Chi-restraints excluded: chain B residue 1160 GLU Chi-restraints excluded: chain B residue 1193 GLU Chi-restraints excluded: chain B residue 1278 THR Chi-restraints excluded: chain B residue 1323 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 262 PHE Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 308 PHE Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 365 LYS Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 413 LYS Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 539 ILE Chi-restraints excluded: chain E residue 543 ASP Chi-restraints excluded: chain E residue 547 ILE Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain G residue 335 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 88 optimal weight: 0.9990 chunk 237 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 264 optimal weight: 0.5980 chunk 219 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 21 optimal weight: 0.0050 chunk 87 optimal weight: 0.0980 chunk 138 optimal weight: 2.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 358 GLN ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1173 ASN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28285 Z= 0.180 Angle : 0.586 12.991 39579 Z= 0.316 Chirality : 0.037 0.237 4370 Planarity : 0.004 0.063 3885 Dihedral : 26.804 175.829 6310 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.42 % Allowed : 29.38 % Favored : 66.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.17), residues: 2447 helix: 1.07 (0.14), residues: 1361 sheet: -0.59 (0.55), residues: 90 loop : -1.06 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP A 261 HIS 0.006 0.001 HIS B 815 PHE 0.037 0.001 PHE G 551 TYR 0.028 0.001 TYR F 281 ARG 0.015 0.000 ARG B 799 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 330 time to evaluate : 2.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 82 GLN cc_start: 0.7843 (pp30) cc_final: 0.7577 (pm20) REVERT: D 275 GLN cc_start: 0.6664 (mm110) cc_final: 0.5968 (mt0) REVERT: D 295 ASN cc_start: 0.7132 (OUTLIER) cc_final: 0.6740 (m-40) REVERT: F 24 GLU cc_start: 0.5096 (mt-10) cc_final: 0.4674 (mm-30) REVERT: F 95 ASP cc_start: 0.2720 (p0) cc_final: 0.2227 (t70) REVERT: F 256 MET cc_start: 0.1505 (OUTLIER) cc_final: 0.0974 (pp-130) REVERT: F 270 GLU cc_start: 0.0557 (OUTLIER) cc_final: -0.0259 (pm20) REVERT: Q 90 ASP cc_start: 0.8469 (t70) cc_final: 0.8183 (t0) REVERT: R 53 SER cc_start: 0.8623 (p) cc_final: 0.8377 (p) REVERT: S 42 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7862 (mtp-110) REVERT: S 73 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7960 (tt0) REVERT: S 129 ARG cc_start: 0.8013 (tpt-90) cc_final: 0.7800 (tpt90) REVERT: S 131 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8321 (mtt180) REVERT: T 25 ASN cc_start: 0.8743 (m-40) cc_final: 0.8013 (m-40) REVERT: T 91 LYS cc_start: 0.8779 (ttmt) cc_final: 0.8564 (tttt) REVERT: U 56 GLU cc_start: 0.8515 (tt0) cc_final: 0.8259 (tt0) REVERT: U 90 ASP cc_start: 0.8191 (t0) cc_final: 0.7970 (t0) REVERT: V 68 GLU cc_start: 0.7373 (mt-10) cc_final: 0.7165 (mt-10) REVERT: V 102 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7508 (tt0) REVERT: V 105 LYS cc_start: 0.8322 (mtpt) cc_final: 0.7858 (mttp) REVERT: A 60 LYS cc_start: 0.6666 (mttm) cc_final: 0.6137 (ptpt) REVERT: A 88 ARG cc_start: 0.8188 (mtm110) cc_final: 0.7709 (mtm180) REVERT: A 189 HIS cc_start: 0.6834 (OUTLIER) cc_final: 0.6001 (p90) REVERT: A 213 GLU cc_start: 0.7457 (tp30) cc_final: 0.7124 (mm-30) REVERT: A 316 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7817 (ptm-80) REVERT: B 666 VAL cc_start: 0.8594 (OUTLIER) cc_final: 0.8169 (t) REVERT: B 670 GLU cc_start: 0.7739 (mp0) cc_final: 0.6868 (mp0) REVERT: B 684 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7676 (mm-30) REVERT: B 812 GLU cc_start: 0.7820 (tp30) cc_final: 0.7411 (tp30) REVERT: B 881 ASP cc_start: 0.8707 (t0) cc_final: 0.8248 (m-30) REVERT: B 910 ARG cc_start: 0.8006 (ttm110) cc_final: 0.7738 (tmt170) REVERT: B 918 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8138 (mp0) REVERT: B 970 LYS cc_start: 0.5620 (OUTLIER) cc_final: 0.5341 (pmmt) REVERT: B 982 LYS cc_start: 0.7402 (mttt) cc_final: 0.6886 (mtmm) REVERT: B 1016 TYR cc_start: 0.7961 (OUTLIER) cc_final: 0.7691 (t80) REVERT: B 1136 PHE cc_start: 0.5821 (OUTLIER) cc_final: 0.5094 (m-10) REVERT: B 1160 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6808 (mp0) REVERT: B 1187 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7204 (mm) REVERT: B 1300 MET cc_start: 0.7986 (tpp) cc_final: 0.7454 (ttt) REVERT: E 262 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.7358 (t80) REVERT: E 282 PHE cc_start: 0.7057 (m-80) cc_final: 0.6618 (m-80) REVERT: E 369 ARG cc_start: 0.7995 (pmm-80) cc_final: 0.7724 (mtm-85) REVERT: E 375 GLU cc_start: 0.8793 (pm20) cc_final: 0.8479 (pm20) REVERT: E 413 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8082 (mppt) REVERT: E 544 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6487 (tm-30) REVERT: E 556 TYR cc_start: 0.8431 (m-10) cc_final: 0.8003 (m-10) outliers start: 98 outliers final: 40 residues processed: 396 average time/residue: 1.3679 time to fit residues: 630.4945 Evaluate side-chains 361 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 302 time to evaluate : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain F residue 81 TYR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 105 LYS Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 73 GLU Chi-restraints excluded: chain S residue 131 ARG Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 62 ILE Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 970 LYS Chi-restraints excluded: chain B residue 1016 TYR Chi-restraints excluded: chain B residue 1136 PHE Chi-restraints excluded: chain B residue 1160 GLU Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1278 THR Chi-restraints excluded: chain B residue 1323 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 262 PHE Chi-restraints excluded: chain E residue 308 PHE Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 365 LYS Chi-restraints excluded: chain E residue 413 LYS Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 544 GLU Chi-restraints excluded: chain E residue 547 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 254 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 150 optimal weight: 1.9990 chunk 192 optimal weight: 0.0980 chunk 149 optimal weight: 0.9990 chunk 222 optimal weight: 9.9990 chunk 147 optimal weight: 0.4980 chunk 263 optimal weight: 4.9990 chunk 164 optimal weight: 0.8980 chunk 160 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 358 GLN ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 76 GLN T 25 ASN U 38 ASN V 92 GLN ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1173 ASN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.5042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28285 Z= 0.211 Angle : 0.600 15.740 39579 Z= 0.321 Chirality : 0.037 0.324 4370 Planarity : 0.004 0.066 3885 Dihedral : 26.792 176.971 6310 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.33 % Allowed : 29.61 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.17), residues: 2447 helix: 1.10 (0.14), residues: 1359 sheet: -0.60 (0.54), residues: 90 loop : -1.00 (0.20), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 261 HIS 0.005 0.001 HIS B 815 PHE 0.029 0.001 PHE G 551 TYR 0.019 0.001 TYR P 88 ARG 0.016 0.000 ARG B 799 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 313 time to evaluate : 2.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 82 GLN cc_start: 0.7905 (pp30) cc_final: 0.7629 (pm20) REVERT: D 275 GLN cc_start: 0.6694 (mm110) cc_final: 0.6005 (mt0) REVERT: D 295 ASN cc_start: 0.7136 (OUTLIER) cc_final: 0.6759 (m-40) REVERT: D 296 MET cc_start: 0.7314 (pmm) cc_final: 0.7100 (pmm) REVERT: D 375 ASN cc_start: 0.8339 (p0) cc_final: 0.7876 (t0) REVERT: F 22 MET cc_start: 0.1379 (mmm) cc_final: 0.1000 (mtt) REVERT: F 24 GLU cc_start: 0.5217 (mt-10) cc_final: 0.4755 (mm-30) REVERT: F 95 ASP cc_start: 0.2606 (p0) cc_final: 0.2160 (t70) REVERT: F 256 MET cc_start: 0.1805 (OUTLIER) cc_final: 0.1199 (pp-130) REVERT: F 270 GLU cc_start: 0.0524 (OUTLIER) cc_final: -0.0228 (pm20) REVERT: Q 90 ASP cc_start: 0.8468 (t70) cc_final: 0.8177 (t0) REVERT: R 32 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7957 (tp30) REVERT: S 42 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7934 (mtp-110) REVERT: S 73 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7981 (tt0) REVERT: S 129 ARG cc_start: 0.8023 (tpt-90) cc_final: 0.7809 (tpt90) REVERT: S 131 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8272 (mtt180) REVERT: T 25 ASN cc_start: 0.8721 (m110) cc_final: 0.8020 (m-40) REVERT: T 91 LYS cc_start: 0.8815 (ttmt) cc_final: 0.8488 (tttt) REVERT: U 56 GLU cc_start: 0.8515 (tt0) cc_final: 0.8256 (tt0) REVERT: V 102 GLU cc_start: 0.7682 (tt0) cc_final: 0.7481 (tt0) REVERT: V 105 LYS cc_start: 0.8331 (mtpt) cc_final: 0.7858 (mttp) REVERT: A 60 LYS cc_start: 0.6667 (mttm) cc_final: 0.6099 (ptpt) REVERT: A 88 ARG cc_start: 0.8172 (mtm110) cc_final: 0.7683 (mtm180) REVERT: A 189 HIS cc_start: 0.6929 (OUTLIER) cc_final: 0.6141 (p90) REVERT: A 316 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7938 (ptm-80) REVERT: A 325 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7554 (mm-30) REVERT: B 666 VAL cc_start: 0.8547 (OUTLIER) cc_final: 0.8191 (t) REVERT: B 670 GLU cc_start: 0.7780 (mp0) cc_final: 0.6912 (mp0) REVERT: B 684 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7654 (mm-30) REVERT: B 799 ARG cc_start: 0.7621 (mmm160) cc_final: 0.6874 (mtt-85) REVERT: B 812 GLU cc_start: 0.7885 (tp30) cc_final: 0.7462 (tp30) REVERT: B 826 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7906 (mmm160) REVERT: B 881 ASP cc_start: 0.8734 (t0) cc_final: 0.8266 (m-30) REVERT: B 910 ARG cc_start: 0.8025 (ttm110) cc_final: 0.7729 (tmt170) REVERT: B 918 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8160 (mp0) REVERT: B 970 LYS cc_start: 0.5604 (OUTLIER) cc_final: 0.5331 (pmmt) REVERT: B 982 LYS cc_start: 0.7381 (mttt) cc_final: 0.6855 (mtmm) REVERT: B 1016 TYR cc_start: 0.7927 (OUTLIER) cc_final: 0.7698 (t80) REVERT: B 1136 PHE cc_start: 0.5874 (OUTLIER) cc_final: 0.5156 (m-10) REVERT: B 1160 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.6828 (mp0) REVERT: B 1187 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7259 (mm) REVERT: B 1289 GLN cc_start: 0.7256 (tm-30) cc_final: 0.6858 (pt0) REVERT: B 1300 MET cc_start: 0.7830 (tpp) cc_final: 0.7497 (ttt) REVERT: E 262 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.7364 (t80) REVERT: E 282 PHE cc_start: 0.7095 (m-80) cc_final: 0.6641 (m-80) REVERT: E 359 GLU cc_start: 0.7661 (pm20) cc_final: 0.7276 (pm20) REVERT: E 369 ARG cc_start: 0.8080 (pmm-80) cc_final: 0.7779 (mtm-85) REVERT: E 375 GLU cc_start: 0.8796 (pm20) cc_final: 0.8479 (pm20) REVERT: E 413 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8080 (mppt) REVERT: E 476 LYS cc_start: 0.7270 (OUTLIER) cc_final: 0.6827 (pmtt) REVERT: E 542 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.8106 (tt) REVERT: E 549 TYR cc_start: 0.8313 (OUTLIER) cc_final: 0.7822 (t80) REVERT: E 556 TYR cc_start: 0.8442 (m-10) cc_final: 0.7926 (m-10) outliers start: 96 outliers final: 50 residues processed: 384 average time/residue: 1.4157 time to fit residues: 629.6422 Evaluate side-chains 368 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 296 time to evaluate : 2.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain F residue 81 TYR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain R residue 32 GLU Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 105 LYS Chi-restraints excluded: chain R residue 113 LYS Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 73 GLU Chi-restraints excluded: chain S residue 131 ARG Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 62 ILE Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 726 TYR Chi-restraints excluded: chain B residue 826 ARG Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 970 LYS Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1016 TYR Chi-restraints excluded: chain B residue 1136 PHE Chi-restraints excluded: chain B residue 1160 GLU Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1278 THR Chi-restraints excluded: chain B residue 1323 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 262 PHE Chi-restraints excluded: chain E residue 308 PHE Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 365 LYS Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain E residue 413 LYS Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 476 LYS Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 547 ILE Chi-restraints excluded: chain E residue 549 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 162 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 167 optimal weight: 0.6980 chunk 179 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 206 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 358 GLN O 76 GLN ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 HIS S 76 GLN ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.5304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 28285 Z= 0.253 Angle : 0.629 16.554 39579 Z= 0.333 Chirality : 0.039 0.341 4370 Planarity : 0.004 0.048 3885 Dihedral : 26.870 176.315 6310 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.60 % Allowed : 29.29 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.17), residues: 2447 helix: 1.04 (0.14), residues: 1368 sheet: -0.71 (0.54), residues: 90 loop : -1.02 (0.20), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 261 HIS 0.005 0.001 HIS B1254 PHE 0.037 0.001 PHE G 551 TYR 0.028 0.002 TYR P 88 ARG 0.012 0.000 ARG B 799 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 315 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 81 TYR cc_start: 0.5683 (OUTLIER) cc_final: 0.4608 (m-80) REVERT: D 82 GLN cc_start: 0.7969 (pp30) cc_final: 0.7621 (pm20) REVERT: D 275 GLN cc_start: 0.6728 (mm110) cc_final: 0.6046 (mt0) REVERT: D 295 ASN cc_start: 0.7199 (OUTLIER) cc_final: 0.6817 (m-40) REVERT: D 296 MET cc_start: 0.7345 (pmm) cc_final: 0.7134 (pmm) REVERT: D 310 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8140 (mp) REVERT: D 354 LEU cc_start: 0.8368 (pp) cc_final: 0.8131 (tm) REVERT: D 358 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7770 (mp10) REVERT: D 375 ASN cc_start: 0.8387 (p0) cc_final: 0.7937 (t0) REVERT: F 22 MET cc_start: 0.1381 (mmm) cc_final: 0.0917 (mtt) REVERT: F 24 GLU cc_start: 0.5378 (mt-10) cc_final: 0.4931 (mm-30) REVERT: F 95 ASP cc_start: 0.2434 (p0) cc_final: 0.2011 (t70) REVERT: F 256 MET cc_start: 0.1718 (OUTLIER) cc_final: 0.1080 (pp-130) REVERT: F 270 GLU cc_start: 0.0487 (OUTLIER) cc_final: -0.0254 (pm20) REVERT: Q 36 LYS cc_start: 0.8328 (ptmt) cc_final: 0.8069 (mmtm) REVERT: Q 90 ASP cc_start: 0.8481 (t70) cc_final: 0.8197 (t0) REVERT: R 32 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7945 (tp30) REVERT: S 42 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7947 (mtp-110) REVERT: S 73 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7991 (tt0) REVERT: S 129 ARG cc_start: 0.8039 (tpt-90) cc_final: 0.7823 (tpt90) REVERT: S 131 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8317 (mtt180) REVERT: T 25 ASN cc_start: 0.8722 (m110) cc_final: 0.8038 (m-40) REVERT: U 56 GLU cc_start: 0.8500 (tt0) cc_final: 0.8251 (tt0) REVERT: V 105 LYS cc_start: 0.8338 (mtpt) cc_final: 0.7863 (mttp) REVERT: A 60 LYS cc_start: 0.6814 (mttm) cc_final: 0.6184 (ptpt) REVERT: A 88 ARG cc_start: 0.8169 (mtm110) cc_final: 0.7662 (mtm180) REVERT: A 189 HIS cc_start: 0.7084 (OUTLIER) cc_final: 0.6317 (p90) REVERT: A 316 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.8009 (ptm-80) REVERT: A 373 MET cc_start: 0.7796 (mpp) cc_final: 0.7529 (mtt) REVERT: B 670 GLU cc_start: 0.7807 (mp0) cc_final: 0.6952 (mp0) REVERT: B 684 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7362 (mm-30) REVERT: B 799 ARG cc_start: 0.7682 (mmm160) cc_final: 0.7374 (mpp-170) REVERT: B 812 GLU cc_start: 0.7926 (tp30) cc_final: 0.7489 (tp30) REVERT: B 826 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7946 (mmm160) REVERT: B 881 ASP cc_start: 0.8753 (t0) cc_final: 0.8282 (m-30) REVERT: B 910 ARG cc_start: 0.8019 (ttm110) cc_final: 0.7728 (tmt170) REVERT: B 918 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: B 970 LYS cc_start: 0.5600 (OUTLIER) cc_final: 0.5330 (pmmt) REVERT: B 982 LYS cc_start: 0.7379 (mttt) cc_final: 0.6858 (mtmm) REVERT: B 1136 PHE cc_start: 0.6007 (OUTLIER) cc_final: 0.5312 (m-10) REVERT: B 1160 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.6786 (mp0) REVERT: B 1187 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7328 (mm) REVERT: B 1300 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7590 (ttt) REVERT: E 262 PHE cc_start: 0.7772 (OUTLIER) cc_final: 0.7411 (t80) REVERT: E 282 PHE cc_start: 0.7117 (m-80) cc_final: 0.6727 (m-80) REVERT: E 369 ARG cc_start: 0.8133 (pmm-80) cc_final: 0.7850 (mtm-85) REVERT: E 476 LYS cc_start: 0.7313 (OUTLIER) cc_final: 0.6833 (pmtt) REVERT: E 549 TYR cc_start: 0.8255 (OUTLIER) cc_final: 0.7774 (t80) REVERT: E 556 TYR cc_start: 0.8547 (m-10) cc_final: 0.8068 (m-10) outliers start: 102 outliers final: 43 residues processed: 388 average time/residue: 1.4593 time to fit residues: 654.2251 Evaluate side-chains 367 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 302 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 TYR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 358 GLN Chi-restraints excluded: chain F residue 81 TYR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain R residue 32 GLU Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 105 LYS Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 73 GLU Chi-restraints excluded: chain S residue 131 ARG Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 62 ILE Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 826 ARG Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 970 LYS Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1136 PHE Chi-restraints excluded: chain B residue 1160 GLU Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1278 THR Chi-restraints excluded: chain B residue 1300 MET Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 262 PHE Chi-restraints excluded: chain E residue 308 PHE Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 365 LYS Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 476 LYS Chi-restraints excluded: chain E residue 539 ILE Chi-restraints excluded: chain E residue 547 ILE Chi-restraints excluded: chain E residue 549 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 239 optimal weight: 20.0000 chunk 252 optimal weight: 20.0000 chunk 229 optimal weight: 5.9990 chunk 245 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 192 optimal weight: 8.9990 chunk 75 optimal weight: 0.7980 chunk 221 optimal weight: 0.9980 chunk 231 optimal weight: 0.9980 chunk 244 optimal weight: 8.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 38 ASN ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 HIS B 974 GLN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.5641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 28285 Z= 0.305 Angle : 0.657 14.352 39579 Z= 0.348 Chirality : 0.040 0.345 4370 Planarity : 0.004 0.061 3885 Dihedral : 26.988 177.323 6310 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.15 % Allowed : 30.01 % Favored : 65.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.17), residues: 2447 helix: 0.84 (0.14), residues: 1375 sheet: -0.55 (0.57), residues: 80 loop : -1.03 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 775 HIS 0.007 0.001 HIS B1254 PHE 0.038 0.002 PHE G 551 TYR 0.032 0.002 TYR P 88 ARG 0.011 0.001 ARG B 770 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 308 time to evaluate : 2.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 82 GLN cc_start: 0.7909 (pp30) cc_final: 0.7526 (pm20) REVERT: D 275 GLN cc_start: 0.6654 (mm110) cc_final: 0.6026 (mt0) REVERT: D 295 ASN cc_start: 0.7371 (OUTLIER) cc_final: 0.6996 (m-40) REVERT: D 296 MET cc_start: 0.7373 (pmm) cc_final: 0.7155 (pmm) REVERT: D 310 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8139 (mp) REVERT: D 375 ASN cc_start: 0.8414 (OUTLIER) cc_final: 0.7971 (t0) REVERT: F 22 MET cc_start: 0.1401 (mmm) cc_final: 0.0922 (mtt) REVERT: F 24 GLU cc_start: 0.5474 (mt-10) cc_final: 0.4942 (mm-30) REVERT: F 95 ASP cc_start: 0.2308 (p0) cc_final: 0.2021 (t0) REVERT: F 256 MET cc_start: 0.1777 (OUTLIER) cc_final: 0.1096 (pp-130) REVERT: F 270 GLU cc_start: 0.0713 (OUTLIER) cc_final: -0.0012 (pm20) REVERT: Q 36 LYS cc_start: 0.8351 (ptmt) cc_final: 0.8079 (mmtm) REVERT: Q 90 ASP cc_start: 0.8463 (t70) cc_final: 0.8185 (t0) REVERT: R 32 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7919 (tp30) REVERT: S 42 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7958 (mtp-110) REVERT: S 73 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8098 (tt0) REVERT: S 79 LYS cc_start: 0.8764 (tttp) cc_final: 0.8197 (tttp) REVERT: S 90 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.8012 (mmm) REVERT: S 131 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8295 (mtt180) REVERT: U 56 GLU cc_start: 0.8507 (tt0) cc_final: 0.8269 (tt0) REVERT: V 105 LYS cc_start: 0.8339 (mtpt) cc_final: 0.7868 (mttp) REVERT: A 60 LYS cc_start: 0.7009 (mttm) cc_final: 0.6238 (ptpt) REVERT: A 88 ARG cc_start: 0.8194 (mtm110) cc_final: 0.7688 (mtm180) REVERT: A 189 HIS cc_start: 0.7312 (OUTLIER) cc_final: 0.6579 (p90) REVERT: A 261 TRP cc_start: 0.7331 (m-90) cc_final: 0.6818 (m-90) REVERT: A 316 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.8105 (ptm-80) REVERT: A 373 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.6935 (mpp) REVERT: B 670 GLU cc_start: 0.7867 (mp0) cc_final: 0.6992 (mp0) REVERT: B 684 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7409 (mm-30) REVERT: B 765 MET cc_start: 0.5296 (mmp) cc_final: 0.4669 (ppp) REVERT: B 799 ARG cc_start: 0.7680 (mmm160) cc_final: 0.7423 (mpp-170) REVERT: B 812 GLU cc_start: 0.7926 (tp30) cc_final: 0.7503 (tp30) REVERT: B 826 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7976 (mmm160) REVERT: B 881 ASP cc_start: 0.8793 (t0) cc_final: 0.8319 (m-30) REVERT: B 907 ARG cc_start: 0.8468 (ptm-80) cc_final: 0.7979 (ptm-80) REVERT: B 910 ARG cc_start: 0.8028 (ttm110) cc_final: 0.7752 (tmt170) REVERT: B 918 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8192 (mp0) REVERT: B 982 LYS cc_start: 0.7382 (mttt) cc_final: 0.6874 (mtmm) REVERT: B 1136 PHE cc_start: 0.6115 (OUTLIER) cc_final: 0.5396 (m-10) REVERT: B 1187 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7353 (mm) REVERT: B 1289 GLN cc_start: 0.7429 (tm-30) cc_final: 0.6994 (pt0) REVERT: B 1300 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7600 (ttt) REVERT: E 262 PHE cc_start: 0.7814 (OUTLIER) cc_final: 0.7600 (t80) REVERT: E 375 GLU cc_start: 0.8778 (pm20) cc_final: 0.8504 (pm20) REVERT: E 476 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.6820 (pmtt) REVERT: E 549 TYR cc_start: 0.8245 (OUTLIER) cc_final: 0.7722 (t80) REVERT: E 556 TYR cc_start: 0.8598 (m-10) cc_final: 0.8137 (m-10) REVERT: G 560 MET cc_start: 0.7939 (mpm) cc_final: 0.7575 (mpt) outliers start: 92 outliers final: 46 residues processed: 371 average time/residue: 1.4961 time to fit residues: 644.6254 Evaluate side-chains 364 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 297 time to evaluate : 2.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 375 ASN Chi-restraints excluded: chain F residue 81 TYR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain R residue 32 GLU Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 105 LYS Chi-restraints excluded: chain R residue 113 LYS Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 73 GLU Chi-restraints excluded: chain S residue 90 MET Chi-restraints excluded: chain S residue 131 ARG Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 726 TYR Chi-restraints excluded: chain B residue 826 ARG Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1136 PHE Chi-restraints excluded: chain B residue 1160 GLU Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1268 LEU Chi-restraints excluded: chain B residue 1278 THR Chi-restraints excluded: chain B residue 1300 MET Chi-restraints excluded: chain B residue 1323 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 262 PHE Chi-restraints excluded: chain E residue 308 PHE Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 365 LYS Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 476 LYS Chi-restraints excluded: chain E residue 539 ILE Chi-restraints excluded: chain E residue 547 ILE Chi-restraints excluded: chain E residue 549 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 161 optimal weight: 0.8980 chunk 259 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 271 optimal weight: 3.9990 chunk 250 optimal weight: 1.9990 chunk 216 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 167 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 358 GLN ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 974 GLN E 410 ASN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.5744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28285 Z= 0.260 Angle : 0.643 14.133 39579 Z= 0.340 Chirality : 0.039 0.366 4370 Planarity : 0.004 0.048 3885 Dihedral : 26.937 176.340 6310 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.61 % Allowed : 30.55 % Favored : 65.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.17), residues: 2447 helix: 0.90 (0.14), residues: 1374 sheet: -0.61 (0.60), residues: 75 loop : -1.05 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B1151 HIS 0.009 0.001 HIS A 43 PHE 0.023 0.002 PHE G 551 TYR 0.037 0.002 TYR P 88 ARG 0.018 0.001 ARG B 770 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 317 time to evaluate : 2.785 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: D 82 GLN cc_start: 0.7933 (pp30) cc_final: 0.7572 (pm20) REVERT: D 275 GLN cc_start: 0.6640 (mm110) cc_final: 0.6007 (mt0) REVERT: D 295 ASN cc_start: 0.7217 (OUTLIER) cc_final: 0.6826 (m-40) REVERT: D 296 MET cc_start: 0.7388 (pmm) cc_final: 0.7138 (pmm) REVERT: D 310 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8141 (mp) REVERT: D 354 LEU cc_start: 0.8312 (pp) cc_final: 0.8108 (tm) REVERT: D 375 ASN cc_start: 0.8392 (OUTLIER) cc_final: 0.7992 (t0) REVERT: F 22 MET cc_start: 0.1438 (mmm) cc_final: 0.0960 (mtt) REVERT: F 24 GLU cc_start: 0.5474 (mt-10) cc_final: 0.4908 (mm-30) REVERT: F 95 ASP cc_start: 0.2340 (p0) cc_final: 0.2101 (t0) REVERT: F 256 MET cc_start: 0.1929 (OUTLIER) cc_final: 0.1252 (pp-130) REVERT: F 270 GLU cc_start: 0.0614 (OUTLIER) cc_final: -0.0040 (pm20) REVERT: Q 36 LYS cc_start: 0.8329 (ptmt) cc_final: 0.8080 (mmtm) REVERT: Q 90 ASP cc_start: 0.8479 (t70) cc_final: 0.8203 (t0) REVERT: S 42 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7915 (mtp-110) REVERT: S 73 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7975 (tt0) REVERT: S 131 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8326 (mtt180) REVERT: T 25 ASN cc_start: 0.8724 (m110) cc_final: 0.8029 (m-40) REVERT: U 56 GLU cc_start: 0.8499 (tt0) cc_final: 0.8244 (tt0) REVERT: V 105 LYS cc_start: 0.8335 (mtpt) cc_final: 0.7861 (mttp) REVERT: A 60 LYS cc_start: 0.6928 (mttm) cc_final: 0.6185 (ptpt) REVERT: A 88 ARG cc_start: 0.8109 (mtm110) cc_final: 0.7653 (mtm180) REVERT: A 189 HIS cc_start: 0.7190 (OUTLIER) cc_final: 0.6447 (p90) REVERT: A 213 GLU cc_start: 0.7537 (tp30) cc_final: 0.7179 (mm-30) REVERT: A 261 TRP cc_start: 0.7373 (m-90) cc_final: 0.6808 (m-90) REVERT: A 316 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.8012 (ptm-80) REVERT: B 670 GLU cc_start: 0.7873 (mp0) cc_final: 0.7009 (mp0) REVERT: B 684 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7274 (mm-30) REVERT: B 765 MET cc_start: 0.5191 (mmp) cc_final: 0.4606 (ppp) REVERT: B 812 GLU cc_start: 0.7902 (tp30) cc_final: 0.7485 (tp30) REVERT: B 826 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7964 (mmm160) REVERT: B 881 ASP cc_start: 0.8789 (t0) cc_final: 0.8341 (m-30) REVERT: B 907 ARG cc_start: 0.8468 (ptm-80) cc_final: 0.7997 (ptm-80) REVERT: B 910 ARG cc_start: 0.8021 (ttm110) cc_final: 0.7754 (tmt170) REVERT: B 918 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8180 (mp0) REVERT: B 982 LYS cc_start: 0.7377 (mttt) cc_final: 0.6870 (mtmm) REVERT: B 1136 PHE cc_start: 0.6080 (OUTLIER) cc_final: 0.5409 (m-80) REVERT: B 1160 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6894 (mp0) REVERT: B 1187 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7267 (mm) REVERT: B 1289 GLN cc_start: 0.7417 (tm-30) cc_final: 0.6998 (pt0) REVERT: B 1300 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7601 (ttt) REVERT: E 262 PHE cc_start: 0.7722 (OUTLIER) cc_final: 0.7435 (t80) REVERT: E 344 ASP cc_start: 0.7925 (m-30) cc_final: 0.7106 (t0) REVERT: E 476 LYS cc_start: 0.7310 (OUTLIER) cc_final: 0.6795 (pmtt) REVERT: E 493 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7322 (mtmt) REVERT: E 549 TYR cc_start: 0.8375 (OUTLIER) cc_final: 0.7645 (t80) REVERT: E 556 TYR cc_start: 0.8638 (m-10) cc_final: 0.8206 (m-10) outliers start: 80 outliers final: 43 residues processed: 377 average time/residue: 1.4723 time to fit residues: 639.4178 Evaluate side-chains 371 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 308 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 375 ASN Chi-restraints excluded: chain F residue 81 TYR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain P residue 24 ASP Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 105 LYS Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 73 GLU Chi-restraints excluded: chain S residue 131 ARG Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 826 ARG Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 974 GLN Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1136 PHE Chi-restraints excluded: chain B residue 1160 GLU Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1278 THR Chi-restraints excluded: chain B residue 1300 MET Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 262 PHE Chi-restraints excluded: chain E residue 308 PHE Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 476 LYS Chi-restraints excluded: chain E residue 493 LYS Chi-restraints excluded: chain E residue 539 ILE Chi-restraints excluded: chain E residue 547 ILE Chi-restraints excluded: chain E residue 549 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 172 optimal weight: 0.0980 chunk 230 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 199 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 216 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 222 optimal weight: 0.0970 chunk 27 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 104 GLN ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 38 ASN ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.122707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.091168 restraints weight = 56031.891| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.95 r_work: 0.3119 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.5772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.178 28285 Z= 0.292 Angle : 0.765 59.163 39579 Z= 0.424 Chirality : 0.041 0.869 4370 Planarity : 0.004 0.049 3885 Dihedral : 26.937 176.350 6310 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.42 % Allowed : 31.10 % Favored : 65.48 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.17), residues: 2447 helix: 0.96 (0.14), residues: 1362 sheet: -0.62 (0.60), residues: 75 loop : -1.03 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B1151 HIS 0.008 0.001 HIS A 43 PHE 0.021 0.002 PHE G 551 TYR 0.073 0.002 TYR A 313 ARG 0.015 0.000 ARG B 799 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10521.29 seconds wall clock time: 185 minutes 14.37 seconds (11114.37 seconds total)