Starting phenix.real_space_refine on Fri Apr 12 21:18:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd5_37125/04_2024/8kd5_37125_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd5_37125/04_2024/8kd5_37125.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd5_37125/04_2024/8kd5_37125.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd5_37125/04_2024/8kd5_37125.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd5_37125/04_2024/8kd5_37125_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd5_37125/04_2024/8kd5_37125_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 319 5.49 5 S 91 5.16 5 C 16088 2.51 5 N 4778 2.21 5 O 5631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 262": "OE1" <-> "OE2" Residue "D GLU 280": "OE1" <-> "OE2" Residue "D GLU 308": "OE1" <-> "OE2" Residue "D ASP 371": "OD1" <-> "OD2" Residue "D TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 89": "OD1" <-> "OD2" Residue "F GLU 255": "OE1" <-> "OE2" Residue "F GLU 280": "OE1" <-> "OE2" Residue "F TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 302": "OE1" <-> "OE2" Residue "F GLU 360": "OE1" <-> "OE2" Residue "O TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 59": "OE1" <-> "OE2" Residue "O ASP 106": "OD1" <-> "OD2" Residue "P GLU 52": "OE1" <-> "OE2" Residue "P PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 56": "OE1" <-> "OE2" Residue "Q ASP 90": "OD1" <-> "OD2" Residue "Q GLU 91": "OE1" <-> "OE2" Residue "R TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 68": "OE1" <-> "OE2" Residue "R GLU 73": "OE1" <-> "OE2" Residue "R GLU 90": "OE1" <-> "OE2" Residue "R GLU 102": "OE1" <-> "OE2" Residue "R TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 106": "OD1" <-> "OD2" Residue "S ASP 123": "OD1" <-> "OD2" Residue "S GLU 133": "OE1" <-> "OE2" Residue "T GLU 53": "OE1" <-> "OE2" Residue "T ASP 85": "OD1" <-> "OD2" Residue "U ASP 90": "OD1" <-> "OD2" Residue "V TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 65": "OD1" <-> "OD2" Residue "V GLU 68": "OE1" <-> "OE2" Residue "V GLU 73": "OE1" <-> "OE2" Residue "V GLU 90": "OE1" <-> "OE2" Residue "V GLU 102": "OE1" <-> "OE2" Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 114": "OD1" <-> "OD2" Residue "A GLU 118": "OE1" <-> "OE2" Residue "A TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 191": "OD1" <-> "OD2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "A ASP 223": "OD1" <-> "OD2" Residue "A ASP 243": "OD1" <-> "OD2" Residue "A TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "A ASP 407": "OD1" <-> "OD2" Residue "A ASP 413": "OD1" <-> "OD2" Residue "B GLU 664": "OE1" <-> "OE2" Residue "B TYR 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 780": "OD1" <-> "OD2" Residue "B GLU 781": "OE1" <-> "OE2" Residue "B TYR 803": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 871": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 986": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1012": "OD1" <-> "OD2" Residue "B TYR 1016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1225": "OE1" <-> "OE2" Residue "B TYR 1232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1259": "OD1" <-> "OD2" Residue "B ASP 1282": "OD1" <-> "OD2" Residue "B ASP 1320": "OD1" <-> "OD2" Residue "E PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 344": "OD1" <-> "OD2" Residue "E TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 507": "OE1" <-> "OE2" Residue "G PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 550": "OD1" <-> "OD2" Residue "G PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 26908 Number of models: 1 Model: "" Number of chains: 17 Chain: "D" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1867 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain breaks: 2 Chain: "F" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1573 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain breaks: 2 Chain: "O" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 822 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} 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: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "R" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 730 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "S" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "U" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "V" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 715 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "X" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 3277 Classifications: {'DNA': 159} Link IDs: {'rna3p': 158} Chain: "Y" Number of atoms: 3261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 3261 Classifications: {'DNA': 160} Link IDs: {'rna3p': 159} 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: 4519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4519 Classifications: {'peptide': 539} Link IDs: {'PTRANS': 12, 'TRANS': 526} Chain breaks: 2 Chain: "E" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2611 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 18, 'TRANS': 298} Chain breaks: 3 Chain: "G" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 724 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.91, per 1000 atoms: 0.52 Number of scatterers: 26908 At special positions: 0 Unit cell: (139.87, 152.65, 188.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 91 16.00 P 319 15.00 O 5631 8.00 N 4778 7.00 C 16088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS G 303 " - pdb=" SG CYS G 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: 12.59 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 188 " 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4754 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 106 helices and 3 sheets defined 51.6% alpha, 2.4% beta 133 base pairs and 266 stacking pairs defined. Time for finding SS restraints: 13.12 Creating SS restraints... Processing helix chain 'D' and resid 99 through 111 Processing helix chain 'D' and resid 226 through 240 Processing helix chain 'D' and resid 254 through 268 Processing helix chain 'D' and resid 274 through 292 Processing helix chain 'D' and resid 300 through 315 removed outlier: 4.505A pdb=" N LEU D 304 " --> pdb=" O ARG D 300 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLN D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 324 No H-bonds generated for 'chain 'D' and resid 322 through 324' Processing helix chain 'D' and resid 328 through 342 Proline residue: D 339 - end of helix Processing helix chain 'D' and resid 349 through 368 Processing helix chain 'D' and resid 392 through 399 Processing helix chain 'F' and resid 99 through 111 Processing helix chain 'F' and resid 230 through 236 Processing helix chain 'F' and resid 254 through 264 removed outlier: 4.054A pdb=" N TYR F 261 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU F 262 " --> pdb=" O LEU F 258 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS F 263 " --> pdb=" O ASN F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 289 removed outlier: 4.374A pdb=" N TYR F 281 " --> pdb=" O GLN F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 312 Processing helix chain 'F' and resid 329 through 342 removed outlier: 3.537A pdb=" N LEU F 332 " --> pdb=" O ILE F 329 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU F 338 " --> pdb=" O ILE F 335 " (cutoff:3.500A) Proline residue: F 339 - end of helix Processing helix chain 'F' and resid 349 through 368 removed outlier: 4.517A pdb=" N MET F 368 " --> pdb=" O VAL F 364 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 56 removed outlier: 3.581A pdb=" N LYS O 56 " --> pdb=" O ARG O 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 64 through 77 removed outlier: 3.970A pdb=" N ASP O 77 " --> pdb=" O GLU O 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 86 through 113 Processing helix chain 'O' and resid 121 through 131 Processing helix chain 'P' and resid 26 through 28 No H-bonds generated for 'chain 'P' and resid 26 through 28' Processing helix chain 'P' and resid 31 through 40 Processing helix chain 'P' and resid 50 through 75 removed outlier: 4.020A pdb=" N ARG P 67 " --> pdb=" O GLU P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 93 removed outlier: 4.020A pdb=" N GLN P 93 " --> pdb=" O ALA P 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 17 through 20 No H-bonds generated for 'chain 'Q' and resid 17 through 20' Processing helix chain 'Q' and resid 27 through 36 Processing helix chain 'Q' and resid 45 through 72 removed outlier: 4.344A pdb=" N VAL Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 89 Processing helix chain 'Q' and resid 91 through 96 Processing helix chain 'R' and resid 35 through 45 removed outlier: 3.622A pdb=" N TYR R 39 " --> pdb=" O ALA R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 80 removed outlier: 3.538A pdb=" N TYR R 80 " --> pdb=" O ARG R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 98 Processing helix chain 'R' and resid 101 through 119 removed outlier: 3.712A pdb=" N LYS R 105 " --> pdb=" O GLU R 102 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N HIS R 106 " --> pdb=" O LEU R 103 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU R 110 " --> pdb=" O ALA R 107 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR R 112 " --> pdb=" O SER R 109 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS R 113 " --> pdb=" O GLU R 110 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR R 116 " --> pdb=" O LYS R 113 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR R 119 " --> pdb=" O THR R 116 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 55 Processing helix chain 'S' and resid 64 through 78 removed outlier: 3.640A pdb=" N ASP S 77 " --> pdb=" O GLU S 73 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE S 78 " --> pdb=" O ILE S 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 86 through 113 Processing helix chain 'S' and resid 121 through 131 Processing helix chain 'T' and resid 26 through 28 No H-bonds generated for 'chain 'T' and resid 26 through 28' Processing helix chain 'T' and resid 31 through 40 Processing helix chain 'T' and resid 50 through 75 removed outlier: 3.826A pdb=" N ARG T 67 " --> pdb=" O GLU T 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 83 through 91 Processing helix chain 'U' and resid 17 through 20 No H-bonds generated for 'chain 'U' and resid 17 through 20' Processing helix chain 'U' and resid 27 through 36 Processing helix chain 'U' and resid 45 through 72 removed outlier: 4.036A pdb=" N VAL U 49 " --> pdb=" O ALA U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 89 Processing helix chain 'U' and resid 91 through 96 Processing helix chain 'V' and resid 35 through 45 Processing helix chain 'V' and resid 53 through 80 Processing helix chain 'V' and resid 88 through 98 Processing helix chain 'V' and resid 101 through 118 removed outlier: 3.750A pdb=" N LYS V 105 " --> pdb=" O GLU V 102 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL V 108 " --> pdb=" O LYS V 105 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU V 110 " --> pdb=" O ALA V 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 54 removed outlier: 3.588A pdb=" N ILE A 45 " --> pdb=" O PRO A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 60 Processing helix chain 'A' and resid 72 through 74 No H-bonds generated for 'chain 'A' and resid 72 through 74' Processing helix chain 'A' and resid 80 through 88 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 99 through 103 removed outlier: 4.104A pdb=" N LYS A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 103' Processing helix chain 'A' and resid 116 through 136 Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 191 through 196 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 244 through 261 Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 288 through 301 removed outlier: 4.007A pdb=" N CYS A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL A 295 " --> pdb=" O HIS A 291 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE A 301 " --> pdb=" O TYR A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 329 removed outlier: 3.723A pdb=" N ARG A 320 " --> pdb=" O ARG A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 346 No H-bonds generated for 'chain 'A' and resid 344 through 346' Processing helix chain 'A' and resid 366 through 382 removed outlier: 4.905A pdb=" N ASN A 382 " --> pdb=" O ALA A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'B' and resid 665 through 676 removed outlier: 4.459A pdb=" N PHE B 669 " --> pdb=" O GLU B 665 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLU B 670 " --> pdb=" O VAL B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 693 Processing helix chain 'B' and resid 699 through 709 removed outlier: 3.628A pdb=" N PHE B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 724 Processing helix chain 'B' and resid 772 through 777 Processing helix chain 'B' and resid 786 through 790 Processing helix chain 'B' and resid 802 through 839 removed outlier: 3.788A pdb=" N TYR B 817 " --> pdb=" O GLU B 813 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP B 818 " --> pdb=" O ARG B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 847 Processing helix chain 'B' and resid 862 through 870 Processing helix chain 'B' and resid 873 through 885 removed outlier: 3.749A pdb=" N PHE B 877 " --> pdb=" O LYS B 873 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU B 878 " --> pdb=" O GLU B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 928 removed outlier: 4.026A pdb=" N LYS B 914 " --> pdb=" O ARG B 910 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL B 915 " --> pdb=" O GLU B 911 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N PHE B 925 " --> pdb=" O GLN B 921 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS B 926 " --> pdb=" O LYS B 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 935 through 942 removed outlier: 4.194A pdb=" N LYS B 940 " --> pdb=" O LYS B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.744A pdb=" N ILE B 955 " --> pdb=" O GLU B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 996 Processing helix chain 'B' and resid 1004 through 1021 removed outlier: 3.787A pdb=" N ILE B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1163 Processing helix chain 'B' and resid 1165 through 1173 removed outlier: 4.121A pdb=" N LYS B1170 " --> pdb=" O GLU B1166 " (cutoff:3.500A) Processing helix chain 'B' and resid 1179 through 1184 Processing helix chain 'B' and resid 1203 through 1216 Processing helix chain 'B' and resid 1221 through 1229 Processing helix chain 'B' and resid 1237 through 1239 No H-bonds generated for 'chain 'B' and resid 1237 through 1239' Processing helix chain 'B' and resid 1242 through 1258 removed outlier: 3.585A pdb=" N THR B1255 " --> pdb=" O LYS B1251 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B1256 " --> pdb=" O HIS B1252 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N MET B1257 " --> pdb=" O ALA B1253 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR B1258 " --> pdb=" O HIS B1254 " (cutoff:3.500A) Processing helix chain 'B' and resid 1260 through 1272 Processing helix chain 'B' and resid 1283 through 1293 Processing helix chain 'B' and resid 1308 through 1310 No H-bonds generated for 'chain 'B' and resid 1308 through 1310' Processing helix chain 'E' and resid 52 through 56 removed outlier: 4.031A pdb=" N SER E 56 " --> pdb=" O ILE E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 295 No H-bonds generated for 'chain 'E' and resid 293 through 295' Processing helix chain 'E' and resid 304 through 309 Processing helix chain 'E' and resid 322 through 329 Processing helix chain 'E' and resid 334 through 344 removed outlier: 4.146A pdb=" N LYS E 338 " --> pdb=" O LYS E 334 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N LEU E 339 " --> pdb=" O ILE E 335 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP E 344 " --> pdb=" O LEU E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 358 No H-bonds generated for 'chain 'E' and resid 355 through 358' Processing helix chain 'E' and resid 383 through 386 No H-bonds generated for 'chain 'E' and resid 383 through 386' Processing helix chain 'E' and resid 403 through 406 Processing helix chain 'E' and resid 431 through 433 No H-bonds generated for 'chain 'E' and resid 431 through 433' Processing helix chain 'E' and resid 544 through 560 removed outlier: 5.112A pdb=" N MET E 560 " --> pdb=" O TYR E 556 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 311 Processing helix chain 'G' and resid 322 through 328 removed outlier: 3.699A pdb=" N ASN G 325 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE G 327 " --> pdb=" O SER G 324 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS G 328 " --> pdb=" O ASN G 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 343 removed outlier: 3.975A pdb=" N ASN G 342 " --> pdb=" O LYS G 338 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE G 343 " --> pdb=" O LEU G 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 338 through 343' Processing helix chain 'G' and resid 542 through 568 Processing sheet with id= A, first strand: chain 'A' and resid 62 through 64 removed outlier: 3.717A pdb=" N GLU A 62 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL A 141 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N PHE A 24 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL A 143 " --> pdb=" O PHE A 24 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N MET A 305 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ASN A 144 " --> pdb=" O MET A 305 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL A 307 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY A 310 " --> pdb=" O CYS A 271 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 1136 through 1140 Processing sheet with id= C, first strand: chain 'E' and resid 272 through 275 removed outlier: 4.115A pdb=" N CYS E 275 " --> pdb=" O LYS E 280 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LYS E 280 " --> pdb=" O CYS E 275 " (cutoff:3.500A) 847 hydrogen bonds defined for protein. 2412 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 348 hydrogen bonds 696 hydrogen bond angles 0 basepair planarities 133 basepair parallelities 266 stacking parallelities Total time for adding SS restraints: 14.66 Time building geometry restraints manager: 13.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7634 1.34 - 1.47: 8286 1.47 - 1.59: 11407 1.59 - 1.72: 636 1.72 - 1.85: 142 Bond restraints: 28105 Sorted by residual: bond pdb=" C MET B 765 " pdb=" N PRO B 766 " ideal model delta sigma weight residual 1.334 1.377 -0.043 1.51e-02 4.39e+03 8.05e+00 bond pdb=" N VAL A 102 " pdb=" CA VAL A 102 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.23e-02 6.61e+03 8.05e+00 bond pdb=" C ASN B1004 " pdb=" N PRO B1005 " ideal model delta sigma weight residual 1.335 1.371 -0.036 1.36e-02 5.41e+03 6.82e+00 bond pdb=" N LYS A 103 " pdb=" CA LYS A 103 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.70e+00 bond pdb=" N ASN E 347 " pdb=" CA ASN E 347 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.45e-02 4.76e+03 5.50e+00 ... (remaining 28100 not shown) Histogram of bond angle deviations from ideal: 98.21 - 105.39: 1630 105.39 - 112.56: 14718 112.56 - 119.73: 9709 119.73 - 126.90: 12244 126.90 - 134.07: 995 Bond angle restraints: 39296 Sorted by residual: angle pdb=" CA MET D 107 " pdb=" CB MET D 107 " pdb=" CG MET D 107 " ideal model delta sigma weight residual 114.10 125.61 -11.51 2.00e+00 2.50e-01 3.31e+01 angle pdb=" CB LYS B 962 " pdb=" CG LYS B 962 " pdb=" CD LYS B 962 " ideal model delta sigma weight residual 111.30 122.72 -11.42 2.30e+00 1.89e-01 2.47e+01 angle pdb=" CB MET S 90 " pdb=" CG MET S 90 " pdb=" SD MET S 90 " ideal model delta sigma weight residual 112.70 127.53 -14.83 3.00e+00 1.11e-01 2.44e+01 angle pdb=" CA GLN F 305 " pdb=" CB GLN F 305 " pdb=" CG GLN F 305 " ideal model delta sigma weight residual 114.10 123.80 -9.70 2.00e+00 2.50e-01 2.35e+01 angle pdb=" CB MET O 90 " pdb=" CG MET O 90 " pdb=" SD MET O 90 " ideal model delta sigma weight residual 112.70 126.23 -13.53 3.00e+00 1.11e-01 2.03e+01 ... (remaining 39291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 14067 35.18 - 70.36: 1981 70.36 - 105.55: 51 105.55 - 140.73: 2 140.73 - 175.91: 1 Dihedral angle restraints: 16102 sinusoidal: 8750 harmonic: 7352 Sorted by residual: dihedral pdb=" CA LEU B1184 " pdb=" C LEU B1184 " pdb=" N ASP B1185 " pdb=" CA ASP B1185 " ideal model delta harmonic sigma weight residual 180.00 154.73 25.27 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA MET F 347 " pdb=" C MET F 347 " pdb=" N ASP F 348 " pdb=" CA ASP F 348 " ideal model delta harmonic sigma weight residual -180.00 -155.39 -24.61 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA HIS E 302 " pdb=" C HIS E 302 " pdb=" N CYS E 303 " pdb=" CA CYS E 303 " ideal model delta harmonic sigma weight residual -180.00 -155.77 -24.23 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 16099 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3613 0.052 - 0.103: 606 0.103 - 0.155: 111 0.155 - 0.207: 11 0.207 - 0.259: 2 Chirality restraints: 4343 Sorted by residual: chirality pdb=" CB ILE F 105 " pdb=" CA ILE F 105 " pdb=" CG1 ILE F 105 " pdb=" CG2 ILE F 105 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB VAL B 777 " pdb=" CA VAL B 777 " pdb=" CG1 VAL B 777 " pdb=" CG2 VAL B 777 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CG LEU F 338 " pdb=" CB LEU F 338 " pdb=" CD1 LEU F 338 " pdb=" CD2 LEU F 338 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 9.68e-01 ... (remaining 4340 not shown) Planarity restraints: 3879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 321 " -0.088 5.00e-02 4.00e+02 1.31e-01 2.75e+01 pdb=" N PRO D 322 " 0.227 5.00e-02 4.00e+02 pdb=" CA PRO D 322 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO D 322 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 292 " 0.044 5.00e-02 4.00e+02 6.66e-02 7.09e+00 pdb=" N PRO E 293 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO E 293 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 293 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 775 " 0.015 2.00e-02 2.50e+03 1.51e-02 5.67e+00 pdb=" CG TRP B 775 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP B 775 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 775 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 775 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 775 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 775 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 775 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 775 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 775 " -0.002 2.00e-02 2.50e+03 ... (remaining 3876 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 345 2.62 - 3.19: 21779 3.19 - 3.76: 48297 3.76 - 4.33: 62563 4.33 - 4.90: 94768 Nonbonded interactions: 227752 Sorted by model distance: nonbonded pdb=" CB HIS A 188 " pdb="ZN ZN A 501 " model vdw 2.044 2.104 nonbonded pdb=" CB ALA A 36 " pdb=" CD2 LEU E 48 " model vdw 2.139 3.880 nonbonded pdb=" O ASN B1165 " pdb=" OG1 THR B1169 " model vdw 2.221 2.440 nonbonded pdb=" O LYS D 243 " pdb=" OG1 THR D 390 " model vdw 2.234 2.440 nonbonded pdb=" O ILE E 395 " pdb=" NZ LYS E 397 " model vdw 2.260 2.520 ... (remaining 227747 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 'O' and resid 36 through 133) selection = chain 'S' } ncs_group { reference = chain 'P' selection = chain 'T' } ncs_group { reference = chain 'Q' selection = chain 'U' } ncs_group { reference = (chain 'R' and resid 29 through 119) selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 7.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 33.980 Check model and map are aligned: 0.440 Set scattering table: 0.270 Process input model: 89.650 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 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 : 0.003 0.058 28105 Z= 0.211 Angle : 0.749 14.828 39296 Z= 0.400 Chirality : 0.040 0.259 4343 Planarity : 0.005 0.131 3879 Dihedral : 24.457 175.912 11345 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.29 % Favored : 95.59 % Rotamer: Outliers : 0.54 % Allowed : 32.75 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.15), residues: 2450 helix: -0.12 (0.13), residues: 1323 sheet: 0.76 (0.67), residues: 81 loop : -1.75 (0.17), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 775 HIS 0.017 0.001 HIS E 302 PHE 0.038 0.001 PHE E 326 TYR 0.032 0.001 TYR A 176 ARG 0.016 0.001 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 315 time to evaluate : 2.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 291 LYS cc_start: 0.8447 (mtpt) cc_final: 0.7906 (mmtt) REVERT: D 350 GLN cc_start: 0.7718 (tm-30) cc_final: 0.7473 (tm-30) REVERT: F 256 MET cc_start: 0.5695 (tpp) cc_final: 0.5075 (pmt) REVERT: P 84 MET cc_start: 0.8088 (tpp) cc_final: 0.7885 (tpp) REVERT: Q 95 LYS cc_start: 0.7854 (ttmp) cc_final: 0.7254 (tptt) REVERT: U 74 LYS cc_start: 0.7341 (mppt) cc_final: 0.7077 (mppt) REVERT: V 60 ASN cc_start: 0.8244 (t0) cc_final: 0.8000 (t0) REVERT: B 726 TYR cc_start: 0.6199 (t80) cc_final: 0.5780 (t80) REVERT: B 757 ARG cc_start: 0.8428 (ttp80) cc_final: 0.8121 (ttp80) REVERT: B 773 MET cc_start: 0.5049 (ppp) cc_final: 0.4287 (ppp) REVERT: B 813 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7888 (mt-10) REVERT: B 1185 ASP cc_start: 0.8091 (t70) cc_final: 0.7787 (t0) REVERT: B 1288 LEU cc_start: 0.7932 (tm) cc_final: 0.7617 (tm) REVERT: E 282 PHE cc_start: 0.6906 (m-10) cc_final: 0.6197 (m-10) outliers start: 12 outliers final: 3 residues processed: 319 average time/residue: 1.2622 time to fit residues: 475.9290 Evaluate side-chains 291 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 288 time to evaluate : 2.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain B residue 785 HIS Chi-restraints excluded: chain E residue 540 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 229 optimal weight: 2.9990 chunk 206 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 110 optimal weight: 0.6980 chunk 213 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 267 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 HIS F 267 GLN F 305 GLN O 39 HIS O 108 ASN ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 85 GLN U 38 ASN A 31 ASN ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 GLN ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1190 GLN ** B1289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1293 HIS ** E 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 516 ASN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 28105 Z= 0.398 Angle : 0.698 12.836 39296 Z= 0.379 Chirality : 0.043 0.221 4343 Planarity : 0.005 0.087 3879 Dihedral : 26.876 179.105 6228 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 5.49 % Allowed : 25.91 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.16), residues: 2450 helix: 0.27 (0.14), residues: 1350 sheet: 0.08 (0.58), residues: 92 loop : -1.42 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 775 HIS 0.009 0.002 HIS A 151 PHE 0.021 0.002 PHE A 24 TYR 0.038 0.002 TYR P 88 ARG 0.007 0.001 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 349 time to evaluate : 2.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 291 LYS cc_start: 0.8798 (mtpt) cc_final: 0.8284 (mmtt) REVERT: D 350 GLN cc_start: 0.7932 (tm-30) cc_final: 0.7657 (tm-30) REVERT: D 364 VAL cc_start: 0.8818 (m) cc_final: 0.8364 (p) REVERT: F 256 MET cc_start: 0.5541 (tpp) cc_final: 0.4977 (pmt) REVERT: F 296 MET cc_start: 0.4083 (mtm) cc_final: 0.3847 (mpp) REVERT: O 59 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7483 (pm20) REVERT: O 115 LYS cc_start: 0.9003 (mmtp) cc_final: 0.8694 (mmtm) REVERT: O 120 MET cc_start: 0.8790 (mmt) cc_final: 0.8538 (mmt) REVERT: O 123 ASP cc_start: 0.8660 (m-30) cc_final: 0.8423 (m-30) REVERT: P 77 LYS cc_start: 0.8480 (mmtt) cc_final: 0.8270 (mmtm) REVERT: P 85 ASP cc_start: 0.8429 (p0) cc_final: 0.8198 (p0) REVERT: Q 99 ARG cc_start: 0.7774 (mpt180) cc_final: 0.7565 (mmm160) REVERT: R 54 LYS cc_start: 0.8428 (mmtt) cc_final: 0.8135 (mmpt) REVERT: R 76 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7774 (ttp80) REVERT: R 105 LYS cc_start: 0.7756 (pttm) cc_final: 0.7460 (ptpp) REVERT: S 59 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7092 (pp20) REVERT: U 29 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.7325 (ttp80) REVERT: U 64 GLU cc_start: 0.7789 (tt0) cc_final: 0.7580 (tt0) REVERT: V 32 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7083 (tp30) REVERT: V 37 TYR cc_start: 0.8552 (m-80) cc_final: 0.8328 (m-80) REVERT: V 40 LYS cc_start: 0.8357 (mttm) cc_final: 0.8117 (mtpt) REVERT: V 102 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7381 (tp30) REVERT: V 110 GLU cc_start: 0.7835 (tp30) cc_final: 0.7596 (mm-30) REVERT: A 89 VAL cc_start: 0.9121 (p) cc_final: 0.8912 (p) REVERT: A 118 GLU cc_start: 0.8266 (mp0) cc_final: 0.7942 (mp0) REVERT: A 267 VAL cc_start: 0.9084 (t) cc_final: 0.8838 (p) REVERT: A 283 CYS cc_start: 0.7233 (m) cc_final: 0.6961 (m) REVERT: A 325 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7842 (mt-10) REVERT: B 726 TYR cc_start: 0.7339 (t80) cc_final: 0.7080 (t80) REVERT: B 825 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8052 (mm) REVERT: B 860 MET cc_start: 0.6527 (mpp) cc_final: 0.5846 (mpt) REVERT: B 868 ARG cc_start: 0.8313 (tpp80) cc_final: 0.7998 (mtt-85) REVERT: B 1155 TYR cc_start: 0.7897 (t80) cc_final: 0.7594 (t80) REVERT: B 1185 ASP cc_start: 0.8313 (t70) cc_final: 0.8062 (t0) REVERT: B 1187 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7095 (mm) REVERT: B 1285 ILE cc_start: 0.8552 (mm) cc_final: 0.8343 (mp) REVERT: E 344 ASP cc_start: 0.7657 (t0) cc_final: 0.7414 (p0) REVERT: E 501 LYS cc_start: 0.6953 (mmtt) cc_final: 0.6408 (mptp) REVERT: E 542 ILE cc_start: 0.7734 (mm) cc_final: 0.7297 (tt) outliers start: 122 outliers final: 36 residues processed: 434 average time/residue: 1.5062 time to fit residues: 756.3673 Evaluate side-chains 335 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 290 time to evaluate : 2.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 53 SER Chi-restraints excluded: chain R residue 76 ARG Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 68 GLN Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 29 ARG Chi-restraints excluded: chain U residue 73 ASN Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 375 ASN Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 798 HIS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1178 VAL Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 343 ILE Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 543 ASP Chi-restraints excluded: chain E residue 546 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 168 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 247 optimal weight: 0.9990 chunk 267 optimal weight: 10.0000 chunk 220 optimal weight: 0.5980 chunk 245 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 198 optimal weight: 0.3980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 GLN ** D 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN ** F 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 ASN V 44 GLN V 60 ASN ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1143 ASN B1221 HIS ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28105 Z= 0.200 Angle : 0.559 10.273 39296 Z= 0.307 Chirality : 0.037 0.180 4343 Planarity : 0.004 0.071 3879 Dihedral : 26.825 176.479 6225 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 5.26 % Allowed : 26.18 % Favored : 68.56 % 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: -0.29 (0.17), residues: 2450 helix: 0.65 (0.14), residues: 1352 sheet: -0.06 (0.59), residues: 87 loop : -1.34 (0.18), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 775 HIS 0.009 0.001 HIS B 785 PHE 0.018 0.001 PHE B 708 TYR 0.019 0.001 TYR A 176 ARG 0.008 0.000 ARG R 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 327 time to evaluate : 3.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 103 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6909 (pp20) REVERT: D 291 LYS cc_start: 0.8777 (mtpt) cc_final: 0.8267 (mmtt) REVERT: D 308 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7428 (mm-30) REVERT: D 350 GLN cc_start: 0.7964 (tm-30) cc_final: 0.7629 (tm-30) REVERT: F 256 MET cc_start: 0.5686 (tpp) cc_final: 0.5121 (pmt) REVERT: F 270 GLU cc_start: 0.0889 (OUTLIER) cc_final: 0.0618 (pt0) REVERT: F 347 MET cc_start: 0.2181 (pp-130) cc_final: 0.1586 (pp-130) REVERT: O 115 LYS cc_start: 0.8958 (mmtp) cc_final: 0.8636 (mmtm) REVERT: P 77 LYS cc_start: 0.8444 (mmtt) cc_final: 0.8236 (mmtm) REVERT: P 85 ASP cc_start: 0.8254 (p0) cc_final: 0.7801 (p0) REVERT: Q 73 ASN cc_start: 0.7837 (p0) cc_final: 0.7354 (m110) REVERT: Q 99 ARG cc_start: 0.7819 (mpt180) cc_final: 0.7600 (mmm160) REVERT: V 40 LYS cc_start: 0.8392 (mttm) cc_final: 0.8067 (mtmt) REVERT: V 82 LYS cc_start: 0.8747 (mmmt) cc_final: 0.8160 (mmtt) REVERT: V 90 GLU cc_start: 0.8347 (mp0) cc_final: 0.7838 (mp0) REVERT: V 102 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7287 (tp30) REVERT: A 60 LYS cc_start: 0.6551 (OUTLIER) cc_final: 0.5813 (ptpt) REVERT: A 89 VAL cc_start: 0.9149 (OUTLIER) cc_final: 0.8934 (p) REVERT: A 118 GLU cc_start: 0.8250 (mp0) cc_final: 0.7812 (mp0) REVERT: A 211 TYR cc_start: 0.7994 (t80) cc_final: 0.7554 (t80) REVERT: A 220 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7045 (mp0) REVERT: A 306 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.7427 (tmm) REVERT: A 373 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.6236 (mpp) REVERT: B 726 TYR cc_start: 0.7428 (t80) cc_final: 0.7209 (t80) REVERT: B 773 MET cc_start: 0.5188 (ppp) cc_final: 0.4454 (ppp) REVERT: B 825 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8062 (mm) REVERT: B 860 MET cc_start: 0.6461 (OUTLIER) cc_final: 0.5801 (mpt) REVERT: B 868 ARG cc_start: 0.8347 (tpp80) cc_final: 0.7972 (mtt-85) REVERT: B 976 ASP cc_start: 0.7209 (OUTLIER) cc_final: 0.6868 (m-30) REVERT: B 1171 GLU cc_start: 0.7551 (tp30) cc_final: 0.7263 (tp30) REVERT: B 1185 ASP cc_start: 0.8317 (t70) cc_final: 0.8098 (t0) REVERT: B 1187 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.6935 (mm) REVERT: E 388 ASN cc_start: 0.3799 (OUTLIER) cc_final: 0.3575 (p0) REVERT: E 500 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.6944 (pttt) REVERT: E 501 LYS cc_start: 0.6843 (mmtt) cc_final: 0.6513 (mmtm) REVERT: E 523 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7424 (pt) REVERT: E 542 ILE cc_start: 0.7842 (mm) cc_final: 0.7320 (tt) REVERT: E 559 LYS cc_start: 0.7325 (OUTLIER) cc_final: 0.6985 (ptmt) outliers start: 117 outliers final: 37 residues processed: 405 average time/residue: 1.6255 time to fit residues: 770.2005 Evaluate side-chains 360 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 308 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 TYR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 112 THR Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 56 LYS Chi-restraints excluded: chain S residue 68 GLN 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 102 GLU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain B residue 798 HIS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 860 MET Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 365 LYS Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 500 LYS Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain E residue 543 ASP Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 559 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 244 optimal weight: 0.7980 chunk 186 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 118 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 248 optimal weight: 10.0000 chunk 262 optimal weight: 0.3980 chunk 129 optimal weight: 2.9990 chunk 235 optimal weight: 6.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 GLN D 275 GLN ** D 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 ASN ** T 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 60 ASN ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 28105 Z= 0.250 Angle : 0.580 9.520 39296 Z= 0.318 Chirality : 0.038 0.189 4343 Planarity : 0.004 0.063 3879 Dihedral : 26.874 177.075 6225 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.90 % Allowed : 26.45 % Favored : 68.65 % 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: -0.11 (0.17), residues: 2450 helix: 0.83 (0.14), residues: 1348 sheet: -0.31 (0.59), residues: 89 loop : -1.27 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 775 HIS 0.008 0.001 HIS B 785 PHE 0.015 0.001 PHE G 551 TYR 0.020 0.002 TYR A 58 ARG 0.009 0.001 ARG R 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 328 time to evaluate : 2.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 103 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6801 (pp20) REVERT: D 275 GLN cc_start: 0.7403 (mm110) cc_final: 0.7163 (mm-40) REVERT: D 291 LYS cc_start: 0.8866 (mtpt) cc_final: 0.8379 (mmtt) REVERT: D 308 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7576 (mm-30) REVERT: D 315 LYS cc_start: 0.7356 (mttm) cc_final: 0.7098 (ptpt) REVERT: D 350 GLN cc_start: 0.8035 (tm-30) cc_final: 0.7675 (tm-30) REVERT: D 361 ASP cc_start: 0.8335 (m-30) cc_final: 0.8019 (m-30) REVERT: F 256 MET cc_start: 0.5711 (tpp) cc_final: 0.5168 (pmt) REVERT: F 317 GLN cc_start: 0.4809 (OUTLIER) cc_final: 0.4458 (pm20) REVERT: O 115 LYS cc_start: 0.8991 (mmtp) cc_final: 0.8669 (mmtm) REVERT: P 85 ASP cc_start: 0.8188 (p0) cc_final: 0.7666 (p0) REVERT: Q 73 ASN cc_start: 0.7806 (p0) cc_final: 0.7497 (m110) REVERT: R 105 LYS cc_start: 0.7769 (pttm) cc_final: 0.7520 (ptpp) REVERT: R 113 LYS cc_start: 0.8632 (ttmm) cc_final: 0.8261 (tttp) REVERT: V 40 LYS cc_start: 0.8406 (mttm) cc_final: 0.8189 (mtpt) REVERT: V 82 LYS cc_start: 0.8752 (mmmt) cc_final: 0.8183 (mmtt) REVERT: V 90 GLU cc_start: 0.8337 (mp0) cc_final: 0.7815 (mp0) REVERT: V 102 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7494 (tp30) REVERT: A 118 GLU cc_start: 0.8283 (mp0) cc_final: 0.7882 (mp0) REVERT: A 138 LYS cc_start: 0.7978 (tppt) cc_final: 0.7557 (tptp) REVERT: A 220 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7212 (mp0) REVERT: A 306 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.7507 (tmm) REVERT: B 726 TYR cc_start: 0.7778 (t80) cc_final: 0.7519 (t80) REVERT: B 812 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7138 (mp0) REVERT: B 813 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8370 (mt-10) REVERT: B 825 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.7996 (mm) REVERT: B 860 MET cc_start: 0.6510 (mpp) cc_final: 0.5848 (mpt) REVERT: B 868 ARG cc_start: 0.8307 (tpp80) cc_final: 0.7920 (mtt-85) REVERT: B 918 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8405 (mp0) REVERT: B 1171 GLU cc_start: 0.7482 (tp30) cc_final: 0.7205 (tp30) REVERT: E 276 ASP cc_start: 0.7190 (m-30) cc_final: 0.6826 (m-30) REVERT: E 388 ASN cc_start: 0.3765 (OUTLIER) cc_final: 0.3528 (p0) REVERT: E 501 LYS cc_start: 0.7068 (mmtt) cc_final: 0.6492 (mptp) REVERT: E 523 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7774 (pt) REVERT: E 542 ILE cc_start: 0.8100 (mm) cc_final: 0.7749 (tt) REVERT: E 559 LYS cc_start: 0.7346 (OUTLIER) cc_final: 0.6976 (ptmt) REVERT: G 552 PHE cc_start: 0.8122 (t80) cc_final: 0.7880 (m-10) outliers start: 109 outliers final: 43 residues processed: 395 average time/residue: 1.5254 time to fit residues: 693.8140 Evaluate side-chains 350 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 297 time to evaluate : 2.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 112 THR Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 68 GLN Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain V residue 116 THR Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 812 GLU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 890 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain B residue 1178 VAL Chi-restraints excluded: chain B residue 1186 LEU Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain E residue 543 ASP Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain E residue 559 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 218 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 224 optimal weight: 0.2980 chunk 181 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 235 optimal weight: 20.0000 chunk 66 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 267 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 ASN F 305 GLN O 76 GLN Q 38 ASN S 108 ASN ** T 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 60 ASN ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 28105 Z= 0.204 Angle : 0.553 9.255 39296 Z= 0.305 Chirality : 0.036 0.174 4343 Planarity : 0.004 0.060 3879 Dihedral : 26.798 175.884 6225 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.59 % Allowed : 27.04 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.17), residues: 2450 helix: 0.99 (0.14), residues: 1347 sheet: -0.43 (0.58), residues: 89 loop : -1.22 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 775 HIS 0.009 0.001 HIS F 369 PHE 0.016 0.001 PHE E 262 TYR 0.023 0.001 TYR V 37 ARG 0.010 0.000 ARG R 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 325 time to evaluate : 2.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 103 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6814 (pp20) REVERT: D 275 GLN cc_start: 0.7405 (mm110) cc_final: 0.7086 (mm-40) REVERT: D 291 LYS cc_start: 0.8863 (mtpt) cc_final: 0.8381 (mmtt) REVERT: D 308 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7568 (mm-30) REVERT: D 315 LYS cc_start: 0.7383 (mttm) cc_final: 0.7140 (ptpt) REVERT: D 350 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7675 (tm-30) REVERT: D 361 ASP cc_start: 0.8348 (m-30) cc_final: 0.8039 (m-30) REVERT: F 256 MET cc_start: 0.5697 (tpp) cc_final: 0.5194 (pmt) REVERT: F 317 GLN cc_start: 0.4756 (OUTLIER) cc_final: 0.4422 (pm20) REVERT: F 347 MET cc_start: 0.2301 (OUTLIER) cc_final: 0.1533 (pp-130) REVERT: O 115 LYS cc_start: 0.8985 (mmtp) cc_final: 0.8662 (mmtm) REVERT: P 77 LYS cc_start: 0.8506 (mmtp) cc_final: 0.8176 (mmtm) REVERT: P 85 ASP cc_start: 0.8209 (p0) cc_final: 0.7758 (p0) REVERT: Q 92 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8018 (mt-10) REVERT: R 105 LYS cc_start: 0.7676 (pttm) cc_final: 0.7460 (ptpp) REVERT: R 113 LYS cc_start: 0.8651 (ttmm) cc_final: 0.8288 (tttp) REVERT: S 42 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7532 (ptm-80) REVERT: V 40 LYS cc_start: 0.8408 (mttm) cc_final: 0.8190 (mtpt) REVERT: V 82 LYS cc_start: 0.8728 (mmmt) cc_final: 0.8177 (mmtt) REVERT: V 90 GLU cc_start: 0.8344 (mp0) cc_final: 0.7854 (mp0) REVERT: V 102 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7549 (tp30) REVERT: A 118 GLU cc_start: 0.8279 (mp0) cc_final: 0.7834 (mp0) REVERT: A 138 LYS cc_start: 0.7949 (tppt) cc_final: 0.7425 (tmtt) REVERT: A 202 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.6145 (ptm-80) REVERT: A 220 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7243 (mp0) REVERT: A 306 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.7498 (tmm) REVERT: B 726 TYR cc_start: 0.7884 (t80) cc_final: 0.7637 (t80) REVERT: B 813 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8385 (mt-10) REVERT: B 825 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8058 (mm) REVERT: B 860 MET cc_start: 0.6506 (OUTLIER) cc_final: 0.5819 (mpt) REVERT: B 868 ARG cc_start: 0.8300 (tpp80) cc_final: 0.7895 (mtt-85) REVERT: B 910 ARG cc_start: 0.7939 (ttp80) cc_final: 0.7699 (ttp80) REVERT: B 1171 GLU cc_start: 0.7544 (tp30) cc_final: 0.7226 (tp30) REVERT: B 1187 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6787 (mm) REVERT: B 1298 GLU cc_start: 0.6801 (tt0) cc_final: 0.6525 (mt-10) REVERT: E 276 ASP cc_start: 0.7254 (m-30) cc_final: 0.6878 (m-30) REVERT: E 316 MET cc_start: 0.1368 (mpm) cc_final: 0.1062 (mpp) REVERT: E 388 ASN cc_start: 0.3817 (OUTLIER) cc_final: 0.3581 (p0) REVERT: E 501 LYS cc_start: 0.6981 (mmtt) cc_final: 0.6482 (mptp) REVERT: E 523 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7793 (pt) REVERT: E 542 ILE cc_start: 0.8141 (mm) cc_final: 0.7784 (tt) REVERT: E 559 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.7094 (ptmt) REVERT: G 552 PHE cc_start: 0.8062 (t80) cc_final: 0.7816 (m-10) outliers start: 102 outliers final: 40 residues processed: 388 average time/residue: 1.5895 time to fit residues: 707.7495 Evaluate side-chains 355 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 302 time to evaluate : 2.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain F residue 347 MET Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 112 THR Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 45 THR Chi-restraints excluded: chain S residue 56 LYS Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 860 MET Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1317 ILE Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain E residue 543 ASP Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 559 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 88 optimal weight: 0.5980 chunk 236 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 263 optimal weight: 0.8980 chunk 218 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 138 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 267 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 GLN Q 38 ASN ** T 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 46 HIS V 60 ASN A 76 GLN ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 28105 Z= 0.207 Angle : 0.558 9.180 39296 Z= 0.307 Chirality : 0.037 0.195 4343 Planarity : 0.004 0.057 3879 Dihedral : 26.804 176.042 6225 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.54 % Allowed : 27.08 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.17), residues: 2450 helix: 1.09 (0.14), residues: 1345 sheet: -0.61 (0.57), residues: 89 loop : -1.18 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 775 HIS 0.008 0.001 HIS B 785 PHE 0.013 0.001 PHE B1147 TYR 0.025 0.001 TYR V 37 ARG 0.011 0.000 ARG R 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 326 time to evaluate : 2.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 103 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6792 (pp20) REVERT: D 275 GLN cc_start: 0.7434 (mm110) cc_final: 0.7076 (mm-40) REVERT: D 291 LYS cc_start: 0.8893 (mtpt) cc_final: 0.8422 (mmtt) REVERT: D 308 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7556 (mm-30) REVERT: D 315 LYS cc_start: 0.7407 (mttm) cc_final: 0.7133 (ptpt) REVERT: D 350 GLN cc_start: 0.8036 (tm-30) cc_final: 0.7688 (tm-30) REVERT: D 361 ASP cc_start: 0.8330 (m-30) cc_final: 0.8045 (m-30) REVERT: F 256 MET cc_start: 0.5726 (tpp) cc_final: 0.5269 (pmt) REVERT: F 317 GLN cc_start: 0.4728 (OUTLIER) cc_final: 0.4468 (pm20) REVERT: F 338 LEU cc_start: 0.8894 (mt) cc_final: 0.8437 (pt) REVERT: F 347 MET cc_start: 0.2357 (pp-130) cc_final: 0.1603 (pp-130) REVERT: O 115 LYS cc_start: 0.8978 (mmtp) cc_final: 0.8652 (mmtm) REVERT: P 77 LYS cc_start: 0.8543 (mmtp) cc_final: 0.8240 (mmtm) REVERT: P 85 ASP cc_start: 0.8191 (p0) cc_final: 0.7735 (p0) REVERT: Q 73 ASN cc_start: 0.7871 (p0) cc_final: 0.7513 (m110) REVERT: Q 92 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7984 (mt-10) REVERT: R 105 LYS cc_start: 0.7690 (pttm) cc_final: 0.7473 (ptpp) REVERT: R 113 LYS cc_start: 0.8657 (ttmm) cc_final: 0.8294 (tttp) REVERT: S 42 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7554 (ptm-80) REVERT: V 40 LYS cc_start: 0.8422 (mttm) cc_final: 0.8196 (mtpt) REVERT: V 82 LYS cc_start: 0.8719 (mmmt) cc_final: 0.8253 (mmtm) REVERT: V 102 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7625 (tp30) REVERT: A 92 ASP cc_start: 0.8769 (p0) cc_final: 0.8494 (m-30) REVERT: A 118 GLU cc_start: 0.8300 (mp0) cc_final: 0.7863 (mp0) REVERT: A 138 LYS cc_start: 0.8020 (tppt) cc_final: 0.7558 (tmtt) REVERT: A 202 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.6111 (ptm-80) REVERT: A 220 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7219 (mp0) REVERT: A 306 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.7509 (tmm) REVERT: B 726 TYR cc_start: 0.8012 (t80) cc_final: 0.7790 (t80) REVERT: B 813 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8403 (mt-10) REVERT: B 825 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8042 (mm) REVERT: B 860 MET cc_start: 0.6524 (OUTLIER) cc_final: 0.5844 (mpt) REVERT: B 868 ARG cc_start: 0.8295 (tpp80) cc_final: 0.7805 (mtt-85) REVERT: B 918 GLU cc_start: 0.8636 (mp0) cc_final: 0.8348 (mp0) REVERT: B 1171 GLU cc_start: 0.7566 (tp30) cc_final: 0.7247 (tp30) REVERT: B 1187 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6887 (mm) REVERT: B 1298 GLU cc_start: 0.6925 (tt0) cc_final: 0.6584 (mt-10) REVERT: E 388 ASN cc_start: 0.3796 (OUTLIER) cc_final: 0.3578 (p0) REVERT: E 500 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7013 (pttt) REVERT: E 501 LYS cc_start: 0.7030 (mmtt) cc_final: 0.6504 (mptp) REVERT: E 523 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7832 (pt) REVERT: E 542 ILE cc_start: 0.8174 (mm) cc_final: 0.7836 (tt) REVERT: E 559 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.7037 (ptmt) REVERT: G 552 PHE cc_start: 0.8051 (t80) cc_final: 0.7805 (m-10) outliers start: 101 outliers final: 48 residues processed: 392 average time/residue: 1.5698 time to fit residues: 705.6481 Evaluate side-chains 369 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 308 time to evaluate : 2.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain F residue 358 GLN Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 112 THR Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 68 GLN Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 860 MET Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain B residue 1178 VAL Chi-restraints excluded: chain B residue 1186 LEU Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1317 ILE Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain E residue 500 LYS Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain E residue 543 ASP Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 559 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 253 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 149 optimal weight: 0.0870 chunk 192 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 221 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 262 optimal weight: 3.9990 chunk 164 optimal weight: 0.7980 chunk 159 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 overall best weight: 0.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 267 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 GLN Q 38 ASN ** T 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 38 ASN V 46 HIS V 60 ASN ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1004 ASN E 521 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28105 Z= 0.207 Angle : 0.563 9.543 39296 Z= 0.309 Chirality : 0.036 0.188 4343 Planarity : 0.004 0.055 3879 Dihedral : 26.806 175.684 6225 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.41 % Allowed : 26.90 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.17), residues: 2450 helix: 1.12 (0.14), residues: 1345 sheet: -0.54 (0.58), residues: 86 loop : -1.19 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 775 HIS 0.009 0.001 HIS E 302 PHE 0.026 0.001 PHE E 262 TYR 0.027 0.001 TYR V 37 ARG 0.014 0.000 ARG R 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 323 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 82 GLN cc_start: 0.7402 (tp40) cc_final: 0.7093 (mm-40) REVERT: D 275 GLN cc_start: 0.7467 (mm110) cc_final: 0.6890 (mm-40) REVERT: D 291 LYS cc_start: 0.8917 (mtpt) cc_final: 0.8432 (mmtt) REVERT: D 308 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7553 (mm-30) REVERT: D 315 LYS cc_start: 0.7312 (mttm) cc_final: 0.7034 (ptpt) REVERT: D 350 GLN cc_start: 0.8057 (tm-30) cc_final: 0.7754 (tm-30) REVERT: D 361 ASP cc_start: 0.8330 (m-30) cc_final: 0.8054 (m-30) REVERT: F 256 MET cc_start: 0.5657 (tpp) cc_final: 0.5243 (pmt) REVERT: F 317 GLN cc_start: 0.4693 (OUTLIER) cc_final: 0.4438 (pm20) REVERT: F 338 LEU cc_start: 0.8937 (mt) cc_final: 0.8474 (pt) REVERT: F 347 MET cc_start: 0.2398 (OUTLIER) cc_final: 0.1519 (pp-130) REVERT: O 115 LYS cc_start: 0.8977 (mmtp) cc_final: 0.8649 (mmtm) REVERT: P 77 LYS cc_start: 0.8574 (mmtp) cc_final: 0.8260 (mmtm) REVERT: P 85 ASP cc_start: 0.8224 (p0) cc_final: 0.7775 (p0) REVERT: Q 73 ASN cc_start: 0.7824 (p0) cc_final: 0.7377 (m110) REVERT: Q 92 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7952 (mt-10) REVERT: R 105 LYS cc_start: 0.7679 (pttm) cc_final: 0.7462 (ptpp) REVERT: R 113 LYS cc_start: 0.8655 (ttmm) cc_final: 0.8294 (tttp) REVERT: S 42 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7526 (ptm-80) REVERT: S 59 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7618 (pm20) REVERT: T 84 MET cc_start: 0.8444 (mmm) cc_final: 0.8184 (mmm) REVERT: V 40 LYS cc_start: 0.8417 (mttm) cc_final: 0.8195 (mtpt) REVERT: V 82 LYS cc_start: 0.8710 (mmmt) cc_final: 0.8268 (mmtm) REVERT: V 90 GLU cc_start: 0.8311 (mp0) cc_final: 0.7874 (mp0) REVERT: V 102 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7649 (tp30) REVERT: A 92 ASP cc_start: 0.8762 (p0) cc_final: 0.8520 (m-30) REVERT: A 99 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8185 (tpp80) REVERT: A 118 GLU cc_start: 0.8282 (mp0) cc_final: 0.7828 (mp0) REVERT: A 202 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.6140 (ptm-80) REVERT: A 306 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.7534 (tmm) REVERT: B 775 TRP cc_start: 0.5955 (m-90) cc_final: 0.5752 (m-90) REVERT: B 813 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8313 (mt-10) REVERT: B 825 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7994 (mm) REVERT: B 860 MET cc_start: 0.6546 (OUTLIER) cc_final: 0.5865 (mpt) REVERT: B 868 ARG cc_start: 0.8304 (tpp80) cc_final: 0.7791 (mtt-85) REVERT: B 1171 GLU cc_start: 0.7526 (tp30) cc_final: 0.7220 (tp30) REVERT: B 1187 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6945 (mm) REVERT: E 500 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7011 (pttt) REVERT: E 501 LYS cc_start: 0.7076 (mmtt) cc_final: 0.6535 (mptp) REVERT: E 523 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7862 (pt) REVERT: E 542 ILE cc_start: 0.8164 (mm) cc_final: 0.7867 (tt) REVERT: E 559 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.7029 (ptmt) REVERT: G 552 PHE cc_start: 0.8057 (t80) cc_final: 0.7802 (m-10) outliers start: 98 outliers final: 46 residues processed: 382 average time/residue: 1.5982 time to fit residues: 703.2856 Evaluate side-chains 361 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 301 time to evaluate : 2.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain F residue 347 MET Chi-restraints excluded: chain F residue 358 GLN Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 112 THR Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 68 GLN Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain A residue 99 ARG Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 860 MET Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain B residue 1178 VAL Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1317 ILE Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain E residue 500 LYS Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain E residue 543 ASP Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain E residue 559 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 162 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 178 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 206 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 267 GLN Q 38 ASN S 39 HIS ** T 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 38 ASN V 60 ASN V 106 HIS ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 521 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 28105 Z= 0.224 Angle : 0.573 10.237 39296 Z= 0.314 Chirality : 0.037 0.193 4343 Planarity : 0.004 0.057 3879 Dihedral : 26.845 175.734 6225 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.87 % Allowed : 27.44 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.17), residues: 2450 helix: 1.08 (0.14), residues: 1346 sheet: -0.71 (0.54), residues: 94 loop : -1.17 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 775 HIS 0.005 0.001 HIS F 369 PHE 0.013 0.001 PHE B1147 TYR 0.027 0.002 TYR V 37 ARG 0.014 0.000 ARG R 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 310 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 82 GLN cc_start: 0.7397 (tp40) cc_final: 0.7081 (mm-40) REVERT: D 275 GLN cc_start: 0.7537 (mm110) cc_final: 0.6944 (mm-40) REVERT: D 291 LYS cc_start: 0.8937 (mtpt) cc_final: 0.8462 (mmtt) REVERT: D 315 LYS cc_start: 0.7339 (mttm) cc_final: 0.7067 (ptpt) REVERT: D 350 GLN cc_start: 0.8064 (tm-30) cc_final: 0.7712 (tm-30) REVERT: D 361 ASP cc_start: 0.8330 (m-30) cc_final: 0.8051 (m-30) REVERT: F 256 MET cc_start: 0.5696 (tpp) cc_final: 0.5331 (pmt) REVERT: F 338 LEU cc_start: 0.8964 (mt) cc_final: 0.8574 (pp) REVERT: F 347 MET cc_start: 0.2430 (OUTLIER) cc_final: 0.1570 (pp-130) REVERT: O 59 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7912 (pm20) REVERT: O 115 LYS cc_start: 0.8982 (mmtp) cc_final: 0.8648 (mmtm) REVERT: P 77 LYS cc_start: 0.8649 (mmtp) cc_final: 0.8339 (mmtm) REVERT: P 85 ASP cc_start: 0.8266 (p0) cc_final: 0.7667 (p0) REVERT: Q 73 ASN cc_start: 0.7772 (p0) cc_final: 0.7413 (m110) REVERT: Q 92 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7963 (mt-10) REVERT: R 105 LYS cc_start: 0.7732 (pttm) cc_final: 0.7464 (ptpp) REVERT: R 113 LYS cc_start: 0.8670 (ttmm) cc_final: 0.8308 (tttp) REVERT: S 42 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7590 (ptm-80) REVERT: S 59 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7662 (pm20) REVERT: V 40 LYS cc_start: 0.8426 (mttm) cc_final: 0.8139 (mtmt) REVERT: V 82 LYS cc_start: 0.8720 (mmmt) cc_final: 0.8281 (mmtm) REVERT: V 102 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7744 (tp30) REVERT: A 99 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8197 (tpp80) REVERT: A 118 GLU cc_start: 0.8309 (mp0) cc_final: 0.7875 (mp0) REVERT: A 160 PHE cc_start: 0.8438 (m-80) cc_final: 0.7986 (m-80) REVERT: A 202 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7878 (mtp-110) REVERT: A 306 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.7565 (tmm) REVERT: B 707 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7424 (t0) REVERT: B 813 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8348 (mt-10) REVERT: B 825 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8001 (mm) REVERT: B 860 MET cc_start: 0.6647 (OUTLIER) cc_final: 0.5929 (mpt) REVERT: B 868 ARG cc_start: 0.8298 (tpp80) cc_final: 0.7790 (mtt-85) REVERT: B 1171 GLU cc_start: 0.7675 (tp30) cc_final: 0.7329 (tp30) REVERT: E 500 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7063 (pttt) REVERT: E 501 LYS cc_start: 0.7097 (mmtt) cc_final: 0.6552 (mptp) REVERT: E 523 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7896 (pt) REVERT: E 542 ILE cc_start: 0.8175 (mm) cc_final: 0.7906 (tt) REVERT: G 316 MET cc_start: 0.3310 (ttm) cc_final: 0.2878 (tpt) REVERT: G 552 PHE cc_start: 0.8076 (t80) cc_final: 0.7812 (m-10) outliers start: 86 outliers final: 49 residues processed: 365 average time/residue: 1.5781 time to fit residues: 664.3085 Evaluate side-chains 354 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 292 time to evaluate : 2.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 347 MET Chi-restraints excluded: chain F residue 358 GLN Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 112 THR Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 99 ARG Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 707 ASP Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 860 MET Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain B residue 1178 VAL Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1317 ILE Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain E residue 500 LYS Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 521 GLN Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain E residue 543 ASP Chi-restraints excluded: chain E residue 546 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 238 optimal weight: 0.0870 chunk 251 optimal weight: 2.9990 chunk 229 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 147 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 191 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 220 optimal weight: 7.9990 chunk 231 optimal weight: 0.9980 chunk 243 optimal weight: 0.8980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 267 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 GLN Q 38 ASN ** T 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 38 ASN V 46 HIS V 60 ASN ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 521 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28105 Z= 0.209 Angle : 0.578 11.346 39296 Z= 0.315 Chirality : 0.037 0.171 4343 Planarity : 0.004 0.059 3879 Dihedral : 26.817 175.642 6225 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.82 % Allowed : 28.07 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.17), residues: 2450 helix: 1.10 (0.14), residues: 1344 sheet: -0.78 (0.54), residues: 94 loop : -1.17 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 775 HIS 0.005 0.001 HIS F 369 PHE 0.016 0.001 PHE B1147 TYR 0.028 0.001 TYR V 37 ARG 0.015 0.000 ARG R 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 298 time to evaluate : 2.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 82 GLN cc_start: 0.7504 (tp40) cc_final: 0.7196 (mm-40) REVERT: D 291 LYS cc_start: 0.8938 (mtpt) cc_final: 0.8472 (mmtt) REVERT: D 315 LYS cc_start: 0.7312 (mttm) cc_final: 0.7023 (ptpt) REVERT: D 361 ASP cc_start: 0.8320 (m-30) cc_final: 0.8043 (m-30) REVERT: F 256 MET cc_start: 0.5700 (tpp) cc_final: 0.5347 (pmt) REVERT: F 338 LEU cc_start: 0.8970 (mt) cc_final: 0.8591 (pp) REVERT: F 347 MET cc_start: 0.2417 (OUTLIER) cc_final: 0.1642 (pp-130) REVERT: O 59 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7896 (pm20) REVERT: O 115 LYS cc_start: 0.8979 (mmtp) cc_final: 0.8710 (mmtm) REVERT: P 77 LYS cc_start: 0.8627 (mmtp) cc_final: 0.8317 (mmtm) REVERT: P 85 ASP cc_start: 0.8325 (p0) cc_final: 0.7939 (p0) REVERT: Q 92 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7960 (mt-10) REVERT: R 105 LYS cc_start: 0.7693 (pttm) cc_final: 0.7450 (ptpp) REVERT: R 113 LYS cc_start: 0.8664 (ttmm) cc_final: 0.8301 (tttp) REVERT: S 42 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7519 (ptm-80) REVERT: S 59 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7661 (pm20) REVERT: V 40 LYS cc_start: 0.8418 (mttm) cc_final: 0.8138 (mtmt) REVERT: V 82 LYS cc_start: 0.8699 (mmmt) cc_final: 0.8258 (mmtm) REVERT: V 90 GLU cc_start: 0.8316 (mp0) cc_final: 0.7875 (mp0) REVERT: V 102 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7688 (tp30) REVERT: A 53 MET cc_start: 0.8054 (mmm) cc_final: 0.7673 (mmp) REVERT: A 99 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8215 (tpp80) REVERT: A 118 GLU cc_start: 0.8285 (mp0) cc_final: 0.7800 (mp0) REVERT: A 160 PHE cc_start: 0.8413 (m-80) cc_final: 0.7969 (m-80) REVERT: A 306 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.7577 (tmm) REVERT: A 422 ARG cc_start: 0.4557 (OUTLIER) cc_final: 0.4292 (mtt180) REVERT: B 707 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7408 (t0) REVERT: B 813 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8285 (mt-10) REVERT: B 825 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8012 (mm) REVERT: B 860 MET cc_start: 0.6676 (OUTLIER) cc_final: 0.5954 (mpt) REVERT: B 868 ARG cc_start: 0.8246 (tpp80) cc_final: 0.7789 (mtt-85) REVERT: B 1171 GLU cc_start: 0.7680 (tp30) cc_final: 0.7349 (tp30) REVERT: E 316 MET cc_start: 0.1341 (mpm) cc_final: 0.1001 (mpp) REVERT: E 500 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7073 (pttt) REVERT: E 501 LYS cc_start: 0.7109 (mmtt) cc_final: 0.6581 (mptp) REVERT: E 523 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7983 (pt) REVERT: E 542 ILE cc_start: 0.8179 (mm) cc_final: 0.7925 (tt) REVERT: G 316 MET cc_start: 0.3369 (ttm) cc_final: 0.2904 (tpt) REVERT: G 552 PHE cc_start: 0.8090 (t80) cc_final: 0.7817 (m-10) outliers start: 85 outliers final: 52 residues processed: 350 average time/residue: 1.6178 time to fit residues: 653.0532 Evaluate side-chains 360 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 295 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 312 LYS Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 347 MET Chi-restraints excluded: chain F residue 358 GLN Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 112 THR Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 68 GLN Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 99 ARG Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 707 ASP Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 804 GLU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 860 MET Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain B residue 1178 VAL Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1317 ILE Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain E residue 500 LYS Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 521 GLN Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain E residue 543 ASP Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 549 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 160 optimal weight: 1.9990 chunk 258 optimal weight: 0.9980 chunk 157 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 270 optimal weight: 5.9990 chunk 249 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 166 optimal weight: 0.3980 chunk 132 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 GLN Q 38 ASN ** T 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 38 ASN V 46 HIS V 60 ASN ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 517 ASN E 519 ASN E 521 GLN G 562 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 28105 Z= 0.308 Angle : 0.636 13.036 39296 Z= 0.344 Chirality : 0.039 0.181 4343 Planarity : 0.004 0.069 3879 Dihedral : 27.066 176.556 6225 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.42 % Allowed : 28.61 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.17), residues: 2450 helix: 0.89 (0.14), residues: 1363 sheet: -0.93 (0.60), residues: 78 loop : -1.16 (0.19), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 775 HIS 0.005 0.001 HIS F 369 PHE 0.016 0.002 PHE B1026 TYR 0.034 0.002 TYR V 37 ARG 0.016 0.001 ARG R 30 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 298 time to evaluate : 2.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 82 GLN cc_start: 0.7645 (tp40) cc_final: 0.7326 (mm-40) REVERT: D 291 LYS cc_start: 0.8995 (mtpt) cc_final: 0.8530 (mmtt) REVERT: D 315 LYS cc_start: 0.7293 (mttm) cc_final: 0.7073 (ptpt) REVERT: D 361 ASP cc_start: 0.8327 (m-30) cc_final: 0.8043 (m-30) REVERT: F 256 MET cc_start: 0.5742 (tpp) cc_final: 0.5375 (pmt) REVERT: F 338 LEU cc_start: 0.8991 (mt) cc_final: 0.8610 (pp) REVERT: F 347 MET cc_start: 0.2591 (OUTLIER) cc_final: 0.1765 (pp-130) REVERT: O 59 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7960 (pm20) REVERT: O 115 LYS cc_start: 0.8998 (mmtp) cc_final: 0.8657 (mmtm) REVERT: P 77 LYS cc_start: 0.8851 (mmtp) cc_final: 0.8428 (mmtm) REVERT: P 85 ASP cc_start: 0.8370 (p0) cc_final: 0.8070 (p0) REVERT: P 92 ARG cc_start: 0.8834 (ptm-80) cc_final: 0.8620 (ptm-80) REVERT: Q 73 ASN cc_start: 0.8084 (p0) cc_final: 0.7639 (m110) REVERT: Q 92 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7974 (mt-10) REVERT: R 105 LYS cc_start: 0.7819 (pttm) cc_final: 0.7537 (ptpp) REVERT: R 113 LYS cc_start: 0.8725 (ttmm) cc_final: 0.8371 (tttp) REVERT: S 59 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7712 (pm20) REVERT: V 82 LYS cc_start: 0.8748 (mmmt) cc_final: 0.8283 (mmtm) REVERT: V 102 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7756 (tp30) REVERT: A 60 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7322 (mttm) REVERT: A 99 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8256 (tpp80) REVERT: A 118 GLU cc_start: 0.8333 (mp0) cc_final: 0.7900 (mp0) REVERT: A 160 PHE cc_start: 0.8547 (m-80) cc_final: 0.8243 (m-80) REVERT: A 165 ASP cc_start: 0.7858 (p0) cc_final: 0.7641 (p0) REVERT: A 306 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.7563 (tmm) REVERT: B 813 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8372 (mt-10) REVERT: B 825 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7908 (mm) REVERT: B 860 MET cc_start: 0.6710 (OUTLIER) cc_final: 0.5981 (mpt) REVERT: B 868 ARG cc_start: 0.8335 (tpp80) cc_final: 0.7922 (mtt-85) REVERT: B 1171 GLU cc_start: 0.7665 (tp30) cc_final: 0.7329 (tp30) REVERT: B 1298 GLU cc_start: 0.6915 (mt-10) cc_final: 0.6702 (mt-10) REVERT: E 316 MET cc_start: 0.1341 (mpm) cc_final: 0.0906 (mpp) REVERT: E 501 LYS cc_start: 0.7207 (mmtt) cc_final: 0.6674 (mptp) REVERT: E 523 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8284 (pt) REVERT: E 542 ILE cc_start: 0.8268 (mm) cc_final: 0.8039 (tt) REVERT: G 316 MET cc_start: 0.3447 (ttm) cc_final: 0.2973 (tpt) REVERT: G 552 PHE cc_start: 0.8176 (t80) cc_final: 0.7851 (m-10) outliers start: 76 outliers final: 46 residues processed: 347 average time/residue: 1.5803 time to fit residues: 629.8575 Evaluate side-chains 346 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 290 time to evaluate : 2.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 347 MET Chi-restraints excluded: chain F residue 358 GLN Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 112 THR Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 99 ARG Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 804 GLU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 860 MET Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain B residue 1178 VAL Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1317 ILE Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain E residue 543 ASP Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 549 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 171 optimal weight: 1.9990 chunk 229 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 198 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 216 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 221 optimal weight: 0.0970 chunk 27 optimal weight: 20.0000 chunk 39 optimal weight: 7.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 GLN Q 38 ASN ** T 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 38 ASN V 46 HIS V 60 ASN ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 521 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.121565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.088870 restraints weight = 55250.973| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.19 r_work: 0.3178 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.5691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28105 Z= 0.214 Angle : 0.603 14.048 39296 Z= 0.327 Chirality : 0.037 0.227 4343 Planarity : 0.004 0.063 3879 Dihedral : 26.924 175.548 6225 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.74 % Allowed : 29.46 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.17), residues: 2450 helix: 0.97 (0.14), residues: 1355 sheet: -0.84 (0.58), residues: 85 loop : -1.19 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP B 775 HIS 0.006 0.001 HIS B 785 PHE 0.023 0.001 PHE E 262 TYR 0.032 0.002 TYR T 88 ARG 0.016 0.000 ARG R 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11343.05 seconds wall clock time: 204 minutes 30.41 seconds (12270.41 seconds total)