Starting phenix.real_space_refine on Tue Feb 20 06:00:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd4_37124/02_2024/8kd4_37124_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd4_37124/02_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_37124/02_2024/8kd4_37124.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd4_37124/02_2024/8kd4_37124.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd4_37124/02_2024/8kd4_37124_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd4_37124/02_2024/8kd4_37124_updated.pdb" } 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 13.57, per 1000 atoms: 0.50 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: 12.38 Conformation dependent library (CDL) restraints added in 4.0 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... running ksdssp... Secondary structure from input PDB file: 102 helices and 4 sheets defined 51.0% alpha, 2.2% beta 140 base pairs and 275 stacking pairs defined. Time for finding SS restraints: 12.52 Creating SS restraints... Processing helix chain 'D' and resid 99 through 112 Processing helix chain 'D' and resid 226 through 240 Processing helix chain 'D' and resid 254 through 268 Processing helix chain 'D' and resid 274 through 294 removed outlier: 5.483A pdb=" N GLY D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 316 removed outlier: 4.625A pdb=" N LEU D 304 " --> pdb=" O ARG D 300 " (cutoff:3.500A) 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 322 through 324 No H-bonds generated for 'chain 'D' and resid 322 through 324' Processing helix chain 'D' and resid 328 through 343 Proline residue: D 339 - end of helix Processing helix chain 'D' and resid 349 through 368 Processing helix chain 'D' and resid 392 through 398 Processing helix chain 'F' and resid 99 through 111 Processing helix chain 'F' and resid 230 through 238 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 254 through 264 removed outlier: 4.075A pdb=" N TYR F 261 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLU F 262 " --> pdb=" O LEU F 258 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS F 263 " --> pdb=" O ASN F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 289 removed outlier: 4.500A pdb=" N TYR F 281 " --> pdb=" O GLN F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 313 Processing helix chain 'F' and resid 329 through 344 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) removed outlier: 4.054A pdb=" N SER F 344 " --> pdb=" O GLU F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 367 Processing helix chain 'O' and resid 45 through 54 Processing helix chain 'O' and resid 64 through 77 removed outlier: 3.544A pdb=" N LEU O 70 " --> pdb=" O PRO O 66 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP O 77 " --> pdb=" O GLU O 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 86 through 113 Processing helix chain 'O' and resid 121 through 131 Processing helix chain 'P' and resid 26 through 28 No H-bonds generated for 'chain 'P' and resid 26 through 28' Processing helix chain 'P' and resid 31 through 40 Processing helix chain 'P' and resid 50 through 75 removed outlier: 4.025A pdb=" N ARG P 67 " --> pdb=" O GLU P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 93 removed outlier: 4.005A pdb=" N GLN P 93 " --> pdb=" O ALA P 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 17 through 20 No H-bonds generated for 'chain 'Q' and resid 17 through 20' Processing helix chain 'Q' and resid 27 through 36 Processing helix chain 'Q' and resid 45 through 72 removed outlier: 4.344A pdb=" N VAL Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 89 Processing helix chain 'Q' and resid 91 through 96 Processing helix chain 'R' and resid 35 through 45 removed outlier: 3.687A pdb=" N TYR R 39 " --> pdb=" O ALA R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 80 Processing helix chain 'R' and resid 88 through 98 Processing helix chain 'R' and resid 101 through 119 removed outlier: 3.924A pdb=" N HIS R 106 " --> pdb=" O LEU R 103 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL R 108 " --> pdb=" O LYS R 105 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU R 110 " --> pdb=" O ALA R 107 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR R 112 " --> pdb=" O SER R 109 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS R 113 " --> pdb=" O GLU R 110 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR R 116 " --> pdb=" O LYS R 113 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR R 119 " --> pdb=" O THR R 116 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 55 Processing helix chain 'S' and resid 64 through 78 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 86 through 113 Processing helix chain 'S' and resid 121 through 131 Processing helix chain 'T' and resid 26 through 28 No H-bonds generated for 'chain 'T' and resid 26 through 28' Processing helix chain 'T' and resid 31 through 40 Processing helix chain 'T' and resid 50 through 75 removed outlier: 3.824A pdb=" N ARG T 67 " --> pdb=" O GLU T 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 83 through 93 removed outlier: 4.137A pdb=" N GLN T 93 " --> pdb=" O ALA T 89 " (cutoff:3.500A) Processing helix chain 'U' and resid 17 through 20 No H-bonds generated for 'chain 'U' and resid 17 through 20' Processing helix chain 'U' and resid 27 through 36 Processing helix chain 'U' and resid 45 through 72 removed outlier: 4.039A pdb=" N VAL U 49 " --> pdb=" O ALA U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 89 Processing helix chain 'U' and resid 91 through 96 Processing helix chain 'V' and resid 35 through 45 Processing helix chain 'V' and resid 53 through 80 Processing helix chain 'V' and resid 88 through 98 Processing helix chain 'V' and resid 101 through 118 removed outlier: 3.615A pdb=" N HIS V 106 " --> pdb=" O LEU V 103 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR V 116 " --> pdb=" O LYS V 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 42 through 55 Processing helix chain 'A' and resid 57 through 60 removed outlier: 3.554A pdb=" N LYS A 60 " --> pdb=" O LEU A 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 57 through 60' Processing helix chain 'A' and resid 80 through 88 Processing helix chain 'A' and resid 99 through 104 Processing helix chain 'A' and resid 116 through 136 Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 191 through 196 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 244 through 261 Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 288 through 299 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 316 through 329 removed outlier: 3.751A pdb=" N ARG A 320 " --> pdb=" O ARG A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 346 No H-bonds generated for 'chain 'A' and resid 344 through 346' Processing helix chain 'A' and resid 366 through 382 removed outlier: 4.969A pdb=" N ASN A 382 " --> pdb=" O ALA A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'B' and resid 665 through 676 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 679 through 693 Processing helix chain 'B' and resid 699 through 709 removed outlier: 3.711A pdb=" N PHE B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 724 Processing helix chain 'B' and resid 772 through 777 Processing helix chain 'B' and resid 786 through 790 Processing helix chain 'B' and resid 802 through 839 removed outlier: 3.604A pdb=" N ASP B 818 " --> pdb=" O ARG B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 847 Processing helix chain 'B' and resid 862 through 870 Processing helix chain 'B' and resid 873 through 885 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 891 through 928 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 935 through 942 removed outlier: 4.290A pdb=" N LYS B 940 " --> pdb=" O LYS B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.606A pdb=" N ILE B 955 " --> pdb=" O GLU B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 996 Processing helix chain 'B' and resid 1004 through 1021 removed outlier: 4.059A pdb=" N ILE B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1163 Processing helix chain 'B' and resid 1165 through 1173 removed outlier: 3.877A pdb=" N LYS B1170 " --> pdb=" O GLU B1166 " (cutoff:3.500A) Processing helix chain 'B' and resid 1179 through 1184 Processing helix chain 'B' and resid 1203 through 1215 Processing helix chain 'B' and resid 1221 through 1229 Processing helix chain 'B' and resid 1237 through 1239 No H-bonds generated for 'chain 'B' and resid 1237 through 1239' Processing helix chain 'B' and resid 1242 through 1258 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) Processing helix chain 'B' and resid 1260 through 1272 Processing helix chain 'B' and resid 1283 through 1293 Processing helix chain 'B' and resid 1308 through 1310 No H-bonds generated for 'chain 'B' and resid 1308 through 1310' Processing helix chain 'E' and resid 52 through 54 No H-bonds generated for 'chain 'E' and resid 52 through 54' Processing helix chain 'E' and resid 293 through 295 No H-bonds generated for 'chain 'E' and resid 293 through 295' Processing helix chain 'E' and resid 304 through 307 No H-bonds generated for 'chain 'E' and resid 304 through 307' Processing helix chain 'E' and resid 322 through 329 removed outlier: 3.734A pdb=" N ILE E 327 " --> pdb=" O GLU E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 344 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) Processing helix chain 'E' and resid 355 through 359 Processing helix chain 'E' and resid 403 through 406 Processing helix chain 'E' and resid 431 through 433 No H-bonds generated for 'chain 'E' and resid 431 through 433' Processing helix chain 'E' and resid 544 through 560 removed outlier: 4.599A pdb=" N MET E 560 " --> pdb=" O TYR E 556 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 325 No H-bonds generated for 'chain 'G' and resid 323 through 325' Processing helix chain 'G' and resid 338 through 343 removed outlier: 4.171A pdb=" N ASN G 342 " --> pdb=" O LYS G 338 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ILE G 343 " --> pdb=" O LEU G 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 338 through 343' Processing helix chain 'G' and resid 542 through 568 Processing sheet with id= A, first strand: chain 'D' and resid 244 through 246 Processing sheet with id= B, first strand: chain 'A' and resid 62 through 64 removed outlier: 3.932A pdb=" N GLU A 62 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR A 23 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL A 141 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N PHE A 24 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL A 143 " --> pdb=" O PHE A 24 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N MET A 305 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ASN A 144 " --> pdb=" O MET A 305 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL A 307 " --> 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) Processing sheet with id= C, first strand: chain 'B' and resid 1136 through 1140 Processing sheet with id= D, first strand: chain 'E' and resid 272 through 274 840 hydrogen bonds defined for protein. 2394 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: 15.90 Time building geometry restraints manager: 13.24 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: 240 2.60 - 3.17: 21452 3.17 - 3.75: 48655 3.75 - 4.32: 63258 4.32 - 4.90: 95653 Nonbonded interactions: 229258 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 229253 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: 12.930 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: 0.000 Extract box with map and model: 33.680 Check model and map are aligned: 0.400 Set scattering table: 0.250 Process input model: 90.830 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.130 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:13.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 153.080 ------------------------------------------------------------------------------- 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= 0.256 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 : 2.520 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: 1.2430 time to fit residues: 530.1519 Evaluate side-chains 319 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 310 time to evaluate : 2.348 ------------------------------------------------------------------------------- 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: 4.9990 chunk 206 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 213 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 247 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 P 27 GLN S 85 GLN 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 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN B1150 HIS E 314 ASN ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 28285 Z= 0.352 Angle : 0.677 12.196 39579 Z= 0.365 Chirality : 0.042 0.242 4370 Planarity : 0.005 0.053 3885 Dihedral : 26.804 179.104 6328 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.66 % Favored : 95.30 % Rotamer: Outliers : 5.77 % Allowed : 26.90 % Favored : 67.33 % 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: -0.95 (0.16), residues: 2447 helix: -0.02 (0.14), residues: 1357 sheet: 0.33 (0.59), residues: 93 loop : -1.52 (0.18), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 775 HIS 0.009 0.002 HIS V 46 PHE 0.018 0.002 PHE E 341 TYR 0.041 0.002 TYR P 88 ARG 0.013 0.001 ARG B 799 *********************** 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 492 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 364 time to evaluate : 2.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 323 ILE cc_start: 0.8472 (pt) cc_final: 0.8227 (pt) REVERT: D 341 LEU cc_start: 0.6340 (OUTLIER) cc_final: 0.6035 (pp) REVERT: F 95 ASP cc_start: 0.3186 (p0) cc_final: 0.2533 (t70) REVERT: F 233 VAL cc_start: 0.2562 (t) cc_final: 0.2271 (m) REVERT: F 234 ASP cc_start: 0.5522 (t70) cc_final: 0.4924 (m-30) REVERT: F 256 MET cc_start: 0.1726 (OUTLIER) cc_final: 0.1258 (pp-130) REVERT: F 261 TYR cc_start: 0.8092 (m-10) cc_final: 0.7888 (m-80) REVERT: F 371 ASP cc_start: 0.5047 (OUTLIER) cc_final: 0.4563 (t70) REVERT: O 59 GLU cc_start: 0.7581 (pm20) cc_final: 0.7201 (pm20) REVERT: P 85 ASP cc_start: 0.8195 (m-30) cc_final: 0.7993 (m-30) REVERT: R 46 HIS cc_start: 0.8351 (OUTLIER) cc_final: 0.7760 (m170) REVERT: R 90 GLU cc_start: 0.8568 (mp0) cc_final: 0.8279 (mp0) REVERT: R 113 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8410 (pttp) REVERT: S 131 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8105 (mtt180) REVERT: T 91 LYS cc_start: 0.8743 (ttmt) cc_final: 0.8437 (tttt) REVERT: U 36 LYS cc_start: 0.8353 (ptmt) cc_final: 0.7959 (ptmm) REVERT: U 95 LYS cc_start: 0.8900 (ttpt) cc_final: 0.8694 (ttmp) REVERT: V 68 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7259 (mt-10) REVERT: V 105 LYS cc_start: 0.8188 (mtpt) cc_final: 0.7695 (mttp) REVERT: A 47 MET cc_start: 0.7589 (ptt) cc_final: 0.7252 (ptp) REVERT: A 88 ARG cc_start: 0.8079 (mtm110) cc_final: 0.7591 (mtm180) REVERT: A 261 TRP cc_start: 0.6910 (m-10) cc_final: 0.6585 (m-10) REVERT: B 670 GLU cc_start: 0.7678 (mp0) cc_final: 0.7381 (pt0) REVERT: B 817 TYR cc_start: 0.8127 (m-80) cc_final: 0.7757 (m-80) REVERT: B 825 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8889 (mm) REVERT: B 910 ARG cc_start: 0.7934 (ttm110) cc_final: 0.7608 (tmt170) REVERT: B 918 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.8006 (mp0) REVERT: B 1136 PHE cc_start: 0.5238 (OUTLIER) cc_final: 0.4773 (m-10) REVERT: B 1187 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7187 (mm) REVERT: B 1257 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7611 (mtm) REVERT: B 1289 GLN cc_start: 0.6611 (OUTLIER) cc_final: 0.6381 (pp30) REVERT: E 262 PHE cc_start: 0.7809 (OUTLIER) cc_final: 0.7347 (t80) REVERT: E 271 SER cc_start: 0.7617 (OUTLIER) cc_final: 0.7333 (m) REVERT: E 282 PHE cc_start: 0.6804 (m-80) cc_final: 0.6495 (m-80) REVERT: E 375 GLU cc_start: 0.8806 (pm20) cc_final: 0.8490 (pm20) REVERT: E 512 ILE cc_start: 0.6600 (OUTLIER) cc_final: 0.5924 (pt) REVERT: E 543 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7905 (p0) REVERT: E 549 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.7895 (t80) outliers start: 128 outliers final: 36 residues processed: 447 average time/residue: 1.4823 time to fit residues: 763.2242 Evaluate side-chains 359 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 306 time to evaluate : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 288 TYR Chi-restraints excluded: chain F residue 371 ASP Chi-restraints excluded: chain O residue 63 ARG Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain R residue 46 HIS Chi-restraints excluded: chain R residue 113 LYS 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 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 373 MET Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 703 VAL 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 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 41 SER Chi-restraints excluded: chain E residue 262 PHE 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 365 LYS 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 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: 0.9980 chunk 68 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 268 optimal weight: 9.9990 chunk 221 optimal weight: 10.0000 chunk 246 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 199 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 358 GLN O 76 GLN O 108 ASN R 106 HIS S 76 GLN S 108 ASN S 125 GLN ** V 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** A 382 ASN A 419 GLN ** B 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 HIS ** B1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 ASN 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 28285 Z= 0.369 Angle : 0.639 11.531 39579 Z= 0.346 Chirality : 0.041 0.194 4370 Planarity : 0.004 0.053 3885 Dihedral : 26.960 179.871 6315 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 6.58 % Allowed : 25.42 % Favored : 68.00 % 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: -0.70 (0.16), residues: 2447 helix: 0.18 (0.14), residues: 1353 sheet: -0.04 (0.56), residues: 90 loop : -1.32 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 775 HIS 0.008 0.001 HIS R 46 PHE 0.022 0.002 PHE G 336 TYR 0.021 0.002 TYR A 176 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 481 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 335 time to evaluate : 2.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 275 GLN cc_start: 0.6973 (mm-40) cc_final: 0.6520 (mp10) REVERT: D 291 LYS cc_start: 0.8583 (mmmt) cc_final: 0.8330 (mmmt) REVERT: D 295 ASN cc_start: 0.7482 (OUTLIER) cc_final: 0.7151 (m-40) REVERT: F 256 MET cc_start: 0.1726 (OUTLIER) cc_final: 0.1140 (pp-130) REVERT: F 270 GLU cc_start: 0.0789 (OUTLIER) cc_final: -0.0214 (pm20) REVERT: Q 51 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8731 (tp) REVERT: Q 90 ASP cc_start: 0.8527 (t70) cc_final: 0.8233 (t0) REVERT: R 90 GLU cc_start: 0.8546 (mp0) cc_final: 0.8258 (mp0) REVERT: R 113 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8466 (pttp) REVERT: S 73 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8041 (tt0) REVERT: S 83 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7127 (mtm180) REVERT: S 131 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8407 (mtt180) REVERT: T 25 ASN cc_start: 0.8661 (m-40) cc_final: 0.8400 (m110) REVERT: U 36 LYS cc_start: 0.8366 (ptmt) cc_final: 0.8034 (mmmt) REVERT: U 56 GLU cc_start: 0.8535 (tt0) cc_final: 0.8291 (tt0) REVERT: V 105 LYS cc_start: 0.8037 (mtpt) cc_final: 0.7573 (mttp) REVERT: A 88 ARG cc_start: 0.8237 (mtm110) cc_final: 0.7841 (mtm180) REVERT: A 189 HIS cc_start: 0.6863 (OUTLIER) cc_final: 0.5798 (p90) REVERT: A 204 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8013 (ttm) REVERT: B 670 GLU cc_start: 0.7712 (mp0) cc_final: 0.6858 (mp0) REVERT: B 817 TYR cc_start: 0.8268 (OUTLIER) cc_final: 0.7965 (m-80) REVERT: B 825 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8890 (mm) REVERT: B 828 ILE cc_start: 0.7263 (OUTLIER) cc_final: 0.6824 (mm) REVERT: B 910 ARG cc_start: 0.7986 (ttm110) cc_final: 0.7703 (tmt170) REVERT: B 918 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8127 (mp0) REVERT: B 982 LYS cc_start: 0.7501 (mtmt) cc_final: 0.7006 (mtmm) REVERT: B 1016 TYR cc_start: 0.7939 (OUTLIER) cc_final: 0.7492 (t80) REVERT: B 1136 PHE cc_start: 0.5803 (OUTLIER) cc_final: 0.5186 (m-10) REVERT: B 1167 ARG cc_start: 0.8033 (mmp-170) cc_final: 0.7796 (mmp-170) REVERT: B 1187 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7167 (mm) REVERT: B 1317 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7837 (mt) REVERT: E 262 PHE cc_start: 0.7835 (OUTLIER) cc_final: 0.7297 (t80) REVERT: E 282 PHE cc_start: 0.6946 (m-80) cc_final: 0.6650 (m-80) REVERT: E 355 ASN cc_start: 0.8494 (m-40) cc_final: 0.7496 (m-40) REVERT: E 375 GLU cc_start: 0.8831 (pm20) cc_final: 0.8521 (pm20) REVERT: E 512 ILE cc_start: 0.7423 (OUTLIER) cc_final: 0.6746 (pt) REVERT: E 543 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7889 (p0) REVERT: E 549 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.7891 (t80) REVERT: E 556 TYR cc_start: 0.8280 (m-10) cc_final: 0.7805 (m-10) outliers start: 146 outliers final: 43 residues processed: 432 average time/residue: 1.4415 time to fit residues: 720.7691 Evaluate side-chains 361 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 296 time to evaluate : 2.468 ------------------------------------------------------------------------------- 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 282 CYS Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 349 LEU 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 O residue 80 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Q residue 74 LYS 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 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 83 ARG 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 115 LEU Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 254 VAL 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 976 ASP Chi-restraints excluded: chain B residue 1016 TYR Chi-restraints excluded: chain B residue 1136 PHE Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1189 SER 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 474 VAL Chi-restraints excluded: chain E residue 512 ILE Chi-restraints excluded: chain E residue 539 ILE Chi-restraints excluded: chain E residue 540 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 245 optimal weight: 0.0970 chunk 186 optimal weight: 0.5980 chunk 128 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 249 optimal weight: 0.8980 chunk 263 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 236 optimal weight: 10.0000 chunk 71 optimal weight: 0.5980 overall best weight: 1.0380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 275 GLN D 358 GLN F 263 HIS S 76 GLN V 46 HIS ** 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** B1150 HIS B1221 HIS E 314 ASN E 410 ASN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4523 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= 0.262 Angle : 0.599 12.189 39579 Z= 0.324 Chirality : 0.038 0.231 4370 Planarity : 0.004 0.050 3885 Dihedral : 26.929 177.914 6313 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 5.59 % Allowed : 26.81 % Favored : 67.60 % 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: -0.48 (0.17), residues: 2447 helix: 0.41 (0.14), residues: 1355 sheet: -0.31 (0.54), residues: 90 loop : -1.26 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 261 HIS 0.006 0.001 HIS B 815 PHE 0.016 0.001 PHE B1147 TYR 0.023 0.001 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 461 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 337 time to evaluate : 2.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 24 GLU cc_start: 0.5020 (mt-10) cc_final: 0.4678 (mm-30) REVERT: F 81 TYR cc_start: 0.3892 (OUTLIER) cc_final: 0.3485 (m-80) REVERT: F 256 MET cc_start: 0.1107 (OUTLIER) cc_final: 0.0498 (pp-130) REVERT: F 270 GLU cc_start: 0.0788 (OUTLIER) cc_final: -0.0068 (pm20) REVERT: F 296 MET cc_start: 0.3991 (mpt) cc_final: 0.3233 (mmm) REVERT: Q 90 ASP cc_start: 0.8477 (t70) cc_final: 0.8087 (t0) REVERT: R 90 GLU cc_start: 0.8500 (mp0) cc_final: 0.8239 (mp0) REVERT: S 73 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8064 (tt0) REVERT: S 83 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7099 (mtm180) REVERT: S 131 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8235 (mtt180) REVERT: T 25 ASN cc_start: 0.8707 (m-40) cc_final: 0.8422 (m110) REVERT: U 36 LYS cc_start: 0.8359 (ptmt) cc_final: 0.8073 (mmmt) REVERT: U 56 GLU cc_start: 0.8517 (tt0) cc_final: 0.8284 (tt0) REVERT: U 92 GLU cc_start: 0.7702 (mp0) cc_final: 0.7484 (mp0) REVERT: V 76 ARG cc_start: 0.7738 (mtp85) cc_final: 0.7375 (mtm-85) REVERT: V 105 LYS cc_start: 0.7996 (mtpt) cc_final: 0.7535 (mttp) REVERT: A 88 ARG cc_start: 0.8233 (mtm110) cc_final: 0.7770 (mtm180) REVERT: A 189 HIS cc_start: 0.6988 (OUTLIER) cc_final: 0.5976 (p90) REVERT: A 306 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7643 (ttm) REVERT: A 325 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7629 (mm-30) REVERT: A 422 ARG cc_start: 0.4750 (OUTLIER) cc_final: 0.4512 (ttt-90) REVERT: B 670 GLU cc_start: 0.7703 (mp0) cc_final: 0.6835 (mp0) REVERT: B 684 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7583 (mm-30) REVERT: B 811 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8328 (tt0) REVERT: B 817 TYR cc_start: 0.8254 (OUTLIER) cc_final: 0.7969 (m-80) REVERT: B 825 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8907 (mm) REVERT: B 826 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7935 (mmm160) REVERT: B 910 ARG cc_start: 0.7988 (ttm110) cc_final: 0.7710 (tmt170) REVERT: B 918 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8105 (mp0) REVERT: B 982 LYS cc_start: 0.7515 (mtmt) cc_final: 0.7010 (mtmm) REVERT: B 1016 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.7532 (t80) REVERT: B 1136 PHE cc_start: 0.5866 (OUTLIER) cc_final: 0.5094 (m-10) REVERT: B 1160 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.6895 (mp0) REVERT: B 1167 ARG cc_start: 0.8053 (mmp-170) cc_final: 0.7745 (mmp-170) REVERT: E 262 PHE cc_start: 0.7807 (OUTLIER) cc_final: 0.7297 (t80) REVERT: E 282 PHE cc_start: 0.6998 (m-80) cc_final: 0.6698 (m-80) REVERT: E 355 ASN cc_start: 0.8213 (m-40) cc_final: 0.7558 (m-40) REVERT: E 359 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7120 (mm-30) REVERT: E 375 GLU cc_start: 0.8827 (pm20) cc_final: 0.8516 (pm20) REVERT: E 543 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7852 (p0) REVERT: E 556 TYR cc_start: 0.8344 (m-10) cc_final: 0.7856 (m-10) outliers start: 124 outliers final: 43 residues processed: 420 average time/residue: 1.4701 time to fit residues: 714.4321 Evaluate side-chains 366 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 305 time to evaluate : 2.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain F residue 81 TYR 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 P residue 96 THR Chi-restraints excluded: chain Q residue 74 LYS 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 83 ARG 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 U residue 115 LEU Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain V residue 109 SER 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 254 VAL Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 817 TYR 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 1016 TYR Chi-restraints excluded: chain B residue 1136 PHE Chi-restraints excluded: chain B residue 1160 GLU 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 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 450 ASP Chi-restraints excluded: chain E residue 452 VAL 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 543 ASP Chi-restraints excluded: chain E residue 547 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 219 optimal weight: 0.6980 chunk 149 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 196 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 225 optimal weight: 0.9980 chunk 182 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 134 optimal weight: 1.9990 chunk 236 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 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 O 39 HIS ** P 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 46 HIS S 76 GLN T 25 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** ** 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 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 410 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: 0.7998 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 28285 Z= 0.278 Angle : 0.608 11.129 39579 Z= 0.329 Chirality : 0.039 0.252 4370 Planarity : 0.004 0.058 3885 Dihedral : 26.981 177.978 6312 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 5.77 % Allowed : 26.54 % Favored : 67.69 % 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: -0.37 (0.17), residues: 2447 helix: 0.49 (0.14), residues: 1353 sheet: -0.68 (0.52), residues: 90 loop : -1.16 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 261 HIS 0.009 0.001 HIS B1221 PHE 0.021 0.001 PHE G 551 TYR 0.024 0.002 TYR A 176 ARG 0.016 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 480 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 352 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 275 GLN cc_start: 0.6832 (mm110) cc_final: 0.6217 (mt0) REVERT: F 24 GLU cc_start: 0.5042 (mt-10) cc_final: 0.4612 (mm-30) REVERT: F 81 TYR cc_start: 0.3929 (OUTLIER) cc_final: 0.3531 (m-80) REVERT: F 95 ASP cc_start: 0.2873 (p0) cc_final: 0.2347 (t70) REVERT: F 234 ASP cc_start: 0.5337 (t70) cc_final: 0.4844 (m-30) REVERT: F 256 MET cc_start: 0.0923 (OUTLIER) cc_final: 0.0579 (pp-130) REVERT: F 270 GLU cc_start: 0.0683 (OUTLIER) cc_final: -0.0212 (pm20) REVERT: F 296 MET cc_start: 0.3932 (OUTLIER) cc_final: 0.3137 (mmm) REVERT: F 363 LEU cc_start: 0.6788 (tp) cc_final: 0.6548 (tt) REVERT: Q 73 ASN cc_start: 0.8341 (p0) cc_final: 0.8110 (p0) REVERT: Q 90 ASP cc_start: 0.8540 (t70) cc_final: 0.8240 (t0) REVERT: R 90 GLU cc_start: 0.8450 (mp0) cc_final: 0.7852 (mp0) REVERT: R 105 LYS cc_start: 0.8495 (tttm) cc_final: 0.8203 (tttp) REVERT: S 73 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7991 (tt0) REVERT: S 83 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7063 (mtm180) REVERT: S 131 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8237 (mtt180) REVERT: T 25 ASN cc_start: 0.8715 (m110) cc_final: 0.8107 (m-40) REVERT: U 36 LYS cc_start: 0.8337 (ptmt) cc_final: 0.8071 (mmmt) REVERT: U 56 GLU cc_start: 0.8501 (tt0) cc_final: 0.8273 (tt0) REVERT: U 92 GLU cc_start: 0.7623 (mp0) cc_final: 0.7307 (pt0) REVERT: V 105 LYS cc_start: 0.7985 (mtpt) cc_final: 0.7463 (mttp) REVERT: A 52 ILE cc_start: 0.7721 (OUTLIER) cc_final: 0.7506 (mp) REVERT: A 60 LYS cc_start: 0.6748 (mttm) cc_final: 0.6217 (ptpt) REVERT: A 88 ARG cc_start: 0.8241 (mtm110) cc_final: 0.7969 (mtm180) REVERT: A 189 HIS cc_start: 0.7251 (OUTLIER) cc_final: 0.6333 (p90) REVERT: A 261 TRP cc_start: 0.7376 (m-90) cc_final: 0.7124 (m-90) REVERT: A 306 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7664 (ttm) REVERT: A 316 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7752 (ptm-80) REVERT: A 325 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7603 (mm-30) REVERT: B 670 GLU cc_start: 0.7750 (mp0) cc_final: 0.6817 (mp0) REVERT: B 684 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7510 (mm-30) REVERT: B 812 GLU cc_start: 0.7723 (tp30) cc_final: 0.7326 (tp30) REVERT: B 817 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.8027 (m-80) REVERT: B 826 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7956 (mmm160) REVERT: B 910 ARG cc_start: 0.8026 (ttm110) cc_final: 0.7749 (tmt170) REVERT: B 918 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8154 (mp0) REVERT: B 970 LYS cc_start: 0.5908 (OUTLIER) cc_final: 0.5646 (pmmt) REVERT: B 982 LYS cc_start: 0.7502 (mttt) cc_final: 0.6988 (mtmm) REVERT: B 1016 TYR cc_start: 0.7951 (OUTLIER) cc_final: 0.7654 (t80) REVERT: B 1020 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8065 (tp) REVERT: B 1136 PHE cc_start: 0.5896 (OUTLIER) cc_final: 0.5213 (m-10) REVERT: B 1160 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.6929 (mp0) REVERT: B 1259 ASP cc_start: 0.8154 (t0) cc_final: 0.7953 (t0) REVERT: E 262 PHE cc_start: 0.7824 (OUTLIER) cc_final: 0.7345 (t80) REVERT: E 282 PHE cc_start: 0.7054 (m-80) cc_final: 0.6590 (m-80) REVERT: E 355 ASN cc_start: 0.8392 (m-40) cc_final: 0.7215 (t0) REVERT: E 359 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7010 (mm-30) REVERT: E 375 GLU cc_start: 0.8829 (pm20) cc_final: 0.8527 (pm20) REVERT: E 388 ASN cc_start: 0.4617 (OUTLIER) cc_final: 0.4276 (m-40) REVERT: E 549 TYR cc_start: 0.8289 (OUTLIER) cc_final: 0.7782 (t80) REVERT: E 556 TYR cc_start: 0.8444 (m-10) cc_final: 0.8043 (m-10) REVERT: G 548 LYS cc_start: 0.4168 (mmmt) cc_final: 0.3909 (mmmt) outliers start: 128 outliers final: 54 residues processed: 441 average time/residue: 1.5205 time to fit residues: 774.4744 Evaluate side-chains 401 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 325 time to evaluate : 2.657 ------------------------------------------------------------------------------- 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 348 ASP Chi-restraints excluded: chain D residue 349 LEU 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 288 TYR Chi-restraints excluded: chain F residue 296 MET 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 61 GLU Chi-restraints excluded: chain Q residue 74 LYS 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 58 THR Chi-restraints excluded: chain S residue 73 GLU Chi-restraints excluded: chain S residue 83 ARG 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 U residue 115 LEU Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 89 VAL 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 254 VAL Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 770 ARG Chi-restraints excluded: chain B residue 817 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 970 LYS Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1016 TYR Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1136 PHE Chi-restraints excluded: chain B residue 1160 GLU Chi-restraints excluded: chain B residue 1228 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 274 CYS 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 388 ASN 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 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 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: 0.2980 chunk 52 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 264 optimal weight: 0.8980 chunk 219 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 87 optimal weight: 0.3980 chunk 138 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 S 76 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** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1222 GLN E 314 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: 0.7966 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28285 Z= 0.201 Angle : 0.589 12.093 39579 Z= 0.319 Chirality : 0.037 0.305 4370 Planarity : 0.004 0.061 3885 Dihedral : 26.894 176.684 6312 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 5.09 % Allowed : 28.03 % Favored : 66.88 % 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: -0.23 (0.17), residues: 2447 helix: 0.60 (0.14), residues: 1364 sheet: -0.68 (0.52), residues: 90 loop : -1.09 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 261 HIS 0.010 0.001 HIS R 46 PHE 0.034 0.001 PHE G 551 TYR 0.025 0.001 TYR F 261 ARG 0.014 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 459 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 346 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 275 GLN cc_start: 0.6792 (mm110) cc_final: 0.6178 (mt0) REVERT: D 295 ASN cc_start: 0.7216 (OUTLIER) cc_final: 0.6735 (m-40) REVERT: D 354 LEU cc_start: 0.8363 (pp) cc_final: 0.8107 (tm) REVERT: D 358 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7828 (mp10) REVERT: F 22 MET cc_start: 0.0939 (mmm) cc_final: 0.0281 (mtt) REVERT: F 24 GLU cc_start: 0.5113 (mt-10) cc_final: 0.4671 (mm-30) REVERT: F 81 TYR cc_start: 0.3834 (OUTLIER) cc_final: 0.3448 (m-80) REVERT: F 95 ASP cc_start: 0.2742 (p0) cc_final: 0.2259 (t70) REVERT: F 234 ASP cc_start: 0.5252 (t70) cc_final: 0.4826 (m-30) REVERT: F 256 MET cc_start: 0.0999 (OUTLIER) cc_final: 0.0749 (pp-130) REVERT: F 270 GLU cc_start: 0.0491 (OUTLIER) cc_final: -0.0217 (pm20) REVERT: F 296 MET cc_start: 0.4137 (mpt) cc_final: 0.3373 (mmm) REVERT: Q 73 ASN cc_start: 0.8194 (p0) cc_final: 0.7963 (p0) REVERT: Q 90 ASP cc_start: 0.8482 (t70) cc_final: 0.8109 (t0) REVERT: R 32 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7958 (tp30) REVERT: R 90 GLU cc_start: 0.8415 (mp0) cc_final: 0.7820 (mp0) REVERT: R 105 LYS cc_start: 0.8490 (tttm) cc_final: 0.8201 (tttp) REVERT: S 42 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7935 (mtp-110) REVERT: S 73 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7955 (tt0) REVERT: S 131 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8238 (mtt180) REVERT: T 25 ASN cc_start: 0.8683 (m110) cc_final: 0.8045 (m-40) REVERT: U 36 LYS cc_start: 0.8310 (ptmt) cc_final: 0.8056 (mmmt) REVERT: U 56 GLU cc_start: 0.8508 (tt0) cc_final: 0.8275 (tt0) REVERT: U 92 GLU cc_start: 0.7589 (mp0) cc_final: 0.7286 (pt0) REVERT: V 105 LYS cc_start: 0.7961 (mtpt) cc_final: 0.7441 (mttp) REVERT: A 52 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7456 (mp) REVERT: A 60 LYS cc_start: 0.6677 (mttm) cc_final: 0.6118 (ptpt) REVERT: A 88 ARG cc_start: 0.8244 (mtm110) cc_final: 0.7850 (mtm180) REVERT: A 189 HIS cc_start: 0.7075 (OUTLIER) cc_final: 0.6088 (p90) REVERT: A 250 VAL cc_start: 0.9112 (p) cc_final: 0.8853 (p) REVERT: A 261 TRP cc_start: 0.7439 (m-10) cc_final: 0.7207 (m-90) REVERT: A 373 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.6675 (mpp) REVERT: B 670 GLU cc_start: 0.7760 (mp0) cc_final: 0.6799 (mp0) REVERT: B 684 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7618 (mm-30) REVERT: B 765 MET cc_start: 0.5633 (OUTLIER) cc_final: 0.4669 (ppp) REVERT: B 812 GLU cc_start: 0.7727 (tp30) cc_final: 0.7320 (tp30) REVERT: B 817 TYR cc_start: 0.8199 (OUTLIER) cc_final: 0.7963 (m-80) REVERT: B 826 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7961 (mmm160) REVERT: B 881 ASP cc_start: 0.8736 (t0) cc_final: 0.8295 (m-30) REVERT: B 910 ARG cc_start: 0.8020 (ttm110) cc_final: 0.7759 (tmt170) REVERT: B 918 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8123 (mp0) REVERT: B 970 LYS cc_start: 0.5969 (OUTLIER) cc_final: 0.5749 (pmmt) REVERT: B 982 LYS cc_start: 0.7472 (mttt) cc_final: 0.6920 (mtmm) REVERT: B 1016 TYR cc_start: 0.7871 (OUTLIER) cc_final: 0.7661 (t80) REVERT: B 1020 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7974 (tp) REVERT: B 1136 PHE cc_start: 0.5873 (OUTLIER) cc_final: 0.5168 (m-10) REVERT: B 1160 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.6940 (mp0) REVERT: B 1167 ARG cc_start: 0.8071 (mmp-170) cc_final: 0.7822 (mmp-170) REVERT: B 1187 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7016 (mm) REVERT: E 262 PHE cc_start: 0.7749 (OUTLIER) cc_final: 0.7310 (t80) REVERT: E 282 PHE cc_start: 0.7059 (m-80) cc_final: 0.6596 (m-80) REVERT: E 355 ASN cc_start: 0.8393 (m-40) cc_final: 0.7117 (t0) REVERT: E 359 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7163 (mm-30) REVERT: E 375 GLU cc_start: 0.8827 (pm20) cc_final: 0.8519 (pm20) REVERT: E 388 ASN cc_start: 0.4871 (OUTLIER) cc_final: 0.4447 (m-40) REVERT: E 515 GLN cc_start: 0.7850 (mp10) cc_final: 0.7384 (mp10) REVERT: E 556 TYR cc_start: 0.8420 (m-10) cc_final: 0.7908 (m-10) REVERT: G 548 LYS cc_start: 0.4177 (mmmt) cc_final: 0.3913 (mmmt) outliers start: 113 outliers final: 52 residues processed: 421 average time/residue: 1.4238 time to fit residues: 690.6763 Evaluate side-chains 405 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 329 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 298 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 235 ASP 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 288 TYR Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain O residue 76 GLN 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 Q residue 61 GLU Chi-restraints excluded: chain Q residue 74 LYS 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 S residue 42 ARG 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 U residue 115 LEU Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 89 VAL 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 B residue 726 TYR Chi-restraints excluded: chain B residue 765 MET Chi-restraints excluded: chain B residue 770 ARG Chi-restraints excluded: chain B residue 817 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 970 LYS Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1016 TYR Chi-restraints excluded: chain B residue 1020 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 1228 LEU Chi-restraints excluded: chain B residue 1278 THR Chi-restraints excluded: chain B residue 1321 ASP 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 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 388 ASN 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 539 ILE Chi-restraints excluded: chain E residue 547 ILE Chi-restraints excluded: chain G residue 335 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 254 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 192 optimal weight: 0.0970 chunk 149 optimal weight: 2.9990 chunk 222 optimal weight: 10.0000 chunk 147 optimal weight: 0.5980 chunk 263 optimal weight: 10.0000 chunk 164 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 46 HIS S 76 GLN ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 GLN ** A 209 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** B 974 GLN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.5299 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= 0.278 Angle : 0.615 11.505 39579 Z= 0.334 Chirality : 0.039 0.304 4370 Planarity : 0.004 0.068 3885 Dihedral : 26.966 177.902 6312 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 5.41 % Allowed : 27.81 % Favored : 66.79 % 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: 0.56 (0.14), residues: 1370 sheet: -0.84 (0.53), residues: 90 loop : -1.11 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 775 HIS 0.007 0.001 HIS B1254 PHE 0.039 0.002 PHE G 551 TYR 0.022 0.002 TYR A 176 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 459 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 339 time to evaluate : 2.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 82 GLN cc_start: 0.7825 (pp30) cc_final: 0.7490 (pm20) REVERT: D 275 GLN cc_start: 0.6673 (mm110) cc_final: 0.6099 (mt0) REVERT: D 295 ASN cc_start: 0.7225 (OUTLIER) cc_final: 0.6925 (m-40) REVERT: D 375 ASN cc_start: 0.8395 (p0) cc_final: 0.7938 (t0) REVERT: F 22 MET cc_start: 0.1044 (mmm) cc_final: 0.0380 (mtt) REVERT: F 24 GLU cc_start: 0.5246 (mt-10) cc_final: 0.4830 (mm-30) REVERT: F 95 ASP cc_start: 0.2560 (p0) cc_final: 0.2103 (t70) REVERT: F 234 ASP cc_start: 0.5278 (t70) cc_final: 0.4862 (m-30) REVERT: F 270 GLU cc_start: 0.0599 (OUTLIER) cc_final: -0.0180 (pm20) REVERT: F 296 MET cc_start: 0.3980 (OUTLIER) cc_final: 0.3208 (mmm) REVERT: Q 73 ASN cc_start: 0.8313 (p0) cc_final: 0.8029 (p0) REVERT: Q 90 ASP cc_start: 0.8518 (t70) cc_final: 0.8227 (t0) REVERT: R 32 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7933 (tp30) REVERT: R 90 GLU cc_start: 0.8421 (mp0) cc_final: 0.7750 (mp0) REVERT: R 105 LYS cc_start: 0.8511 (tttm) cc_final: 0.8181 (tttp) REVERT: S 42 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8067 (mtp-110) REVERT: S 64 LYS cc_start: 0.8427 (mptm) cc_final: 0.8165 (mppt) REVERT: S 73 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7985 (tt0) REVERT: S 115 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8854 (mmtm) REVERT: S 131 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8241 (mtt180) REVERT: T 25 ASN cc_start: 0.8713 (m110) cc_final: 0.8094 (m-40) REVERT: U 36 LYS cc_start: 0.8357 (ptmt) cc_final: 0.8089 (mmmt) REVERT: U 56 GLU cc_start: 0.8505 (tt0) cc_final: 0.8271 (tt0) REVERT: U 92 GLU cc_start: 0.7594 (mp0) cc_final: 0.7283 (pt0) REVERT: V 105 LYS cc_start: 0.7974 (mtpt) cc_final: 0.7483 (mttp) REVERT: A 52 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7472 (mp) REVERT: A 60 LYS cc_start: 0.6872 (mttm) cc_final: 0.6270 (ptpt) REVERT: A 88 ARG cc_start: 0.8218 (mtm110) cc_final: 0.8015 (mtm110) REVERT: A 189 HIS cc_start: 0.7311 (OUTLIER) cc_final: 0.6368 (p90) REVERT: A 250 VAL cc_start: 0.9127 (p) cc_final: 0.8867 (p) REVERT: A 261 TRP cc_start: 0.7617 (m-10) cc_final: 0.7293 (m-90) REVERT: A 306 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.7530 (tmm) REVERT: A 325 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7555 (mm-30) REVERT: A 373 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7548 (mtt) REVERT: B 670 GLU cc_start: 0.7797 (mp0) cc_final: 0.6863 (mp0) REVERT: B 684 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7497 (mm-30) REVERT: B 765 MET cc_start: 0.5355 (OUTLIER) cc_final: 0.4568 (pp-130) REVERT: B 799 ARG cc_start: 0.7662 (mmm160) cc_final: 0.6896 (mtt-85) REVERT: B 812 GLU cc_start: 0.7781 (tp30) cc_final: 0.7358 (tp30) REVERT: B 817 TYR cc_start: 0.8195 (OUTLIER) cc_final: 0.7963 (m-80) REVERT: B 826 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7968 (mmm160) REVERT: B 881 ASP cc_start: 0.8793 (t0) cc_final: 0.8356 (m-30) REVERT: B 910 ARG cc_start: 0.8021 (ttm110) cc_final: 0.7751 (tmt170) REVERT: B 918 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7382 (mp0) REVERT: B 970 LYS cc_start: 0.5981 (OUTLIER) cc_final: 0.5759 (pmmt) REVERT: B 982 LYS cc_start: 0.7454 (mttt) cc_final: 0.6801 (mtmm) REVERT: B 1020 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8092 (tp) REVERT: B 1136 PHE cc_start: 0.5964 (OUTLIER) cc_final: 0.5298 (m-10) REVERT: B 1160 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.6940 (mp0) REVERT: B 1167 ARG cc_start: 0.8070 (mmp-170) cc_final: 0.7802 (mmp-170) REVERT: B 1185 ASP cc_start: 0.8092 (t0) cc_final: 0.7714 (t0) REVERT: B 1187 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.6980 (mm) REVERT: E 262 PHE cc_start: 0.7755 (OUTLIER) cc_final: 0.7359 (t80) REVERT: E 282 PHE cc_start: 0.7129 (m-80) cc_final: 0.6719 (m-80) REVERT: E 355 ASN cc_start: 0.8458 (m-40) cc_final: 0.7243 (t0) REVERT: E 359 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7174 (mm-30) REVERT: E 375 GLU cc_start: 0.8842 (pm20) cc_final: 0.8536 (pm20) REVERT: E 388 ASN cc_start: 0.4715 (OUTLIER) cc_final: 0.4330 (m-40) REVERT: E 404 ASP cc_start: 0.8556 (m-30) cc_final: 0.8306 (p0) REVERT: E 476 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.6774 (pmtt) REVERT: E 549 TYR cc_start: 0.8245 (OUTLIER) cc_final: 0.7782 (t80) REVERT: E 556 TYR cc_start: 0.8543 (m-10) cc_final: 0.8059 (m-10) REVERT: G 548 LYS cc_start: 0.4237 (mmmt) cc_final: 0.3968 (mmmt) outliers start: 120 outliers final: 55 residues processed: 420 average time/residue: 1.5080 time to fit residues: 730.9948 Evaluate side-chains 397 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 317 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 235 ASP Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain F residue 288 TYR Chi-restraints excluded: chain F residue 296 MET Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain O residue 76 GLN 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 Q residue 61 GLU Chi-restraints excluded: chain Q residue 74 LYS 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 S residue 42 ARG Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 73 GLU Chi-restraints excluded: chain S residue 115 LYS 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 U residue 115 LEU Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 89 VAL 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 306 MET 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 726 TYR Chi-restraints excluded: chain B residue 765 MET Chi-restraints excluded: chain B residue 817 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 970 LYS Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1020 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 1193 GLU Chi-restraints excluded: chain B residue 1228 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 274 CYS 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 388 ASN 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 542 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 162 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 167 optimal weight: 0.5980 chunk 179 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 206 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 S 76 GLN ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 GLN A 177 HIS ** A 209 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 974 GLN B1222 GLN E 410 ASN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 28285 Z= 0.305 Angle : 0.637 14.738 39579 Z= 0.342 Chirality : 0.039 0.337 4370 Planarity : 0.004 0.047 3885 Dihedral : 27.054 177.186 6312 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.91 % Allowed : 28.48 % Favored : 66.61 % 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: -0.32 (0.17), residues: 2447 helix: 0.53 (0.14), residues: 1372 sheet: -0.92 (0.53), residues: 90 loop : -1.12 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B1151 HIS 0.008 0.001 HIS B1254 PHE 0.021 0.001 PHE B 708 TYR 0.028 0.002 TYR A 347 ARG 0.013 0.001 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 445 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 336 time to evaluate : 2.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 82 GLN cc_start: 0.7876 (pp30) cc_final: 0.7513 (pm20) REVERT: D 275 GLN cc_start: 0.6559 (mm110) cc_final: 0.6027 (mt0) REVERT: D 295 ASN cc_start: 0.7284 (OUTLIER) cc_final: 0.6992 (m-40) REVERT: D 354 LEU cc_start: 0.8319 (pp) cc_final: 0.8105 (tm) REVERT: D 358 GLN cc_start: 0.8015 (mp-120) cc_final: 0.7802 (mp10) REVERT: D 375 ASN cc_start: 0.8448 (OUTLIER) cc_final: 0.8003 (t0) REVERT: F 22 MET cc_start: 0.1117 (mmm) cc_final: 0.0444 (mtt) REVERT: F 24 GLU cc_start: 0.5442 (mt-10) cc_final: 0.4929 (mm-30) REVERT: F 95 ASP cc_start: 0.2355 (p0) cc_final: 0.1938 (t70) REVERT: F 270 GLU cc_start: 0.0748 (OUTLIER) cc_final: 0.0122 (pm20) REVERT: F 296 MET cc_start: 0.3932 (OUTLIER) cc_final: 0.3699 (mmm) REVERT: Q 73 ASN cc_start: 0.8325 (p0) cc_final: 0.8042 (p0) REVERT: Q 90 ASP cc_start: 0.8483 (t70) cc_final: 0.8110 (t0) REVERT: Q 92 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7888 (mm-30) REVERT: R 30 ARG cc_start: 0.7049 (mtm-85) cc_final: 0.6712 (mtt-85) REVERT: R 32 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7938 (tp30) REVERT: R 90 GLU cc_start: 0.8438 (mp0) cc_final: 0.7804 (mp0) REVERT: R 105 LYS cc_start: 0.8533 (tttm) cc_final: 0.8197 (tttp) REVERT: S 42 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8046 (mtp-110) REVERT: S 64 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8156 (mppt) REVERT: S 131 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8266 (mtt180) REVERT: U 36 LYS cc_start: 0.8353 (ptmt) cc_final: 0.8095 (mmmt) REVERT: U 56 GLU cc_start: 0.8503 (tt0) cc_final: 0.8275 (tt0) REVERT: U 90 ASP cc_start: 0.8293 (t0) cc_final: 0.8061 (t0) REVERT: U 92 GLU cc_start: 0.7606 (mp0) cc_final: 0.7138 (pt0) REVERT: V 105 LYS cc_start: 0.7989 (mtpt) cc_final: 0.7506 (mttp) REVERT: A 52 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7474 (mp) REVERT: A 60 LYS cc_start: 0.7059 (mttm) cc_final: 0.6341 (ptpt) REVERT: A 189 HIS cc_start: 0.7398 (OUTLIER) cc_final: 0.6487 (p90) REVERT: A 250 VAL cc_start: 0.9145 (p) cc_final: 0.8872 (p) REVERT: A 261 TRP cc_start: 0.7770 (m-10) cc_final: 0.7458 (m-90) REVERT: A 306 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.7528 (tmm) REVERT: A 316 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7957 (ptm-80) REVERT: A 325 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7647 (mp0) REVERT: A 373 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7605 (mtt) REVERT: B 670 GLU cc_start: 0.7846 (mp0) cc_final: 0.6929 (mp0) REVERT: B 684 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7331 (mm-30) REVERT: B 765 MET cc_start: 0.5217 (OUTLIER) cc_final: 0.4593 (pp-130) REVERT: B 812 GLU cc_start: 0.7790 (tp30) cc_final: 0.7391 (tp30) REVERT: B 817 TYR cc_start: 0.8185 (OUTLIER) cc_final: 0.7948 (m-80) REVERT: B 826 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.8000 (mmm160) REVERT: B 881 ASP cc_start: 0.8812 (t0) cc_final: 0.8389 (m-30) REVERT: B 918 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: B 982 LYS cc_start: 0.7381 (mttt) cc_final: 0.6840 (mtmm) REVERT: B 1136 PHE cc_start: 0.5995 (OUTLIER) cc_final: 0.5334 (m-10) REVERT: B 1156 GLU cc_start: 0.7150 (mt-10) cc_final: 0.6574 (mt-10) REVERT: B 1160 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: B 1185 ASP cc_start: 0.8110 (t0) cc_final: 0.7740 (t0) REVERT: B 1187 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.6995 (mm) REVERT: E 262 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.7540 (t80) REVERT: E 282 PHE cc_start: 0.7203 (m-80) cc_final: 0.6923 (m-80) REVERT: E 355 ASN cc_start: 0.8491 (m-40) cc_final: 0.7217 (t0) REVERT: E 359 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7338 (mm-30) REVERT: E 375 GLU cc_start: 0.8845 (pm20) cc_final: 0.8549 (pm20) REVERT: E 388 ASN cc_start: 0.5009 (OUTLIER) cc_final: 0.4456 (m-40) REVERT: E 404 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8335 (p0) REVERT: E 476 LYS cc_start: 0.7366 (OUTLIER) cc_final: 0.6771 (pmtt) REVERT: E 543 ASP cc_start: 0.7815 (p0) cc_final: 0.7574 (p0) REVERT: E 549 TYR cc_start: 0.8465 (OUTLIER) cc_final: 0.7632 (t80) REVERT: E 556 TYR cc_start: 0.8607 (m-10) cc_final: 0.8162 (m-10) REVERT: G 548 LYS cc_start: 0.4274 (mmmt) cc_final: 0.3982 (mmmt) outliers start: 109 outliers final: 54 residues processed: 409 average time/residue: 1.4289 time to fit residues: 676.0078 Evaluate side-chains 393 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 314 time to evaluate : 2.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 254 VAL Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain F residue 288 TYR Chi-restraints excluded: chain F residue 296 MET 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 Q residue 74 LYS Chi-restraints excluded: chain Q residue 76 THR 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 S residue 42 ARG Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 64 LYS 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 U residue 115 LEU Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 97 PHE 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 306 MET Chi-restraints excluded: chain A residue 316 ARG 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 726 TYR Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 765 MET Chi-restraints excluded: chain B residue 817 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 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 1228 LEU Chi-restraints excluded: chain B residue 1278 THR Chi-restraints excluded: chain B residue 1321 ASP 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 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 388 ASN Chi-restraints excluded: chain E residue 404 ASP 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 542 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 239 optimal weight: 8.9990 chunk 252 optimal weight: 4.9990 chunk 229 optimal weight: 7.9990 chunk 245 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 192 optimal weight: 0.0040 chunk 75 optimal weight: 0.5980 chunk 221 optimal weight: 5.9990 chunk 231 optimal weight: 2.9990 chunk 244 optimal weight: 0.0980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 46 HIS S 39 HIS T 25 ASN ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN ** B 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 974 GLN ** E 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7980 moved from start: 0.5514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28285 Z= 0.196 Angle : 0.628 15.846 39579 Z= 0.332 Chirality : 0.037 0.338 4370 Planarity : 0.004 0.076 3885 Dihedral : 26.926 175.813 6312 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.38 % Allowed : 30.24 % Favored : 66.38 % 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: -0.19 (0.17), residues: 2447 helix: 0.65 (0.14), residues: 1363 sheet: -0.87 (0.56), residues: 85 loop : -1.07 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 775 HIS 0.005 0.001 HIS B1254 PHE 0.031 0.001 PHE E 341 TYR 0.023 0.001 TYR A 176 ARG 0.018 0.000 ARG B 799 *********************** 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 421 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 346 time to evaluate : 2.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 82 GLN cc_start: 0.7929 (pp30) cc_final: 0.7527 (pm20) REVERT: D 275 GLN cc_start: 0.6423 (mm110) cc_final: 0.5847 (mt0) REVERT: D 295 ASN cc_start: 0.6914 (OUTLIER) cc_final: 0.6604 (m-40) REVERT: D 375 ASN cc_start: 0.8367 (OUTLIER) cc_final: 0.7920 (t0) REVERT: F 22 MET cc_start: 0.1115 (mmm) cc_final: 0.0522 (mtt) REVERT: F 24 GLU cc_start: 0.5434 (mt-10) cc_final: 0.4910 (mm-30) REVERT: F 95 ASP cc_start: 0.2352 (p0) cc_final: 0.1982 (t70) REVERT: F 270 GLU cc_start: 0.0644 (OUTLIER) cc_final: -0.0028 (pm20) REVERT: F 297 LEU cc_start: 0.5033 (pt) cc_final: 0.4407 (tp) REVERT: Q 73 ASN cc_start: 0.8155 (p0) cc_final: 0.7881 (p0) REVERT: Q 90 ASP cc_start: 0.8509 (t70) cc_final: 0.8232 (t0) REVERT: R 90 GLU cc_start: 0.8390 (mp0) cc_final: 0.7809 (mp0) REVERT: R 105 LYS cc_start: 0.8476 (tttm) cc_final: 0.8151 (tttp) REVERT: S 42 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7993 (mtp-110) REVERT: S 64 LYS cc_start: 0.8382 (mptm) cc_final: 0.8134 (mppt) REVERT: S 131 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8249 (mtt180) REVERT: T 25 ASN cc_start: 0.8796 (m-40) cc_final: 0.8478 (m-40) REVERT: U 36 LYS cc_start: 0.8326 (ptmt) cc_final: 0.8067 (mmmt) REVERT: U 56 GLU cc_start: 0.8502 (tt0) cc_final: 0.8273 (tt0) REVERT: U 90 ASP cc_start: 0.8247 (t0) cc_final: 0.7995 (t0) REVERT: U 92 GLU cc_start: 0.7561 (mp0) cc_final: 0.7110 (pt0) REVERT: V 105 LYS cc_start: 0.7944 (mtpt) cc_final: 0.7451 (mttp) REVERT: A 60 LYS cc_start: 0.6918 (mttm) cc_final: 0.6279 (ptpt) REVERT: A 189 HIS cc_start: 0.7127 (OUTLIER) cc_final: 0.6171 (p90) REVERT: A 213 GLU cc_start: 0.7398 (tp30) cc_final: 0.7077 (mm-30) REVERT: A 250 VAL cc_start: 0.9091 (p) cc_final: 0.8864 (p) REVERT: A 261 TRP cc_start: 0.7623 (m-10) cc_final: 0.7264 (m-90) REVERT: A 316 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7959 (ptm-80) REVERT: A 325 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7689 (mp0) REVERT: A 373 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.7526 (mtt) REVERT: B 670 GLU cc_start: 0.7845 (mp0) cc_final: 0.6910 (mp0) REVERT: B 684 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7323 (mm-30) REVERT: B 765 MET cc_start: 0.5109 (OUTLIER) cc_final: 0.4673 (pp-130) REVERT: B 799 ARG cc_start: 0.7708 (mmm160) cc_final: 0.6909 (mtt-85) REVERT: B 812 GLU cc_start: 0.7736 (tp30) cc_final: 0.7316 (tp30) REVERT: B 826 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7985 (mmm160) REVERT: B 881 ASP cc_start: 0.8805 (t0) cc_final: 0.8347 (m-30) REVERT: B 918 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7356 (mp0) REVERT: B 982 LYS cc_start: 0.7318 (mttt) cc_final: 0.6793 (mtmm) REVERT: B 1136 PHE cc_start: 0.5992 (OUTLIER) cc_final: 0.5268 (m-10) REVERT: B 1160 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6937 (mp0) REVERT: B 1167 ARG cc_start: 0.8044 (mmp-170) cc_final: 0.7832 (mmp-170) REVERT: B 1185 ASP cc_start: 0.8070 (t0) cc_final: 0.7708 (t0) REVERT: B 1187 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7011 (mm) REVERT: B 1289 GLN cc_start: 0.7458 (pp30) cc_final: 0.7173 (pt0) REVERT: B 1317 ILE cc_start: 0.8244 (pt) cc_final: 0.7993 (mt) REVERT: E 262 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.7449 (t80) REVERT: E 282 PHE cc_start: 0.7133 (m-80) cc_final: 0.6720 (m-80) REVERT: E 355 ASN cc_start: 0.8472 (m-40) cc_final: 0.7167 (t0) REVERT: E 359 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7232 (mm-30) REVERT: E 375 GLU cc_start: 0.8811 (pm20) cc_final: 0.8501 (pm20) REVERT: E 404 ASP cc_start: 0.8526 (m-30) cc_final: 0.8287 (p0) REVERT: E 476 LYS cc_start: 0.7266 (OUTLIER) cc_final: 0.6717 (pmtt) REVERT: E 515 GLN cc_start: 0.7727 (mp10) cc_final: 0.7337 (mp10) REVERT: E 549 TYR cc_start: 0.8421 (OUTLIER) cc_final: 0.7556 (t80) REVERT: E 556 TYR cc_start: 0.8581 (m-10) cc_final: 0.8084 (m-10) REVERT: G 548 LYS cc_start: 0.4291 (mmmt) cc_final: 0.3979 (mmmt) outliers start: 75 outliers final: 37 residues processed: 397 average time/residue: 1.4810 time to fit residues: 678.8684 Evaluate side-chains 377 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 323 time to evaluate : 2.717 ------------------------------------------------------------------------------- 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 295 ASN 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 254 VAL Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain F residue 288 TYR 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 33 SER Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 58 THR 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 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 360 MET 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 765 MET 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 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 E residue 262 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 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 542 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 161 optimal weight: 0.7980 chunk 259 optimal weight: 7.9990 chunk 158 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 180 optimal weight: 0.9990 chunk 271 optimal weight: 1.9990 chunk 250 optimal weight: 3.9990 chunk 216 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 167 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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** R 46 HIS S 39 HIS ** T 25 ASN ** 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** ** 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** B 974 GLN B1222 GLN ** E 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8015 moved from start: 0.5645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 28285 Z= 0.269 Angle : 0.651 16.335 39579 Z= 0.343 Chirality : 0.039 0.371 4370 Planarity : 0.004 0.071 3885 Dihedral : 26.929 177.225 6312 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.33 % Allowed : 30.51 % Favored : 66.16 % 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: -0.21 (0.17), residues: 2447 helix: 0.62 (0.14), residues: 1370 sheet: -0.89 (0.54), residues: 90 loop : -1.08 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B1151 HIS 0.006 0.001 HIS B1254 PHE 0.022 0.001 PHE B 708 TYR 0.027 0.002 TYR D 288 ARG 0.018 0.001 ARG B 799 ********************** 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 407 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 333 time to evaluate : 2.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 82 GLN cc_start: 0.7910 (pp30) cc_final: 0.7613 (pm20) REVERT: D 275 GLN cc_start: 0.6408 (mm110) cc_final: 0.5761 (mt0) REVERT: D 295 ASN cc_start: 0.7069 (OUTLIER) cc_final: 0.6801 (m-40) REVERT: D 354 LEU cc_start: 0.8651 (tm) cc_final: 0.8346 (pp) REVERT: D 375 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.7974 (t0) REVERT: F 22 MET cc_start: 0.1180 (mmm) cc_final: 0.0556 (mtt) REVERT: F 24 GLU cc_start: 0.5470 (mt-10) cc_final: 0.4912 (mm-30) REVERT: F 95 ASP cc_start: 0.2340 (p0) cc_final: 0.2030 (t0) REVERT: F 270 GLU cc_start: 0.0586 (OUTLIER) cc_final: -0.0015 (pm20) REVERT: F 297 LEU cc_start: 0.5191 (pt) cc_final: 0.4561 (tp) REVERT: Q 73 ASN cc_start: 0.8246 (p0) cc_final: 0.7952 (p0) REVERT: Q 90 ASP cc_start: 0.8466 (t70) cc_final: 0.8103 (t0) REVERT: R 30 ARG cc_start: 0.7023 (mtm-85) cc_final: 0.6821 (mtt-85) REVERT: R 90 GLU cc_start: 0.8417 (mp0) cc_final: 0.7830 (mp0) REVERT: R 105 LYS cc_start: 0.8501 (tttm) cc_final: 0.8216 (tttp) REVERT: S 42 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8013 (mtp-110) REVERT: S 64 LYS cc_start: 0.8435 (mptm) cc_final: 0.8162 (mppt) REVERT: S 73 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7894 (tt0) REVERT: S 131 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8199 (mtt180) REVERT: T 25 ASN cc_start: 0.8800 (m-40) cc_final: 0.8246 (m-40) REVERT: U 36 LYS cc_start: 0.8344 (ptmt) cc_final: 0.8081 (mmmt) REVERT: U 56 GLU cc_start: 0.8504 (tt0) cc_final: 0.8281 (tt0) REVERT: U 90 ASP cc_start: 0.8254 (t0) cc_final: 0.8014 (t0) REVERT: U 92 GLU cc_start: 0.7583 (mp0) cc_final: 0.7115 (pt0) REVERT: V 105 LYS cc_start: 0.7975 (mtpt) cc_final: 0.7484 (mttp) REVERT: A 60 LYS cc_start: 0.6943 (mttm) cc_final: 0.6247 (ptpt) REVERT: A 72 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7233 (mp10) REVERT: A 128 MET cc_start: 0.8641 (mtt) cc_final: 0.8417 (ptt) REVERT: A 189 HIS cc_start: 0.7308 (OUTLIER) cc_final: 0.6377 (p90) REVERT: A 250 VAL cc_start: 0.9118 (p) cc_final: 0.8869 (p) REVERT: A 261 TRP cc_start: 0.7704 (m-10) cc_final: 0.7396 (m-90) REVERT: A 306 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.7496 (tmm) REVERT: A 316 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7966 (ptm-80) REVERT: A 325 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7651 (mp0) REVERT: A 373 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7585 (mtt) REVERT: B 670 GLU cc_start: 0.7885 (mp0) cc_final: 0.6967 (mp0) REVERT: B 684 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7332 (mm-30) REVERT: B 765 MET cc_start: 0.5127 (OUTLIER) cc_final: 0.4748 (pp-130) REVERT: B 799 ARG cc_start: 0.7746 (mmm160) cc_final: 0.6933 (mtt-85) REVERT: B 812 GLU cc_start: 0.7781 (tp30) cc_final: 0.7394 (tp30) REVERT: B 826 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7989 (mmm160) REVERT: B 881 ASP cc_start: 0.8829 (t0) cc_final: 0.8372 (m-30) REVERT: B 918 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: B 982 LYS cc_start: 0.7302 (mttt) cc_final: 0.6766 (mtmm) REVERT: B 1136 PHE cc_start: 0.6038 (OUTLIER) cc_final: 0.5337 (m-10) REVERT: B 1160 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: B 1185 ASP cc_start: 0.8102 (t0) cc_final: 0.7737 (t0) REVERT: B 1187 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7016 (mm) REVERT: E 282 PHE cc_start: 0.7179 (m-80) cc_final: 0.6906 (m-80) REVERT: E 355 ASN cc_start: 0.8496 (m-40) cc_final: 0.8044 (m-40) REVERT: E 375 GLU cc_start: 0.8837 (pm20) cc_final: 0.8544 (pm20) REVERT: E 404 ASP cc_start: 0.8540 (m-30) cc_final: 0.8312 (p0) REVERT: E 476 LYS cc_start: 0.7317 (OUTLIER) cc_final: 0.6751 (pmtt) REVERT: E 515 GLN cc_start: 0.7765 (mp10) cc_final: 0.7339 (mp10) REVERT: E 544 GLU cc_start: 0.7531 (tm-30) cc_final: 0.7327 (tm-30) REVERT: E 556 TYR cc_start: 0.8618 (m-10) cc_final: 0.8165 (m-10) REVERT: G 548 LYS cc_start: 0.4311 (mmmt) cc_final: 0.4001 (mmmt) outliers start: 74 outliers final: 40 residues processed: 378 average time/residue: 1.4819 time to fit residues: 646.3414 Evaluate side-chains 380 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 322 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 295 ASN 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 254 VAL 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 33 SER Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain S residue 42 ARG 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 A residue 72 GLN 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 306 MET Chi-restraints excluded: chain A residue 316 ARG 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 699 LEU Chi-restraints excluded: chain B residue 707 ASP Chi-restraints excluded: chain B residue 726 TYR Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 765 MET 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 974 GLN 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 1228 LEU Chi-restraints excluded: chain B residue 1278 THR Chi-restraints excluded: chain E residue 43 ASN 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 172 optimal weight: 0.4980 chunk 230 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 199 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 60 optimal weight: 0.9980 chunk 216 optimal weight: 8.9990 chunk 90 optimal weight: 0.9990 chunk 222 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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** R 46 HIS S 39 HIS T 25 ASN ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN ** 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** B 974 GLN B1222 GLN ** E 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.120418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.088464 restraints weight = 55772.792| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.96 r_work: 0.3073 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.5927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 28285 Z= 0.374 Angle : 0.690 15.749 39579 Z= 0.366 Chirality : 0.042 0.362 4370 Planarity : 0.004 0.066 3885 Dihedral : 27.070 178.308 6312 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.74 % Allowed : 30.24 % Favored : 66.02 % 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: -0.31 (0.17), residues: 2447 helix: 0.51 (0.14), residues: 1363 sheet: -0.95 (0.56), residues: 78 loop : -1.07 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP B1151 HIS 0.008 0.001 HIS B1254 PHE 0.035 0.002 PHE E 341 TYR 0.034 0.002 TYR D 288 ARG 0.016 0.001 ARG B 799 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11373.50 seconds wall clock time: 202 minutes 52.33 seconds (12172.33 seconds total)