Starting phenix.real_space_refine on Wed Jul 24 21:53:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd6_37126/07_2024/8kd6_37126_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd6_37126/07_2024/8kd6_37126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd6_37126/07_2024/8kd6_37126.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd6_37126/07_2024/8kd6_37126.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd6_37126/07_2024/8kd6_37126_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd6_37126/07_2024/8kd6_37126_neut.cif" } resolution = 3.07 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 563 atoms to isotropic. 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 92 5.16 5 C 16098 2.51 5 N 4797 2.21 5 O 5666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ASP 234": "OD1" <-> "OD2" Residue "D TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 290": "OD1" <-> "OD2" Residue "D TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 360": "OE1" <-> "OE2" Residue "D ASP 376": "OD1" <-> "OD2" Residue "D TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 307": "OD1" <-> "OD2" Residue "F GLU 340": "OE1" <-> "OE2" Residue "O ASP 106": "OD1" <-> "OD2" Residue "R TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 73": "OE1" <-> "OE2" Residue "R GLU 102": "OE1" <-> "OE2" Residue "S PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 105": "OE1" <-> "OE2" Residue "U GLU 41": "OE1" <-> "OE2" Residue "U TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 90": "OD1" <-> "OD2" Residue "U GLU 91": "OE1" <-> "OE2" Residue "U GLU 92": "OE1" <-> "OE2" Residue "V GLU 32": "OE1" <-> "OE2" Residue "V GLU 68": "OE1" <-> "OE2" Residue "V TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "A ASP 114": "OD1" <-> "OD2" Residue "A TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 140": "OD1" <-> "OD2" Residue "A ASP 165": "OD1" <-> "OD2" Residue "A TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "B PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 695": "OD1" <-> "OD2" Residue "B TYR 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 776": "OE1" <-> "OE2" Residue "B ASP 818": "OD1" <-> "OD2" Residue "B TYR 871": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 920": "OE1" <-> "OE2" Residue "B PHE 1017": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1160": "OE1" <-> "OE2" Residue "B ASP 1243": "OD1" <-> "OD2" Residue "E PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 323": "OE1" <-> "OE2" Residue "G PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 550": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 26982 Number of models: 1 Model: "" Number of chains: 17 Chain: "D" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1875 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 8, 'TRANS': 221} Chain breaks: 2 Chain: "F" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1627 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain breaks: 2 Chain: "O" 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: "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: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, '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: 4505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4505 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 12, 'TRANS': 524} Chain breaks: 2 Chain: "E" Number of atoms: 2475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2475 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 283} Chain breaks: 5 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 718 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.84, per 1000 atoms: 0.62 Number of scatterers: 26982 At special positions: 0 Unit cell: (138.45, 158.33, 176.08, 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 92 16.00 P 328 15.00 O 5666 8.00 N 4797 7.00 C 16098 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: 12.19 Conformation dependent library (CDL) restraints added in 3.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 188 " 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4724 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 16 sheets defined 58.6% alpha, 3.3% beta 140 base pairs and 270 stacking pairs defined. Time for finding SS restraints: 11.63 Creating SS restraints... Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.611A pdb=" N TRP D 88 " --> pdb=" O LYS D 85 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP D 89 " --> pdb=" O SER D 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 85 through 89' Processing helix chain 'D' and resid 98 through 113 Processing helix chain 'D' and resid 225 through 241 Processing helix chain 'D' and resid 253 through 269 removed outlier: 3.718A pdb=" N LEU D 269 " --> pdb=" O VAL D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 292 Processing helix chain 'D' and resid 302 through 315 Processing helix chain 'D' and resid 327 through 337 removed outlier: 4.042A pdb=" N LEU D 331 " --> pdb=" O GLY D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 344 Processing helix chain 'D' and resid 348 through 369 Processing helix chain 'D' and resid 369 through 374 removed outlier: 3.636A pdb=" N TYR D 373 " --> pdb=" O HIS D 369 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE D 374 " --> pdb=" O VAL D 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 369 through 374' Processing helix chain 'D' and resid 391 through 399 Processing helix chain 'F' and resid 98 through 112 removed outlier: 3.911A pdb=" N GLU F 102 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 239 removed outlier: 3.715A pdb=" N VAL F 233 " --> pdb=" O LYS F 229 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU F 237 " --> pdb=" O VAL F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 262 removed outlier: 4.114A pdb=" N TYR F 261 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLU F 262 " --> pdb=" O LEU F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 290 removed outlier: 4.371A pdb=" N TYR F 281 " --> pdb=" O GLN F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 314 Processing helix chain 'F' and resid 330 through 338 Processing helix chain 'F' and resid 338 through 343 removed outlier: 3.545A pdb=" N SER F 343 " --> pdb=" O PRO F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 348 through 369 removed outlier: 3.994A pdb=" N CYS F 352 " --> pdb=" O ASP F 348 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N MET F 368 " --> pdb=" O VAL F 364 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS F 369 " --> pdb=" O TRP F 365 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 57 removed outlier: 3.556A pdb=" N LYS O 56 " --> pdb=" O ARG O 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 76 Processing helix chain 'O' and resid 85 through 114 removed outlier: 3.564A pdb=" N GLU O 94 " --> pdb=" O MET O 90 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA O 95 " --> pdb=" O ALA O 91 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA O 110 " --> pdb=" O ASP O 106 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA O 111 " --> pdb=" O THR O 107 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE O 112 " --> pdb=" O ASN O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 120 through 132 Processing helix chain 'P' and resid 25 through 29 removed outlier: 3.959A pdb=" N ILE P 29 " --> pdb=" O ILE P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 41 Processing helix chain 'P' and resid 49 through 76 removed outlier: 3.689A pdb=" N GLU P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG P 67 " --> pdb=" O GLU P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 92 removed outlier: 3.592A pdb=" N VAL P 86 " --> pdb=" O THR P 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 21 Processing helix chain 'Q' and resid 26 through 37 Processing helix chain 'Q' and resid 45 through 73 removed outlier: 4.367A pdb=" N VAL Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN Q 73 " --> pdb=" O ALA Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 90 Processing helix chain 'Q' and resid 90 through 97 Processing helix chain 'R' and resid 34 through 46 removed outlier: 3.554A pdb=" N TYR R 39 " --> pdb=" O ALA R 35 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL R 45 " --> pdb=" O VAL R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 81 Processing helix chain 'R' and resid 87 through 99 removed outlier: 3.550A pdb=" N ARG R 96 " --> pdb=" O GLN R 92 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 120 removed outlier: 3.979A pdb=" N HIS R 106 " --> pdb=" O GLU R 102 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA R 107 " --> pdb=" O LEU R 103 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 56 removed outlier: 3.524A pdb=" N LYS S 56 " --> pdb=" O ARG S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 77 removed outlier: 3.525A pdb=" N PHE S 67 " --> pdb=" O ARG S 63 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP S 77 " --> pdb=" O GLU S 73 " (cutoff:3.500A) Processing helix chain 'S' and resid 85 through 114 Processing helix chain 'S' and resid 120 through 132 removed outlier: 3.544A pdb=" N ILE S 124 " --> pdb=" O MET S 120 " (cutoff:3.500A) Processing helix chain 'T' and resid 24 through 29 removed outlier: 3.719A pdb=" N GLN T 27 " --> pdb=" O ASP T 24 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE T 29 " --> pdb=" O ILE T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 30 through 41 Processing helix chain 'T' and resid 49 through 76 removed outlier: 3.627A pdb=" N GLY T 56 " --> pdb=" O GLU T 52 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG T 67 " --> pdb=" O GLU T 63 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA T 76 " --> pdb=" O TYR T 72 " (cutoff:3.500A) Processing helix chain 'T' and resid 82 through 92 Processing helix chain 'U' and resid 16 through 21 removed outlier: 3.556A pdb=" N ARG U 20 " --> pdb=" O THR U 16 " (cutoff:3.500A) Processing helix chain 'U' and resid 26 through 37 removed outlier: 3.608A pdb=" N VAL U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 73 removed outlier: 4.077A pdb=" N VAL U 49 " --> pdb=" O ALA U 45 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN U 73 " --> pdb=" O ALA U 69 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 90 removed outlier: 3.520A pdb=" N ASP U 90 " --> pdb=" O ALA U 86 " (cutoff:3.500A) Processing helix chain 'U' and resid 90 through 97 removed outlier: 3.865A pdb=" N LYS U 95 " --> pdb=" O GLU U 91 " (cutoff:3.500A) Processing helix chain 'V' and resid 34 through 46 removed outlier: 3.520A pdb=" N VAL V 45 " --> pdb=" O VAL V 41 " (cutoff:3.500A) Processing helix chain 'V' and resid 52 through 81 removed outlier: 3.575A pdb=" N ASN V 81 " --> pdb=" O LEU V 77 " (cutoff:3.500A) Processing helix chain 'V' and resid 87 through 99 Processing helix chain 'V' and resid 101 through 119 removed outlier: 4.218A pdb=" N LYS V 105 " --> pdb=" O GLY V 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 55 removed outlier: 4.318A pdb=" N MET A 47 " --> pdb=" O HIS A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 61 removed outlier: 3.567A pdb=" N LYS A 60 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET A 61 " --> pdb=" O TYR A 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 57 through 61' Processing helix chain 'A' and resid 71 through 75 Processing helix chain 'A' and resid 79 through 88 Processing helix chain 'A' and resid 90 through 94 removed outlier: 3.735A pdb=" N ASN A 93 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 94 " --> pdb=" O PRO A 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 90 through 94' Processing helix chain 'A' and resid 98 through 104 removed outlier: 3.568A pdb=" N VAL A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 137 removed outlier: 3.635A pdb=" N TYR A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 175 removed outlier: 3.991A pdb=" N LEU A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 removed outlier: 4.012A pdb=" N GLU A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 243 through 262 Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 274 through 276 No H-bonds generated for 'chain 'A' and resid 274 through 276' Processing helix chain 'A' and resid 287 through 300 removed outlier: 4.007A pdb=" N CYS A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL A 295 " --> pdb=" O HIS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 330 Processing helix chain 'A' and resid 365 through 381 Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'B' and resid 664 through 666 No H-bonds generated for 'chain 'B' and resid 664 through 666' Processing helix chain 'B' and resid 667 through 677 Processing helix chain 'B' and resid 678 through 694 Processing helix chain 'B' and resid 698 through 710 removed outlier: 3.649A pdb=" N PHE B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 725 Processing helix chain 'B' and resid 771 through 778 Processing helix chain 'B' and resid 785 through 791 removed outlier: 3.874A pdb=" N ALA B 789 " --> pdb=" O HIS B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 838 Processing helix chain 'B' and resid 839 through 841 No H-bonds generated for 'chain 'B' and resid 839 through 841' Processing helix chain 'B' and resid 842 through 848 removed outlier: 3.968A pdb=" N ASN B 848 " --> pdb=" O ASN B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 871 Processing helix chain 'B' and resid 872 through 886 removed outlier: 3.925A pdb=" N PHE B 877 " --> pdb=" O LYS B 873 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU B 878 " --> pdb=" O GLU B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 929 removed outlier: 4.046A pdb=" N LYS B 914 " --> pdb=" O ARG B 910 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N VAL B 915 " --> pdb=" O GLU B 911 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N PHE B 925 " --> pdb=" O GLN B 921 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS B 926 " --> pdb=" O LYS B 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 934 through 942 removed outlier: 4.768A pdb=" N LYS B 940 " --> pdb=" O LYS B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 967 Processing helix chain 'B' and resid 982 through 996 removed outlier: 3.979A pdb=" N TYR B 986 " --> pdb=" O LYS B 982 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1022 removed outlier: 3.701A pdb=" N ILE B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE B1022 " --> pdb=" O ILE B1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1164 removed outlier: 4.049A pdb=" N MET B1164 " --> pdb=" O GLU B1160 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1174 removed outlier: 4.047A pdb=" N LYS B1170 " --> pdb=" O GLU B1166 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B1174 " --> pdb=" O LYS B1170 " (cutoff:3.500A) Processing helix chain 'B' and resid 1178 through 1185 Processing helix chain 'B' and resid 1202 through 1217 Processing helix chain 'B' and resid 1221 through 1232 removed outlier: 3.516A pdb=" N TYR B1232 " --> pdb=" O LEU B1228 " (cutoff:3.500A) Processing helix chain 'B' and resid 1236 through 1240 removed outlier: 4.227A pdb=" N LEU B1239 " --> pdb=" O ALA B1236 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR B1240 " --> pdb=" O PHE B1237 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1236 through 1240' Processing helix chain 'B' and resid 1241 through 1259 removed outlier: 3.583A pdb=" N THR B1255 " --> pdb=" O LYS B1251 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU B1256 " --> pdb=" O HIS B1252 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N MET B1257 " --> pdb=" O ALA B1253 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR B1258 " --> pdb=" O HIS B1254 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP B1259 " --> pdb=" O THR B1255 " (cutoff:3.500A) Processing helix chain 'B' and resid 1259 through 1273 Processing helix chain 'B' and resid 1282 through 1294 removed outlier: 3.534A pdb=" N MET B1294 " --> pdb=" O VAL B1290 " (cutoff:3.500A) Processing helix chain 'B' and resid 1307 through 1310 removed outlier: 3.690A pdb=" N LEU B1310 " --> pdb=" O LYS B1307 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1307 through 1310' Processing helix chain 'E' and resid 51 through 55 removed outlier: 3.629A pdb=" N ILE E 54 " --> pdb=" O ARG E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 296 removed outlier: 3.748A pdb=" N LEU E 296 " --> pdb=" O PRO E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 310 Processing helix chain 'E' and resid 321 through 330 Processing helix chain 'E' and resid 333 through 345 removed outlier: 4.221A pdb=" N LYS E 338 " --> pdb=" O LYS E 334 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU E 339 " --> pdb=" O ILE E 335 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP E 344 " --> pdb=" O LEU E 340 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER E 345 " --> pdb=" O PHE E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 361 removed outlier: 3.656A pdb=" N LYS E 358 " --> pdb=" O PRO E 354 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU E 359 " --> pdb=" O ASN E 355 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR E 360 " --> pdb=" O TYR E 356 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE E 361 " --> pdb=" O ILE E 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 354 through 361' Processing helix chain 'E' and resid 402 through 406 Processing helix chain 'E' and resid 430 through 434 Processing helix chain 'E' and resid 543 through 558 Processing helix chain 'G' and resid 305 through 312 Processing helix chain 'G' and resid 321 through 325 removed outlier: 3.586A pdb=" N SER G 324 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN G 325 " --> pdb=" O ILE G 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 321 through 325' Processing helix chain 'G' and resid 337 through 342 removed outlier: 4.191A pdb=" N PHE G 341 " --> pdb=" O ALA G 337 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASN G 342 " --> pdb=" O LYS G 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 337 through 342' Processing helix chain 'G' and resid 541 through 569 Processing sheet with id=AA1, first strand: chain 'D' and resid 244 through 245 Processing sheet with id=AA2, first strand: chain 'O' and resid 83 through 84 removed outlier: 6.644A pdb=" N ARG O 83 " --> pdb=" O VAL P 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'P' and resid 96 through 98 removed outlier: 6.137A pdb=" N THR P 96 " --> pdb=" O THR U 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'Q' and resid 42 through 43 removed outlier: 7.454A pdb=" N ARG Q 42 " --> pdb=" O ILE R 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'Q' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'Q' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'S' and resid 83 through 84 removed outlier: 6.942A pdb=" N ARG S 83 " --> pdb=" O VAL T 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'U' and resid 42 through 43 removed outlier: 6.912A pdb=" N ARG U 42 " --> pdb=" O ILE V 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'U' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'A' and resid 233 through 236 removed outlier: 8.232A pdb=" N VAL A 234 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N THR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL A 236 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N SER A 207 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL A 180 " --> pdb=" O MET A 204 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N CYS A 206 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR A 182 " --> pdb=" O CYS A 206 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N PHE A 208 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ASP A 184 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN A 270 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VAL A 267 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VAL A 308 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N LEU A 269 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N GLY A 310 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N CYS A 271 " --> pdb=" O GLY A 310 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA A 142 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N GLY A 309 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ASN A 144 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N GLY A 311 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA A 22 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU A 62 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR A 64 " --> pdb=" O TYR A 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1136 through 1140 Processing sheet with id=AB3, first strand: chain 'E' and resid 273 through 274 Processing sheet with id=AB4, first strand: chain 'E' and resid 365 through 366 removed outlier: 3.708A pdb=" N SER E 373 " --> pdb=" O LYS E 365 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 437 through 438 Processing sheet with id=AB6, first strand: chain 'E' and resid 505 through 506 removed outlier: 6.350A pdb=" N TYR E 505 " --> pdb=" O ILE E 539 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 521 through 522 removed outlier: 5.809A pdb=" N GLN E 521 " --> pdb=" O ILE E 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 963 hydrogen bonds defined for protein. 2826 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 369 hydrogen bonds 738 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 270 stacking parallelities Total time for adding SS restraints: 15.80 Time building geometry restraints manager: 13.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7513 1.34 - 1.46: 8211 1.46 - 1.58: 11674 1.58 - 1.71: 655 1.71 - 1.83: 144 Bond restraints: 28197 Sorted by residual: bond pdb=" CG PRO E 279 " pdb=" CD PRO E 279 " ideal model delta sigma weight residual 1.503 1.374 0.129 3.40e-02 8.65e+02 1.43e+01 bond pdb=" N PRO E 279 " pdb=" CD PRO E 279 " ideal model delta sigma weight residual 1.473 1.519 -0.046 1.40e-02 5.10e+03 1.08e+01 bond pdb=" CB PRO E 279 " pdb=" CG PRO E 279 " ideal model delta sigma weight residual 1.492 1.646 -0.154 5.00e-02 4.00e+02 9.45e+00 bond pdb=" CB ASP B1185 " pdb=" CG ASP B1185 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.50e-02 1.60e+03 4.06e+00 bond pdb=" N PRO E 279 " pdb=" CA PRO E 279 " ideal model delta sigma weight residual 1.469 1.444 0.025 1.28e-02 6.10e+03 3.67e+00 ... (remaining 28192 not shown) Histogram of bond angle deviations from ideal: 89.18 - 101.91: 329 101.91 - 114.64: 18473 114.64 - 127.37: 19923 127.37 - 140.10: 727 140.10 - 152.82: 1 Bond angle restraints: 39453 Sorted by residual: angle pdb=" N MET F 296 " pdb=" CA MET F 296 " pdb=" C MET F 296 " ideal model delta sigma weight residual 110.80 152.82 -42.02 2.13e+00 2.20e-01 3.89e+02 angle pdb=" N LEU F 297 " pdb=" CA LEU F 297 " pdb=" CB LEU F 297 " ideal model delta sigma weight residual 110.45 89.35 21.10 1.26e+00 6.30e-01 2.80e+02 angle pdb=" CA PRO E 279 " pdb=" N PRO E 279 " pdb=" CD PRO E 279 " ideal model delta sigma weight residual 112.00 94.72 17.28 1.40e+00 5.10e-01 1.52e+02 angle pdb=" C MET F 296 " pdb=" CA MET F 296 " pdb=" CB MET F 296 " ideal model delta sigma weight residual 110.42 89.18 21.24 1.99e+00 2.53e-01 1.14e+02 angle pdb=" N PRO E 279 " pdb=" CD PRO E 279 " pdb=" CG PRO E 279 " ideal model delta sigma weight residual 103.20 92.70 10.50 1.50e+00 4.44e-01 4.90e+01 ... (remaining 39448 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.10: 14045 35.10 - 70.20: 2008 70.20 - 105.30: 59 105.30 - 140.40: 2 140.40 - 175.50: 1 Dihedral angle restraints: 16115 sinusoidal: 8808 harmonic: 7307 Sorted by residual: dihedral pdb=" N MET F 296 " pdb=" C MET F 296 " pdb=" CA MET F 296 " pdb=" CB MET F 296 " ideal model delta harmonic sigma weight residual 122.80 147.99 -25.19 0 2.50e+00 1.60e-01 1.02e+02 dihedral pdb=" N LEU F 297 " pdb=" C LEU F 297 " pdb=" CA LEU F 297 " pdb=" CB LEU F 297 " ideal model delta harmonic sigma weight residual 122.80 97.71 25.09 0 2.50e+00 1.60e-01 1.01e+02 dihedral pdb=" C MET F 296 " pdb=" N MET F 296 " pdb=" CA MET F 296 " pdb=" CB MET F 296 " ideal model delta harmonic sigma weight residual -122.60 -144.67 22.07 0 2.50e+00 1.60e-01 7.79e+01 ... (remaining 16112 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.335: 4353 0.335 - 0.671: 1 0.671 - 1.006: 0 1.006 - 1.341: 0 1.341 - 1.676: 1 Chirality restraints: 4355 Sorted by residual: chirality pdb=" CA MET F 296 " pdb=" N MET F 296 " pdb=" C MET F 296 " pdb=" CB MET F 296 " both_signs ideal model delta sigma weight residual False 2.51 0.83 1.68 2.00e-01 2.50e+01 7.02e+01 chirality pdb=" CA LEU F 297 " pdb=" N LEU F 297 " pdb=" C LEU F 297 " pdb=" CB LEU F 297 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" CA PRO E 279 " pdb=" N PRO E 279 " pdb=" C PRO E 279 " pdb=" CB PRO E 279 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 4352 not shown) Planarity restraints: 3868 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS E 278 " -0.072 5.00e-02 4.00e+02 9.71e-02 1.51e+01 pdb=" N PRO E 279 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO E 279 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO E 279 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B1175 " -0.237 9.50e-02 1.11e+02 1.07e-01 8.41e+00 pdb=" NE ARG B1175 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG B1175 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG B1175 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B1175 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 365 " 0.019 2.00e-02 2.50e+03 1.77e-02 7.81e+00 pdb=" CG TRP D 365 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP D 365 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP D 365 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 365 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 365 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 365 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 365 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 365 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 365 " 0.000 2.00e-02 2.50e+03 ... (remaining 3865 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 111 2.49 - 3.09: 17250 3.09 - 3.70: 45778 3.70 - 4.30: 64072 4.30 - 4.90: 96689 Nonbonded interactions: 223900 Sorted by model distance: nonbonded pdb=" CD2 LEU Q 23 " pdb=" OE1 GLU Q 56 " model vdw 1.891 3.460 nonbonded pdb=" CB ALA A 36 " pdb=" CD2 LEU E 48 " model vdw 2.114 3.880 nonbonded pdb=" CD2 HIS A 188 " pdb="ZN ZN A 501 " model vdw 2.147 1.960 nonbonded pdb=" CB HIS A 188 " pdb="ZN ZN A 501 " model vdw 2.161 2.104 nonbonded pdb=" OG1 THR A 90 " pdb=" OD1 ASN A 93 " model vdw 2.226 2.440 ... (remaining 223895 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 \ 372)) selection = chain 'F' } ncs_group { reference = chain 'O' selection = chain 'S' } ncs_group { reference = chain 'P' selection = chain 'T' } ncs_group { reference = chain 'Q' selection = (chain 'U' and resid 11 through 116) } 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=0.00 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: 27.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.030 Extract box with map and model: 2.360 Check model and map are aligned: 0.000 Set scattering table: 0.120 Process input model: 92.530 Find NCS groups from input model: 0.570 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: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 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 0.154 28197 Z= 0.236 Angle : 0.873 42.023 39453 Z= 0.451 Chirality : 0.050 1.676 4355 Planarity : 0.006 0.107 3868 Dihedral : 24.626 175.502 11388 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.48 % Favored : 95.48 % Rotamer: Outliers : 0.77 % Allowed : 34.89 % Favored : 64.34 % Cbeta Deviations : 0.08 % 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: -1.98 (0.15), residues: 2433 helix: -0.96 (0.13), residues: 1333 sheet: -0.11 (0.64), residues: 84 loop : -1.79 (0.17), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP D 365 HIS 0.019 0.001 HIS D 263 PHE 0.037 0.001 PHE B 669 TYR 0.032 0.001 TYR F 261 ARG 0.021 0.001 ARG B1175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 311 time to evaluate : 2.385 Fit side-chains revert: symmetry clash REVERT: D 223 GLN cc_start: 0.7255 (pp30) cc_final: 0.6886 (pt0) REVERT: F 296 MET cc_start: 0.3825 (mpp) cc_final: 0.2793 (mtt) REVERT: A 255 ILE cc_start: 0.3325 (mm) cc_final: 0.3005 (mm) REVERT: A 368 TYR cc_start: 0.5064 (t80) cc_final: 0.3913 (t80) REVERT: E 316 MET cc_start: 0.6508 (tpt) cc_final: 0.5929 (pmm) REVERT: G 332 ASN cc_start: 0.8113 (m-40) cc_final: 0.7504 (t0) REVERT: G 560 MET cc_start: 0.6012 (tmm) cc_final: 0.5612 (mtp) outliers start: 17 outliers final: 13 residues processed: 320 average time/residue: 0.3785 time to fit residues: 192.8108 Evaluate side-chains 291 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 278 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 261 TYR Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 419 GLN Chi-restraints excluded: chain B residue 1221 HIS Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 321 LYS Chi-restraints excluded: chain E residue 401 TYR Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain G residue 346 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 6.9990 chunk 206 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 213 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 159 optimal weight: 0.1980 chunk 247 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 259 ASN O 93 GLN ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1222 GLN B1254 HIS ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 459 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 28197 Z= 0.242 Angle : 0.582 8.648 39453 Z= 0.316 Chirality : 0.037 0.196 4355 Planarity : 0.004 0.053 3868 Dihedral : 26.368 173.256 6328 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.71 % Allowed : 29.27 % 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: -0.68 (0.16), residues: 2433 helix: 0.34 (0.14), residues: 1351 sheet: 0.16 (0.64), residues: 81 loop : -1.58 (0.18), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 365 HIS 0.008 0.001 HIS P 75 PHE 0.027 0.002 PHE A 160 TYR 0.018 0.002 TYR V 37 ARG 0.008 0.001 ARG R 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 321 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 223 GLN cc_start: 0.7444 (pp30) cc_final: 0.7219 (pt0) REVERT: D 308 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8198 (pp20) REVERT: D 311 LYS cc_start: 0.8386 (pttt) cc_final: 0.8069 (pttt) REVERT: D 395 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6843 (mt-10) REVERT: F 296 MET cc_start: 0.4275 (mpp) cc_final: 0.4000 (mmt) REVERT: O 37 LYS cc_start: 0.7499 (tppp) cc_final: 0.6364 (tptp) REVERT: O 59 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6096 (pm20) REVERT: P 59 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8035 (ttmt) REVERT: R 65 ASP cc_start: 0.8442 (t0) cc_final: 0.8143 (t0) REVERT: S 42 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.6751 (pmm-80) REVERT: S 59 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.6973 (pp20) REVERT: S 97 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7982 (mt-10) REVERT: S 115 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8416 (mptt) REVERT: U 56 GLU cc_start: 0.8047 (tt0) cc_final: 0.7843 (tt0) REVERT: V 54 LYS cc_start: 0.8586 (mmtt) cc_final: 0.8180 (mmmt) REVERT: V 65 ASP cc_start: 0.8678 (t70) cc_final: 0.8375 (t0) REVERT: A 88 ARG cc_start: 0.7395 (mtm110) cc_final: 0.7012 (mtm110) REVERT: A 140 ASP cc_start: 0.6742 (t0) cc_final: 0.6274 (t0) REVERT: A 172 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.5786 (tm-30) REVERT: A 199 THR cc_start: 0.6815 (p) cc_final: 0.6574 (p) REVERT: A 280 ARG cc_start: 0.6065 (OUTLIER) cc_final: 0.5516 (mtm-85) REVERT: A 350 ASP cc_start: 0.8225 (p0) cc_final: 0.7983 (p0) REVERT: A 360 MET cc_start: 0.8076 (mmt) cc_final: 0.7867 (mmm) REVERT: B 694 GLN cc_start: 0.7368 (OUTLIER) cc_final: 0.6877 (tp40) REVERT: B 890 THR cc_start: 0.3690 (OUTLIER) cc_final: 0.3409 (t) REVERT: B 1164 MET cc_start: 0.7910 (ppp) cc_final: 0.7602 (ppp) REVERT: E 305 GLU cc_start: 0.5275 (OUTLIER) cc_final: 0.4900 (pp20) REVERT: G 560 MET cc_start: 0.6049 (tmm) cc_final: 0.5615 (mtm) outliers start: 104 outliers final: 49 residues processed: 389 average time/residue: 0.4032 time to fit residues: 243.8206 Evaluate side-chains 341 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 280 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 373 TYR Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain P residue 59 LYS Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain R residue 53 SER Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 56 LYS Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 92 LEU Chi-restraints excluded: chain S residue 115 LYS Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 91 GLU Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 694 GLN Chi-restraints excluded: chain B residue 890 THR Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 999 THR Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1221 HIS Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 321 LYS Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 401 TYR Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 505 TYR Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain G residue 346 HIS 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: 0.8980 chunk 168 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 268 optimal weight: 6.9990 chunk 221 optimal weight: 3.9990 chunk 246 optimal weight: 5.9990 chunk 84 optimal weight: 0.0980 chunk 199 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 ASN D 275 GLN D 350 GLN R 64 ASN ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1150 HIS ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 294 ASN ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 28197 Z= 0.327 Angle : 0.647 11.961 39453 Z= 0.350 Chirality : 0.041 0.185 4355 Planarity : 0.005 0.074 3868 Dihedral : 26.998 175.026 6316 Min Nonbonded Distance : 1.563 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 5.48 % Allowed : 27.32 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.17), residues: 2433 helix: 0.60 (0.14), residues: 1340 sheet: -0.82 (0.53), residues: 104 loop : -1.54 (0.18), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 365 HIS 0.022 0.002 HIS F 330 PHE 0.029 0.002 PHE E 311 TYR 0.041 0.002 TYR F 261 ARG 0.009 0.001 ARG R 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 334 time to evaluate : 2.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 295 ASN cc_start: 0.4785 (t0) cc_final: 0.4247 (t0) REVERT: D 305 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.7035 (tt0) REVERT: D 308 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8159 (pp20) REVERT: D 311 LYS cc_start: 0.8529 (pttt) cc_final: 0.8205 (pttt) REVERT: D 324 ARG cc_start: 0.7498 (mmt-90) cc_final: 0.6974 (mmt-90) REVERT: D 347 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.6880 (pmt) REVERT: F 241 LYS cc_start: 0.3128 (OUTLIER) cc_final: 0.2355 (mmtm) REVERT: F 296 MET cc_start: 0.4630 (mpp) cc_final: 0.4340 (mmt) REVERT: F 347 MET cc_start: 0.5698 (pmm) cc_final: 0.5228 (mpp) REVERT: F 363 LEU cc_start: 0.8796 (mt) cc_final: 0.8362 (tp) REVERT: O 106 ASP cc_start: 0.8085 (m-30) cc_final: 0.7738 (m-30) REVERT: P 31 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8769 (tttp) REVERT: Q 36 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8004 (ttpp) REVERT: R 31 LYS cc_start: 0.7036 (OUTLIER) cc_final: 0.6089 (ptpt) REVERT: S 59 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7272 (pp20) REVERT: S 77 ASP cc_start: 0.8536 (m-30) cc_final: 0.8216 (m-30) REVERT: T 63 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7844 (mt-10) REVERT: U 56 GLU cc_start: 0.8332 (tt0) cc_final: 0.7996 (tt0) REVERT: V 65 ASP cc_start: 0.8665 (t70) cc_final: 0.8462 (t0) REVERT: A 88 ARG cc_start: 0.7898 (mtm110) cc_final: 0.7396 (mtm110) REVERT: A 140 ASP cc_start: 0.6941 (t0) cc_final: 0.6370 (t0) REVERT: A 172 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.6378 (tm-30) REVERT: A 270 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.6867 (tm-30) REVERT: A 344 TYR cc_start: 0.7670 (t80) cc_final: 0.7218 (t80) REVERT: A 350 ASP cc_start: 0.8373 (p0) cc_final: 0.8147 (p0) REVERT: A 353 LEU cc_start: 0.8248 (tp) cc_final: 0.7988 (tt) REVERT: A 412 LYS cc_start: 0.8114 (tppt) cc_final: 0.7908 (tppt) REVERT: B 704 GLU cc_start: 0.8260 (pp20) cc_final: 0.7819 (pp20) REVERT: B 775 TRP cc_start: 0.7517 (m100) cc_final: 0.7178 (m100) REVERT: B 1257 MET cc_start: 0.5795 (OUTLIER) cc_final: 0.5440 (mmt) REVERT: B 1300 MET cc_start: 0.5829 (mmt) cc_final: 0.5603 (mmt) REVERT: E 305 GLU cc_start: 0.5517 (OUTLIER) cc_final: 0.5275 (pp20) REVERT: E 316 MET cc_start: 0.6453 (tpt) cc_final: 0.6238 (mtt) REVERT: E 474 VAL cc_start: 0.6272 (m) cc_final: 0.6051 (t) REVERT: G 560 MET cc_start: 0.6350 (tmm) cc_final: 0.5927 (mtm) outliers start: 121 outliers final: 57 residues processed: 414 average time/residue: 0.4121 time to fit residues: 262.1446 Evaluate side-chains 361 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 292 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 275 GLN Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 352 CYS Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain P residue 31 LYS Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 36 LYS Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain R residue 31 LYS Chi-restraints excluded: chain S residue 56 LYS Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 92 LEU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain V residue 46 HIS Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 999 THR Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1249 LEU Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 321 LYS Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 505 TYR Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain G residue 346 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 245 optimal weight: 6.9990 chunk 186 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 249 optimal weight: 0.7980 chunk 263 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 236 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 263 HIS S 108 ASN ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1299 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 28197 Z= 0.327 Angle : 0.614 10.759 39453 Z= 0.335 Chirality : 0.040 0.230 4355 Planarity : 0.005 0.106 3868 Dihedral : 27.057 176.705 6310 Min Nonbonded Distance : 1.666 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.44 % Allowed : 27.91 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.17), residues: 2433 helix: 0.77 (0.14), residues: 1342 sheet: -1.30 (0.49), residues: 114 loop : -1.50 (0.18), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B1151 HIS 0.005 0.001 HIS A 151 PHE 0.016 0.002 PHE S 78 TYR 0.019 0.002 TYR B 692 ARG 0.013 0.001 ARG B1175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 319 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 82 GLN cc_start: 0.7547 (pm20) cc_final: 0.7157 (pm20) REVERT: D 243 LYS cc_start: 0.7828 (mmmm) cc_final: 0.7473 (mmtm) REVERT: D 263 HIS cc_start: 0.7696 (m90) cc_final: 0.7321 (m170) REVERT: D 295 ASN cc_start: 0.5165 (t0) cc_final: 0.4678 (t0) REVERT: D 311 LYS cc_start: 0.8602 (pttt) cc_final: 0.8268 (pttt) REVERT: D 347 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6777 (pmt) REVERT: F 241 LYS cc_start: 0.3039 (OUTLIER) cc_final: 0.2224 (mmtm) REVERT: F 296 MET cc_start: 0.4409 (mpp) cc_final: 0.4083 (mmt) REVERT: F 309 LEU cc_start: 0.2099 (OUTLIER) cc_final: 0.1824 (tt) REVERT: O 106 ASP cc_start: 0.8044 (m-30) cc_final: 0.7761 (m-30) REVERT: Q 36 LYS cc_start: 0.8506 (ptmt) cc_final: 0.8143 (ttpp) REVERT: Q 71 ARG cc_start: 0.7955 (ptp-110) cc_final: 0.7704 (ptp-170) REVERT: Q 113 SER cc_start: 0.8707 (m) cc_final: 0.8417 (p) REVERT: R 31 LYS cc_start: 0.7098 (OUTLIER) cc_final: 0.6119 (ptpt) REVERT: S 77 ASP cc_start: 0.8589 (m-30) cc_final: 0.8364 (m-30) REVERT: U 56 GLU cc_start: 0.8336 (tt0) cc_final: 0.8046 (tt0) REVERT: A 172 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.6511 (tm-30) REVERT: A 280 ARG cc_start: 0.6706 (OUTLIER) cc_final: 0.6493 (ttm170) REVERT: A 353 LEU cc_start: 0.8566 (tp) cc_final: 0.8210 (tt) REVERT: A 360 MET cc_start: 0.8225 (mmm) cc_final: 0.7944 (mmm) REVERT: B 704 GLU cc_start: 0.8450 (pp20) cc_final: 0.7952 (pp20) REVERT: B 809 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.7028 (ptpt) REVERT: B 912 TRP cc_start: 0.8100 (m100) cc_final: 0.7625 (m100) REVERT: B 1164 MET cc_start: 0.8432 (ppp) cc_final: 0.8125 (ppp) REVERT: B 1257 MET cc_start: 0.5714 (OUTLIER) cc_final: 0.5332 (mmt) REVERT: B 1289 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.8052 (pp30) REVERT: E 305 GLU cc_start: 0.5391 (OUTLIER) cc_final: 0.5146 (pp20) REVERT: E 316 MET cc_start: 0.6624 (tpt) cc_final: 0.5986 (pmm) outliers start: 98 outliers final: 60 residues processed: 383 average time/residue: 0.4174 time to fit residues: 247.7283 Evaluate side-chains 362 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 292 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain R residue 31 LYS Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 56 LYS Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain S residue 92 LEU Chi-restraints excluded: chain S residue 124 ILE 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 32 GLU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 809 LYS Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1197 ASP Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1249 LEU Chi-restraints excluded: chain B residue 1250 VAL Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain B residue 1289 GLN Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 321 LYS Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 505 TYR Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain G residue 346 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 219 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 chunk 3 optimal weight: 0.0270 chunk 196 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 225 optimal weight: 2.9990 chunk 182 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 134 optimal weight: 1.9990 chunk 236 optimal weight: 5.9990 chunk 66 optimal weight: 0.3980 overall best weight: 1.8844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 ASN D 350 GLN ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1150 HIS ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 ASN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.5697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 28197 Z= 0.361 Angle : 0.643 11.344 39453 Z= 0.351 Chirality : 0.042 0.316 4355 Planarity : 0.004 0.094 3868 Dihedral : 27.386 176.457 6310 Min Nonbonded Distance : 1.628 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 5.98 % Allowed : 27.10 % Favored : 66.92 % 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: -0.40 (0.17), residues: 2433 helix: 0.65 (0.14), residues: 1363 sheet: -1.38 (0.51), residues: 104 loop : -1.42 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 916 HIS 0.007 0.001 HIS B1252 PHE 0.019 0.002 PHE B 764 TYR 0.028 0.002 TYR T 88 ARG 0.011 0.001 ARG U 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 317 time to evaluate : 2.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 295 ASN cc_start: 0.5767 (t0) cc_final: 0.4431 (t0) REVERT: D 296 MET cc_start: 0.6005 (mpt) cc_final: 0.4977 (mpt) REVERT: D 311 LYS cc_start: 0.8650 (pttt) cc_final: 0.8364 (ptpt) REVERT: D 347 MET cc_start: 0.7027 (OUTLIER) cc_final: 0.6687 (pmt) REVERT: D 381 ARG cc_start: 0.8147 (ptp90) cc_final: 0.7930 (ptp90) REVERT: F 241 LYS cc_start: 0.3122 (OUTLIER) cc_final: 0.2308 (mmtm) REVERT: F 296 MET cc_start: 0.4460 (mpp) cc_final: 0.4142 (mmt) REVERT: F 309 LEU cc_start: 0.1477 (OUTLIER) cc_final: 0.1154 (tt) REVERT: F 361 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7766 (m-30) REVERT: F 363 LEU cc_start: 0.8685 (mp) cc_final: 0.8273 (tp) REVERT: O 37 LYS cc_start: 0.7852 (tppt) cc_final: 0.7460 (tppt) REVERT: O 106 ASP cc_start: 0.8068 (m-30) cc_final: 0.7775 (m-30) REVERT: P 31 LYS cc_start: 0.8904 (tttp) cc_final: 0.8611 (tttm) REVERT: Q 36 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8141 (ttpp) REVERT: Q 113 SER cc_start: 0.8807 (m) cc_final: 0.8563 (p) REVERT: R 31 LYS cc_start: 0.7190 (OUTLIER) cc_final: 0.6189 (ptpt) REVERT: R 105 LYS cc_start: 0.8545 (pptt) cc_final: 0.8256 (pttp) REVERT: S 59 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7288 (pp20) REVERT: S 77 ASP cc_start: 0.8601 (m-30) cc_final: 0.8392 (m-30) REVERT: S 115 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8521 (mptt) REVERT: U 56 GLU cc_start: 0.8337 (tt0) cc_final: 0.8063 (tt0) REVERT: V 65 ASP cc_start: 0.8629 (t0) cc_final: 0.8391 (t0) REVERT: A 172 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.6758 (tm-30) REVERT: A 186 ASP cc_start: 0.6508 (OUTLIER) cc_final: 0.5909 (p0) REVERT: A 213 GLU cc_start: 0.7240 (tp30) cc_final: 0.6856 (tp30) REVERT: A 338 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7891 (tp) REVERT: A 353 LEU cc_start: 0.8633 (tp) cc_final: 0.8118 (tt) REVERT: B 704 GLU cc_start: 0.8581 (pp20) cc_final: 0.8106 (pp20) REVERT: B 722 ASN cc_start: 0.8232 (m110) cc_final: 0.7985 (m110) REVERT: B 809 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7563 (ptpt) REVERT: B 912 TRP cc_start: 0.8128 (m100) cc_final: 0.7734 (m100) REVERT: B 1164 MET cc_start: 0.8156 (ppp) cc_final: 0.7690 (ppp) REVERT: B 1257 MET cc_start: 0.5841 (OUTLIER) cc_final: 0.5423 (mmt) REVERT: E 305 GLU cc_start: 0.5602 (OUTLIER) cc_final: 0.5357 (pp20) REVERT: E 316 MET cc_start: 0.6603 (tpt) cc_final: 0.5995 (pmm) REVERT: E 473 LYS cc_start: 0.7514 (ptmt) cc_final: 0.7077 (ptmt) REVERT: G 560 MET cc_start: 0.6548 (tmm) cc_final: 0.6118 (mtp) outliers start: 132 outliers final: 81 residues processed: 408 average time/residue: 0.4102 time to fit residues: 258.0499 Evaluate side-chains 386 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 291 time to evaluate : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 352 CYS Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain O residue 90 MET Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 36 LYS Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain R residue 31 LYS Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 56 LYS Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain S residue 92 LEU Chi-restraints excluded: chain S residue 115 LYS Chi-restraints excluded: chain S residue 124 ILE Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain V residue 46 HIS Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 809 LYS Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 999 THR Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain B residue 1197 ASP Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1249 LEU Chi-restraints excluded: chain B residue 1250 VAL Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain B residue 1289 GLN Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 321 LYS Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 505 TYR Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain G residue 346 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 88 optimal weight: 0.5980 chunk 237 optimal weight: 20.0000 chunk 52 optimal weight: 0.4980 chunk 154 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 264 optimal weight: 1.9990 chunk 219 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 87 optimal weight: 0.0980 chunk 138 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 350 GLN O 108 ASN ** T 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 ASN ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28197 Z= 0.183 Angle : 0.569 10.215 39453 Z= 0.312 Chirality : 0.038 0.307 4355 Planarity : 0.004 0.087 3868 Dihedral : 27.098 177.455 6310 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.35 % Allowed : 28.45 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.17), residues: 2433 helix: 0.94 (0.14), residues: 1361 sheet: -1.28 (0.51), residues: 104 loop : -1.38 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 916 HIS 0.021 0.001 HIS E 283 PHE 0.016 0.001 PHE B 669 TYR 0.033 0.001 TYR T 88 ARG 0.013 0.000 ARG U 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 319 time to evaluate : 2.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 295 ASN cc_start: 0.5603 (t0) cc_final: 0.4240 (t0) REVERT: D 296 MET cc_start: 0.5801 (mpt) cc_final: 0.4783 (mpt) REVERT: D 311 LYS cc_start: 0.8605 (pttt) cc_final: 0.8322 (ptpt) REVERT: D 324 ARG cc_start: 0.7601 (mmt-90) cc_final: 0.7114 (mmt-90) REVERT: D 347 MET cc_start: 0.6992 (OUTLIER) cc_final: 0.6652 (pmt) REVERT: F 241 LYS cc_start: 0.3022 (OUTLIER) cc_final: 0.2187 (mmtm) REVERT: F 296 MET cc_start: 0.4335 (mpp) cc_final: 0.4035 (mmt) REVERT: F 309 LEU cc_start: 0.2216 (OUTLIER) cc_final: 0.1945 (tt) REVERT: F 361 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7773 (m-30) REVERT: F 363 LEU cc_start: 0.8716 (mp) cc_final: 0.8239 (tp) REVERT: O 37 LYS cc_start: 0.7767 (tppt) cc_final: 0.7352 (tppt) REVERT: O 87 SER cc_start: 0.9082 (t) cc_final: 0.8774 (p) REVERT: O 106 ASP cc_start: 0.7931 (m-30) cc_final: 0.7615 (m-30) REVERT: Q 113 SER cc_start: 0.8804 (m) cc_final: 0.8533 (p) REVERT: Q 114 VAL cc_start: 0.9245 (p) cc_final: 0.8985 (m) REVERT: R 65 ASP cc_start: 0.8578 (t0) cc_final: 0.8048 (t0) REVERT: R 105 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8212 (pttp) REVERT: S 59 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7228 (pp20) REVERT: S 77 ASP cc_start: 0.8599 (m-30) cc_final: 0.8374 (m-30) REVERT: S 115 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8519 (mptt) REVERT: T 92 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8398 (ptm160) REVERT: U 56 GLU cc_start: 0.8324 (tt0) cc_final: 0.8074 (tt0) REVERT: V 65 ASP cc_start: 0.8627 (t0) cc_final: 0.8366 (t0) REVERT: A 134 LEU cc_start: 0.8530 (mp) cc_final: 0.8207 (mp) REVERT: A 213 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6603 (tp30) REVERT: A 259 MET cc_start: 0.8659 (mmt) cc_final: 0.8458 (mmm) REVERT: A 353 LEU cc_start: 0.8741 (tp) cc_final: 0.8165 (tt) REVERT: A 360 MET cc_start: 0.8314 (mmm) cc_final: 0.8095 (mmm) REVERT: A 420 TYR cc_start: 0.7532 (t80) cc_final: 0.7259 (t80) REVERT: B 704 GLU cc_start: 0.8562 (pp20) cc_final: 0.8032 (pp20) REVERT: B 722 ASN cc_start: 0.8211 (m110) cc_final: 0.7972 (m110) REVERT: B 912 TRP cc_start: 0.8205 (m100) cc_final: 0.7828 (m100) REVERT: B 1164 MET cc_start: 0.8173 (ppp) cc_final: 0.7831 (ppp) REVERT: B 1257 MET cc_start: 0.5789 (OUTLIER) cc_final: 0.5153 (tpt) REVERT: E 305 GLU cc_start: 0.5662 (OUTLIER) cc_final: 0.5420 (pp20) REVERT: E 316 MET cc_start: 0.6672 (tpt) cc_final: 0.6047 (pmm) REVERT: E 473 LYS cc_start: 0.7426 (ptmt) cc_final: 0.6986 (ptmt) REVERT: E 493 LYS cc_start: 0.7837 (mmmt) cc_final: 0.7624 (mmtt) REVERT: G 560 MET cc_start: 0.6469 (tmm) cc_final: 0.5930 (mtm) outliers start: 96 outliers final: 61 residues processed: 383 average time/residue: 0.4192 time to fit residues: 246.7485 Evaluate side-chains 363 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 291 time to evaluate : 2.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain R residue 105 LYS Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 56 LYS Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain S residue 115 LYS Chi-restraints excluded: chain S residue 124 ILE Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 92 ARG 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 79 ILE Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1197 ASP Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 307 LYS Chi-restraints excluded: chain E residue 321 LYS Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 505 TYR Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain G residue 346 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 254 optimal weight: 0.9990 chunk 29 optimal weight: 0.0670 chunk 150 optimal weight: 3.9990 chunk 192 optimal weight: 0.9980 chunk 149 optimal weight: 7.9990 chunk 222 optimal weight: 9.9990 chunk 147 optimal weight: 0.6980 chunk 263 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 160 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 350 GLN ** T 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28197 Z= 0.200 Angle : 0.574 11.117 39453 Z= 0.312 Chirality : 0.038 0.302 4355 Planarity : 0.004 0.079 3868 Dihedral : 27.007 177.842 6310 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.21 % Allowed : 28.59 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.17), residues: 2433 helix: 1.10 (0.14), residues: 1349 sheet: -1.23 (0.51), residues: 104 loop : -1.29 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 719 HIS 0.005 0.001 HIS A 38 PHE 0.022 0.001 PHE A 208 TYR 0.019 0.001 TYR F 261 ARG 0.014 0.000 ARG U 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 315 time to evaluate : 2.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 295 ASN cc_start: 0.5597 (t0) cc_final: 0.5274 (t0) REVERT: D 324 ARG cc_start: 0.7585 (mmt-90) cc_final: 0.7106 (mmt-90) REVERT: D 347 MET cc_start: 0.6984 (OUTLIER) cc_final: 0.6647 (pmt) REVERT: F 241 LYS cc_start: 0.3028 (OUTLIER) cc_final: 0.2199 (mmtm) REVERT: F 296 MET cc_start: 0.4388 (mpp) cc_final: 0.4077 (mmt) REVERT: F 309 LEU cc_start: 0.2178 (OUTLIER) cc_final: 0.1884 (tt) REVERT: O 37 LYS cc_start: 0.7785 (tppt) cc_final: 0.7357 (tppt) REVERT: O 106 ASP cc_start: 0.7928 (m-30) cc_final: 0.7629 (m-30) REVERT: P 92 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8043 (ptm160) REVERT: Q 113 SER cc_start: 0.8811 (m) cc_final: 0.8546 (p) REVERT: Q 114 VAL cc_start: 0.9253 (p) cc_final: 0.9003 (m) REVERT: R 31 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6122 (ptpt) REVERT: R 65 ASP cc_start: 0.8571 (t0) cc_final: 0.8045 (t0) REVERT: R 90 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7736 (mp0) REVERT: R 105 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8216 (pttp) REVERT: S 59 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7238 (pp20) REVERT: S 77 ASP cc_start: 0.8606 (m-30) cc_final: 0.8380 (m-30) REVERT: S 115 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8486 (mptt) REVERT: T 88 TYR cc_start: 0.8564 (m-80) cc_final: 0.8359 (m-10) REVERT: T 92 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.8343 (ptm160) REVERT: U 51 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8563 (tp) REVERT: U 56 GLU cc_start: 0.8320 (tt0) cc_final: 0.8044 (tt0) REVERT: V 65 ASP cc_start: 0.8639 (t0) cc_final: 0.8373 (t0) REVERT: A 156 GLU cc_start: 0.8091 (tp30) cc_final: 0.7820 (tp30) REVERT: A 213 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6648 (tp30) REVERT: A 259 MET cc_start: 0.8641 (mmt) cc_final: 0.8399 (mmm) REVERT: A 353 LEU cc_start: 0.8537 (tp) cc_final: 0.8170 (tt) REVERT: A 420 TYR cc_start: 0.7552 (t80) cc_final: 0.7289 (t80) REVERT: B 704 GLU cc_start: 0.8597 (pp20) cc_final: 0.8031 (pp20) REVERT: B 722 ASN cc_start: 0.8224 (m110) cc_final: 0.7979 (m110) REVERT: B 912 TRP cc_start: 0.8224 (m100) cc_final: 0.7745 (m100) REVERT: B 916 TRP cc_start: 0.7542 (m-10) cc_final: 0.7268 (m-10) REVERT: B 1164 MET cc_start: 0.8187 (ppp) cc_final: 0.7827 (ppp) REVERT: B 1257 MET cc_start: 0.5858 (OUTLIER) cc_final: 0.5162 (tpp) REVERT: E 305 GLU cc_start: 0.5635 (OUTLIER) cc_final: 0.5365 (pp20) REVERT: E 316 MET cc_start: 0.6626 (tpt) cc_final: 0.6006 (pmm) REVERT: E 473 LYS cc_start: 0.7507 (ptmt) cc_final: 0.7082 (ptmt) REVERT: G 560 MET cc_start: 0.6597 (tmm) cc_final: 0.6038 (mtm) outliers start: 93 outliers final: 63 residues processed: 372 average time/residue: 0.4377 time to fit residues: 253.0827 Evaluate side-chains 378 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 301 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain P residue 92 ARG Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain R residue 31 LYS Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain R residue 105 LYS Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 56 LYS Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain S residue 115 LYS Chi-restraints excluded: chain S residue 124 ILE Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 92 ARG Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1197 ASP Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 321 LYS Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 505 TYR Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain G residue 316 MET Chi-restraints excluded: chain G residue 346 HIS 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: 0.6980 chunk 157 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 167 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 206 optimal weight: 3.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.5930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 28197 Z= 0.280 Angle : 0.611 12.691 39453 Z= 0.329 Chirality : 0.040 0.289 4355 Planarity : 0.004 0.083 3868 Dihedral : 27.150 176.732 6310 Min Nonbonded Distance : 1.674 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.30 % Allowed : 28.45 % Favored : 67.24 % 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: -0.01 (0.17), residues: 2433 helix: 1.00 (0.14), residues: 1350 sheet: -1.35 (0.50), residues: 104 loop : -1.27 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 719 HIS 0.005 0.001 HIS B1252 PHE 0.023 0.001 PHE A 208 TYR 0.019 0.001 TYR F 261 ARG 0.013 0.000 ARG U 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 304 time to evaluate : 2.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 295 ASN cc_start: 0.5827 (t0) cc_final: 0.5531 (t0) REVERT: D 311 LYS cc_start: 0.8647 (pttt) cc_final: 0.8374 (ptpt) REVERT: D 324 ARG cc_start: 0.7630 (mmt-90) cc_final: 0.7163 (mmt-90) REVERT: D 347 MET cc_start: 0.6973 (OUTLIER) cc_final: 0.6642 (pmt) REVERT: D 360 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: F 241 LYS cc_start: 0.3121 (OUTLIER) cc_final: 0.2252 (mmtm) REVERT: F 296 MET cc_start: 0.4471 (mpp) cc_final: 0.4125 (mmt) REVERT: F 309 LEU cc_start: 0.2148 (OUTLIER) cc_final: 0.1884 (tt) REVERT: F 363 LEU cc_start: 0.8710 (mp) cc_final: 0.8252 (tt) REVERT: O 37 LYS cc_start: 0.7851 (tppt) cc_final: 0.7413 (tppt) REVERT: O 106 ASP cc_start: 0.8034 (m-30) cc_final: 0.7735 (m-30) REVERT: P 92 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8112 (ptm160) REVERT: Q 113 SER cc_start: 0.8848 (m) cc_final: 0.8613 (p) REVERT: Q 114 VAL cc_start: 0.9251 (p) cc_final: 0.9001 (m) REVERT: R 31 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.6351 (pttt) REVERT: R 105 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8200 (pttp) REVERT: S 59 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7284 (pp20) REVERT: S 77 ASP cc_start: 0.8602 (m-30) cc_final: 0.8386 (m-30) REVERT: S 115 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8484 (mptt) REVERT: T 92 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8324 (ptm160) REVERT: U 41 GLU cc_start: 0.8020 (mp0) cc_final: 0.7766 (mp0) REVERT: U 56 GLU cc_start: 0.8322 (tt0) cc_final: 0.8076 (tt0) REVERT: V 39 TYR cc_start: 0.7983 (t80) cc_final: 0.7564 (t80) REVERT: V 65 ASP cc_start: 0.8645 (t0) cc_final: 0.8289 (t0) REVERT: A 156 GLU cc_start: 0.8182 (tp30) cc_final: 0.7970 (tp30) REVERT: A 186 ASP cc_start: 0.6367 (OUTLIER) cc_final: 0.5826 (p0) REVERT: A 213 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6783 (tp30) REVERT: A 353 LEU cc_start: 0.8556 (tp) cc_final: 0.8211 (tt) REVERT: B 704 GLU cc_start: 0.8625 (pp20) cc_final: 0.8052 (pp20) REVERT: B 722 ASN cc_start: 0.8229 (m110) cc_final: 0.7935 (m-40) REVERT: B 912 TRP cc_start: 0.8300 (m100) cc_final: 0.7816 (m100) REVERT: B 1164 MET cc_start: 0.8222 (ppp) cc_final: 0.7770 (ppp) REVERT: B 1257 MET cc_start: 0.5929 (OUTLIER) cc_final: 0.5283 (tpp) REVERT: E 305 GLU cc_start: 0.5726 (OUTLIER) cc_final: 0.5462 (pp20) REVERT: E 316 MET cc_start: 0.6655 (tpt) cc_final: 0.6002 (pmm) REVERT: E 473 LYS cc_start: 0.7600 (ptmt) cc_final: 0.7235 (ptmt) REVERT: E 493 LYS cc_start: 0.7766 (mmmt) cc_final: 0.7419 (mmmt) REVERT: G 560 MET cc_start: 0.6695 (tmm) cc_final: 0.6120 (mtm) outliers start: 95 outliers final: 66 residues processed: 367 average time/residue: 0.4214 time to fit residues: 238.2537 Evaluate side-chains 376 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 296 time to evaluate : 2.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain P residue 92 ARG Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain R residue 31 LYS Chi-restraints excluded: chain R residue 105 LYS Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 56 LYS Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain S residue 115 LYS Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 92 ARG Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 64 GLU Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1197 ASP Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 321 LYS Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 505 TYR Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain G residue 346 HIS 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: 8.9990 chunk 229 optimal weight: 0.7980 chunk 245 optimal weight: 9.9990 chunk 147 optimal weight: 0.6980 chunk 106 optimal weight: 0.5980 chunk 192 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 221 optimal weight: 8.9990 chunk 231 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 350 GLN ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.5910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28197 Z= 0.207 Angle : 0.589 11.040 39453 Z= 0.318 Chirality : 0.038 0.285 4355 Planarity : 0.004 0.086 3868 Dihedral : 27.016 177.075 6310 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.94 % Allowed : 28.95 % Favored : 67.10 % 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: 0.10 (0.17), residues: 2433 helix: 1.10 (0.14), residues: 1344 sheet: -1.29 (0.51), residues: 104 loop : -1.22 (0.20), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 719 HIS 0.006 0.001 HIS R 46 PHE 0.018 0.001 PHE A 208 TYR 0.036 0.001 TYR T 88 ARG 0.014 0.000 ARG U 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 316 time to evaluate : 2.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 295 ASN cc_start: 0.5728 (t0) cc_final: 0.5444 (t0) REVERT: D 311 LYS cc_start: 0.8635 (pttt) cc_final: 0.8380 (ptpt) REVERT: D 324 ARG cc_start: 0.7586 (mmt-90) cc_final: 0.7124 (mmt-90) REVERT: D 347 MET cc_start: 0.6948 (OUTLIER) cc_final: 0.6616 (pmt) REVERT: F 241 LYS cc_start: 0.3097 (OUTLIER) cc_final: 0.2242 (mmtm) REVERT: F 296 MET cc_start: 0.4476 (mpp) cc_final: 0.4105 (mmt) REVERT: F 309 LEU cc_start: 0.2242 (OUTLIER) cc_final: 0.2017 (tt) REVERT: F 349 LEU cc_start: 0.8558 (mp) cc_final: 0.8021 (pp) REVERT: F 363 LEU cc_start: 0.8744 (mp) cc_final: 0.8299 (tt) REVERT: O 37 LYS cc_start: 0.7845 (tppt) cc_final: 0.7405 (tppt) REVERT: O 106 ASP cc_start: 0.7939 (m-30) cc_final: 0.7634 (m-30) REVERT: P 92 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8035 (ptm160) REVERT: Q 113 SER cc_start: 0.8828 (m) cc_final: 0.8583 (p) REVERT: Q 114 VAL cc_start: 0.9257 (p) cc_final: 0.9023 (m) REVERT: R 31 LYS cc_start: 0.7327 (OUTLIER) cc_final: 0.6322 (pttt) REVERT: R 65 ASP cc_start: 0.8567 (t0) cc_final: 0.8048 (t0) REVERT: R 105 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8231 (pttp) REVERT: S 59 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7174 (pp20) REVERT: S 77 ASP cc_start: 0.8611 (m-30) cc_final: 0.8390 (m-30) REVERT: S 115 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8488 (mptt) REVERT: T 92 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8280 (ptm160) REVERT: U 41 GLU cc_start: 0.8022 (mp0) cc_final: 0.7781 (mp0) REVERT: U 56 GLU cc_start: 0.8313 (tt0) cc_final: 0.8044 (tt0) REVERT: U 71 ARG cc_start: 0.7701 (mtm110) cc_final: 0.7497 (ttp-110) REVERT: V 65 ASP cc_start: 0.8632 (t70) cc_final: 0.8327 (t0) REVERT: A 165 ASP cc_start: 0.8365 (p0) cc_final: 0.7998 (p0) REVERT: A 213 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6722 (tp30) REVERT: A 259 MET cc_start: 0.8104 (mmp) cc_final: 0.7853 (mmm) REVERT: A 360 MET cc_start: 0.8254 (mmm) cc_final: 0.8038 (mmm) REVERT: A 420 TYR cc_start: 0.7631 (t80) cc_final: 0.7387 (t80) REVERT: B 704 GLU cc_start: 0.8619 (pp20) cc_final: 0.8035 (pp20) REVERT: B 722 ASN cc_start: 0.8250 (m110) cc_final: 0.7953 (m-40) REVERT: B 912 TRP cc_start: 0.8257 (m100) cc_final: 0.7798 (m100) REVERT: B 1164 MET cc_start: 0.8228 (ppp) cc_final: 0.7816 (ppp) REVERT: B 1257 MET cc_start: 0.5891 (OUTLIER) cc_final: 0.5108 (tpp) REVERT: B 1289 GLN cc_start: 0.8079 (pp30) cc_final: 0.7858 (pp30) REVERT: E 305 GLU cc_start: 0.5727 (OUTLIER) cc_final: 0.5465 (pp20) REVERT: E 316 MET cc_start: 0.6654 (tpt) cc_final: 0.6002 (pmm) REVERT: G 560 MET cc_start: 0.6729 (tmm) cc_final: 0.6182 (mtm) outliers start: 87 outliers final: 64 residues processed: 371 average time/residue: 0.4230 time to fit residues: 240.9051 Evaluate side-chains 377 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 301 time to evaluate : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain P residue 92 ARG Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain R residue 31 LYS Chi-restraints excluded: chain R residue 105 LYS Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 56 LYS Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain S residue 115 LYS Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 92 ARG Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 36 LYS Chi-restraints excluded: chain U residue 64 GLU Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1197 ASP Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 321 LYS Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 505 TYR Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain G residue 346 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 161 optimal weight: 3.9990 chunk 259 optimal weight: 0.8980 chunk 158 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 180 optimal weight: 7.9990 chunk 271 optimal weight: 10.0000 chunk 250 optimal weight: 0.0980 chunk 216 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 167 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 275 GLN ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.5951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 28197 Z= 0.208 Angle : 0.601 11.614 39453 Z= 0.322 Chirality : 0.038 0.275 4355 Planarity : 0.004 0.083 3868 Dihedral : 26.993 177.235 6310 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.76 % Allowed : 29.36 % 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: 0.07 (0.17), residues: 2433 helix: 1.06 (0.14), residues: 1351 sheet: -1.43 (0.48), residues: 114 loop : -1.20 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP E 492 HIS 0.006 0.001 HIS A 38 PHE 0.021 0.001 PHE A 208 TYR 0.019 0.001 TYR F 261 ARG 0.013 0.000 ARG U 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 309 time to evaluate : 2.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 295 ASN cc_start: 0.5693 (t0) cc_final: 0.5413 (t0) REVERT: D 311 LYS cc_start: 0.8641 (pttt) cc_final: 0.8394 (ptpt) REVERT: D 324 ARG cc_start: 0.7602 (mmt-90) cc_final: 0.7145 (mmt-90) REVERT: D 347 MET cc_start: 0.6923 (OUTLIER) cc_final: 0.6566 (pmt) REVERT: D 360 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: F 241 LYS cc_start: 0.3086 (OUTLIER) cc_final: 0.2241 (mmtm) REVERT: F 296 MET cc_start: 0.4528 (mpp) cc_final: 0.4149 (mmt) REVERT: F 309 LEU cc_start: 0.2231 (OUTLIER) cc_final: 0.1999 (tt) REVERT: F 349 LEU cc_start: 0.8561 (mp) cc_final: 0.8016 (pp) REVERT: F 363 LEU cc_start: 0.8782 (mp) cc_final: 0.8347 (tt) REVERT: O 37 LYS cc_start: 0.7859 (tppt) cc_final: 0.6644 (tmtt) REVERT: P 92 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8024 (ptm160) REVERT: Q 113 SER cc_start: 0.8823 (m) cc_final: 0.8588 (p) REVERT: Q 114 VAL cc_start: 0.9257 (p) cc_final: 0.9021 (m) REVERT: R 31 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.6346 (pttt) REVERT: R 65 ASP cc_start: 0.8560 (t0) cc_final: 0.8049 (t0) REVERT: R 90 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7791 (mp0) REVERT: R 105 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8238 (pttp) REVERT: S 59 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7237 (pp20) REVERT: S 77 ASP cc_start: 0.8607 (m-30) cc_final: 0.8390 (m-30) REVERT: S 115 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8471 (mptt) REVERT: T 92 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8315 (ptm160) REVERT: U 41 GLU cc_start: 0.8009 (mp0) cc_final: 0.7788 (mp0) REVERT: U 56 GLU cc_start: 0.8312 (tt0) cc_final: 0.8044 (tt0) REVERT: U 71 ARG cc_start: 0.7677 (mtm110) cc_final: 0.7464 (ttp-110) REVERT: V 65 ASP cc_start: 0.8625 (t70) cc_final: 0.8335 (t0) REVERT: A 165 ASP cc_start: 0.8363 (p0) cc_final: 0.8006 (p0) REVERT: A 213 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6714 (tp30) REVERT: A 360 MET cc_start: 0.8229 (mmm) cc_final: 0.8009 (mmm) REVERT: A 420 TYR cc_start: 0.7661 (t80) cc_final: 0.7302 (t80) REVERT: B 704 GLU cc_start: 0.8617 (pp20) cc_final: 0.8036 (pp20) REVERT: B 722 ASN cc_start: 0.8264 (m110) cc_final: 0.7973 (m110) REVERT: B 860 MET cc_start: 0.6148 (mmm) cc_final: 0.5502 (tpt) REVERT: B 912 TRP cc_start: 0.8281 (m100) cc_final: 0.7832 (m100) REVERT: B 1164 MET cc_start: 0.8242 (ppp) cc_final: 0.7789 (ppp) REVERT: B 1257 MET cc_start: 0.6014 (OUTLIER) cc_final: 0.5210 (tpp) REVERT: B 1289 GLN cc_start: 0.8104 (pp30) cc_final: 0.7889 (pp30) REVERT: E 305 GLU cc_start: 0.5725 (OUTLIER) cc_final: 0.5459 (pp20) REVERT: E 316 MET cc_start: 0.6688 (tpt) cc_final: 0.6058 (pmm) REVERT: G 336 PHE cc_start: 0.2455 (OUTLIER) cc_final: 0.1845 (p90) REVERT: G 560 MET cc_start: 0.6739 (tmm) cc_final: 0.6188 (mtm) outliers start: 83 outliers final: 66 residues processed: 362 average time/residue: 0.4091 time to fit residues: 228.9101 Evaluate side-chains 378 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 297 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain P residue 92 ARG Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain R residue 31 LYS Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain R residue 105 LYS Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain S residue 115 LYS Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 92 ARG Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 36 LYS Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 64 GLU Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain B residue 1197 ASP Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 321 LYS Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 505 TYR Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain G residue 336 PHE Chi-restraints excluded: chain G residue 346 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 172 optimal weight: 0.7980 chunk 230 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 199 optimal weight: 10.0000 chunk 31 optimal weight: 0.5980 chunk 60 optimal weight: 0.3980 chunk 216 optimal weight: 0.0470 chunk 90 optimal weight: 0.0570 chunk 222 optimal weight: 0.0970 chunk 27 optimal weight: 0.1980 chunk 39 optimal weight: 0.5980 overall best weight: 0.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 815 HIS ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.129857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.092412 restraints weight = 68195.911| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.19 r_work: 0.3368 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.5782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 28197 Z= 0.161 Angle : 0.585 11.984 39453 Z= 0.314 Chirality : 0.037 0.266 4355 Planarity : 0.004 0.084 3868 Dihedral : 26.763 177.455 6310 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.40 % Allowed : 29.90 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.17), residues: 2433 helix: 1.14 (0.14), residues: 1357 sheet: -1.25 (0.52), residues: 104 loop : -1.22 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP E 492 HIS 0.004 0.001 HIS R 46 PHE 0.061 0.001 PHE A 160 TYR 0.039 0.001 TYR T 88 ARG 0.014 0.000 ARG U 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7449.28 seconds wall clock time: 133 minutes 23.87 seconds (8003.87 seconds total)