Starting phenix.real_space_refine on Sat Mar 16 00:46:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k79_22697/03_2024/7k79_22697.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k79_22697/03_2024/7k79_22697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k79_22697/03_2024/7k79_22697.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k79_22697/03_2024/7k79_22697.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k79_22697/03_2024/7k79_22697.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k79_22697/03_2024/7k79_22697.pdb" } resolution = 4.0 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= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 8616 2.51 5 N 2175 2.21 5 O 2423 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K ARG 17": "NH1" <-> "NH2" Residue "K ARG 55": "NH1" <-> "NH2" Residue "K ARG 64": "NH1" <-> "NH2" Residue "K GLU 89": "OE1" <-> "OE2" Residue "K ARG 95": "NH1" <-> "NH2" Residue "K ARG 128": "NH1" <-> "NH2" Residue "K GLU 188": "OE1" <-> "OE2" Residue "K ARG 262": "NH1" <-> "NH2" Residue "K GLU 268": "OE1" <-> "OE2" Residue "K GLU 285": "OE1" <-> "OE2" Residue "K ARG 308": "NH1" <-> "NH2" Residue "K GLU 311": "OE1" <-> "OE2" Residue "K ARG 313": "NH1" <-> "NH2" Residue "K ARG 322": "NH1" <-> "NH2" Residue "K ARG 330": "NH1" <-> "NH2" Residue "K GLU 374": "OE1" <-> "OE2" Residue "K ARG 409": "NH1" <-> "NH2" Residue "K GLU 417": "OE1" <-> "OE2" Residue "K ARG 463": "NH1" <-> "NH2" Residue "K ARG 468": "NH1" <-> "NH2" Residue "L GLU 56": "OE1" <-> "OE2" Residue "L GLU 97": "OE1" <-> "OE2" Residue "L GLU 98": "OE1" <-> "OE2" Residue "L GLU 141": "OE1" <-> "OE2" Residue "L ARG 147": "NH1" <-> "NH2" Residue "L GLU 177": "OE1" <-> "OE2" Residue "L GLU 181": "OE1" <-> "OE2" Residue "L GLU 190": "OE1" <-> "OE2" Residue "L GLU 201": "OE1" <-> "OE2" Residue "L GLU 282": "OE1" <-> "OE2" Residue "L ARG 307": "NH1" <-> "NH2" Residue "L GLU 337": "OE1" <-> "OE2" Residue "L GLU 338": "OE1" <-> "OE2" Residue "L GLU 342": "OE1" <-> "OE2" Residue "L ARG 375": "NH1" <-> "NH2" Residue "L GLU 376": "OE1" <-> "OE2" Residue "L ARG 392": "NH1" <-> "NH2" Residue "L ARG 397": "NH1" <-> "NH2" Residue "L GLU 451": "OE1" <-> "OE2" Residue "L PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 512": "OE1" <-> "OE2" Residue "L GLU 549": "OE1" <-> "OE2" Residue "L GLU 554": "OE1" <-> "OE2" Residue "L ARG 591": "NH1" <-> "NH2" Residue "L GLU 595": "OE1" <-> "OE2" Residue "L GLU 600": "OE1" <-> "OE2" Residue "O GLU 69": "OE1" <-> "OE2" Residue "O GLU 98": "OE1" <-> "OE2" Residue "O GLU 135": "OE1" <-> "OE2" Residue "O GLU 141": "OE1" <-> "OE2" Residue "O GLU 342": "OE1" <-> "OE2" Residue "O GLU 376": "OE1" <-> "OE2" Residue "O GLU 389": "OE1" <-> "OE2" Residue "O ARG 392": "NH1" <-> "NH2" Residue "O GLU 451": "OE1" <-> "OE2" Residue "O GLU 491": "OE1" <-> "OE2" Residue "O GLU 512": "OE1" <-> "OE2" Residue "O ARG 591": "NH1" <-> "NH2" Residue "O GLU 596": "OE1" <-> "OE2" Residue "N ARG 25": "NH1" <-> "NH2" Residue "N ARG 83": "NH1" <-> "NH2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "N ARG 121": "NH1" <-> "NH2" Residue "N GLU 156": "OE1" <-> "OE2" Residue "N ARG 159": "NH1" <-> "NH2" Residue "N ARG 161": "NH1" <-> "NH2" Residue "N GLU 165": "OE1" <-> "OE2" Residue "N ARG 168": "NH1" <-> "NH2" Residue "N PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 179": "OE1" <-> "OE2" Residue "N GLU 180": "OE1" <-> "OE2" Residue "N GLU 181": "OE1" <-> "OE2" Residue "N ARG 185": "NH1" <-> "NH2" Residue "N ARG 186": "NH1" <-> "NH2" Residue "N GLU 189": "OE1" <-> "OE2" Residue "N GLU 192": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13272 Number of models: 1 Model: "" Number of chains: 4 Chain: "K" Number of atoms: 3413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3413 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 397} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "L" Number of atoms: 4355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4355 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 507} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "O" Number of atoms: 4284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4284 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 499} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1220 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 7.14, per 1000 atoms: 0.54 Number of scatterers: 13272 At special positions: 0 Unit cell: (113.42, 125.08, 98.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 2423 8.00 N 2175 7.00 C 8616 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS L 99 " - pdb=" SG CYS L 215 " 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: 5.79 Conformation dependent library (CDL) restraints added in 2.4 seconds 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3118 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 5 sheets defined 57.6% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'K' and resid 13 through 24 removed outlier: 3.857A pdb=" N TYR K 21 " --> pdb=" O ARG K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 66 Processing helix chain 'K' and resid 69 through 74 Processing helix chain 'K' and resid 85 through 91 removed outlier: 4.212A pdb=" N GLU K 89 " --> pdb=" O GLU K 85 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA K 91 " --> pdb=" O TRP K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 107 Processing helix chain 'K' and resid 143 through 151 removed outlier: 3.632A pdb=" N LYS K 149 " --> pdb=" O LYS K 145 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TRP K 150 " --> pdb=" O GLU K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 185 removed outlier: 3.953A pdb=" N SER K 185 " --> pdb=" O ASP K 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 192 through 196 Processing helix chain 'K' and resid 257 through 266 removed outlier: 4.281A pdb=" N ILE K 261 " --> pdb=" O SER K 257 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG K 262 " --> pdb=" O ILE K 258 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR K 263 " --> pdb=" O SER K 259 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE K 264 " --> pdb=" O VAL K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 280 through 288 removed outlier: 3.975A pdb=" N TYR K 284 " --> pdb=" O GLY K 280 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU K 286 " --> pdb=" O LYS K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 304 through 308 removed outlier: 4.031A pdb=" N ARG K 307 " --> pdb=" O ILE K 304 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG K 308 " --> pdb=" O VAL K 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 304 through 308' Processing helix chain 'K' and resid 346 through 350 Processing helix chain 'K' and resid 368 through 371 removed outlier: 3.695A pdb=" N ASN K 371 " --> pdb=" O LYS K 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 368 through 371' Processing helix chain 'K' and resid 372 through 380 Processing helix chain 'K' and resid 383 through 390 removed outlier: 3.971A pdb=" N LEU K 390 " --> pdb=" O THR K 386 " (cutoff:3.500A) Processing helix chain 'K' and resid 398 through 402 removed outlier: 4.151A pdb=" N LYS K 401 " --> pdb=" O LYS K 398 " (cutoff:3.500A) Processing helix chain 'K' and resid 423 through 434 removed outlier: 3.671A pdb=" N SER K 433 " --> pdb=" O ILE K 429 " (cutoff:3.500A) Processing helix chain 'K' and resid 455 through 460 Processing helix chain 'L' and resid 58 through 72 removed outlier: 3.696A pdb=" N LEU L 62 " --> pdb=" O LEU L 58 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU L 63 " --> pdb=" O PRO L 59 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N PHE L 64 " --> pdb=" O ASP L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 106 removed outlier: 4.307A pdb=" N PHE L 101 " --> pdb=" O GLU L 97 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU L 106 " --> pdb=" O TRP L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 122 removed outlier: 3.575A pdb=" N LEU L 122 " --> pdb=" O ALA L 118 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 145 Processing helix chain 'L' and resid 153 through 173 removed outlier: 3.519A pdb=" N LYS L 157 " --> pdb=" O SER L 153 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR L 173 " --> pdb=" O MET L 169 " (cutoff:3.500A) Processing helix chain 'L' and resid 175 through 181 removed outlier: 4.103A pdb=" N GLU L 181 " --> pdb=" O GLU L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 190 removed outlier: 4.112A pdb=" N HIS L 189 " --> pdb=" O VAL L 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 203 through 224 Processing helix chain 'L' and resid 230 through 241 removed outlier: 4.221A pdb=" N VAL L 234 " --> pdb=" O ASP L 230 " (cutoff:3.500A) Processing helix chain 'L' and resid 244 through 249 Processing helix chain 'L' and resid 249 through 266 removed outlier: 3.506A pdb=" N ALA L 253 " --> pdb=" O GLU L 249 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN L 266 " --> pdb=" O HIS L 262 " (cutoff:3.500A) Processing helix chain 'L' and resid 279 through 302 removed outlier: 3.598A pdb=" N LEU L 302 " --> pdb=" O GLY L 298 " (cutoff:3.500A) Processing helix chain 'L' and resid 343 through 357 removed outlier: 3.536A pdb=" N ASP L 354 " --> pdb=" O SER L 350 " (cutoff:3.500A) Processing helix chain 'L' and resid 358 through 360 No H-bonds generated for 'chain 'L' and resid 358 through 360' Processing helix chain 'L' and resid 366 through 384 removed outlier: 3.963A pdb=" N LEU L 370 " --> pdb=" O PRO L 366 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TYR L 382 " --> pdb=" O ASP L 378 " (cutoff:3.500A) Processing helix chain 'L' and resid 393 through 422 removed outlier: 3.884A pdb=" N ARG L 397 " --> pdb=" O SER L 393 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER L 411 " --> pdb=" O ILE L 407 " (cutoff:3.500A) Processing helix chain 'L' and resid 428 through 445 Processing helix chain 'L' and resid 451 through 456 removed outlier: 3.667A pdb=" N ASN L 454 " --> pdb=" O GLU L 451 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS L 456 " --> pdb=" O PHE L 453 " (cutoff:3.500A) Processing helix chain 'L' and resid 458 through 477 removed outlier: 3.649A pdb=" N ILE L 463 " --> pdb=" O VAL L 459 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR L 464 " --> pdb=" O MET L 460 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE L 475 " --> pdb=" O SER L 471 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N PHE L 476 " --> pdb=" O PHE L 472 " (cutoff:3.500A) Processing helix chain 'L' and resid 481 through 494 Processing helix chain 'L' and resid 501 through 522 removed outlier: 3.856A pdb=" N LEU L 519 " --> pdb=" O SER L 515 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU L 520 " --> pdb=" O LYS L 516 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP L 522 " --> pdb=" O LYS L 518 " (cutoff:3.500A) Processing helix chain 'L' and resid 536 through 552 removed outlier: 4.612A pdb=" N GLN L 542 " --> pdb=" O PHE L 538 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE L 545 " --> pdb=" O LEU L 541 " (cutoff:3.500A) Processing helix chain 'L' and resid 554 through 562 Processing helix chain 'L' and resid 590 through 601 Processing helix chain 'O' and resid 56 through 73 removed outlier: 4.370A pdb=" N ASP O 60 " --> pdb=" O GLU O 56 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE O 64 " --> pdb=" O ASP O 60 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN O 66 " --> pdb=" O LEU O 62 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ASN O 67 " --> pdb=" O LEU O 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 98 through 103 Processing helix chain 'O' and resid 107 through 118 Processing helix chain 'O' and resid 125 through 129 removed outlier: 3.724A pdb=" N GLY O 128 " --> pdb=" O LEU O 125 " (cutoff:3.500A) Processing helix chain 'O' and resid 133 through 147 Processing helix chain 'O' and resid 154 through 171 removed outlier: 3.650A pdb=" N MET O 169 " --> pdb=" O SER O 165 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 174 No H-bonds generated for 'chain 'O' and resid 172 through 174' Processing helix chain 'O' and resid 175 through 182 removed outlier: 3.729A pdb=" N LEU O 179 " --> pdb=" O PRO O 175 " (cutoff:3.500A) Processing helix chain 'O' and resid 203 through 224 removed outlier: 4.186A pdb=" N CYS O 209 " --> pdb=" O GLN O 205 " (cutoff:3.500A) Processing helix chain 'O' and resid 230 through 232 No H-bonds generated for 'chain 'O' and resid 230 through 232' Processing helix chain 'O' and resid 233 through 241 removed outlier: 3.790A pdb=" N ILE O 239 " --> pdb=" O GLN O 235 " (cutoff:3.500A) Processing helix chain 'O' and resid 244 through 249 Processing helix chain 'O' and resid 249 through 266 removed outlier: 3.505A pdb=" N ALA O 253 " --> pdb=" O GLU O 249 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER O 255 " --> pdb=" O LEU O 251 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN O 266 " --> pdb=" O HIS O 262 " (cutoff:3.500A) Processing helix chain 'O' and resid 279 through 304 removed outlier: 3.747A pdb=" N SER O 283 " --> pdb=" O ASP O 279 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG O 291 " --> pdb=" O VAL O 287 " (cutoff:3.500A) Processing helix chain 'O' and resid 340 through 344 removed outlier: 3.649A pdb=" N VAL O 343 " --> pdb=" O SER O 340 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU O 344 " --> pdb=" O THR O 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 340 through 344' Processing helix chain 'O' and resid 346 through 357 removed outlier: 4.783A pdb=" N ASP O 354 " --> pdb=" O SER O 350 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU O 355 " --> pdb=" O LEU O 351 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP O 356 " --> pdb=" O ASP O 352 " (cutoff:3.500A) Processing helix chain 'O' and resid 366 through 386 removed outlier: 4.500A pdb=" N LEU O 370 " --> pdb=" O PRO O 366 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA O 372 " --> pdb=" O LYS O 368 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP O 378 " --> pdb=" O ARG O 374 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE O 379 " --> pdb=" O ARG O 375 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL O 384 " --> pdb=" O PHE O 380 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP O 385 " --> pdb=" O GLN O 381 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER O 386 " --> pdb=" O TYR O 382 " (cutoff:3.500A) Processing helix chain 'O' and resid 393 through 422 removed outlier: 3.915A pdb=" N ARG O 397 " --> pdb=" O SER O 393 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET O 417 " --> pdb=" O LYS O 413 " (cutoff:3.500A) Processing helix chain 'O' and resid 426 through 435 Processing helix chain 'O' and resid 435 through 445 removed outlier: 4.173A pdb=" N ILE O 439 " --> pdb=" O SER O 435 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN O 445 " --> pdb=" O LEU O 441 " (cutoff:3.500A) Processing helix chain 'O' and resid 451 through 456 Processing helix chain 'O' and resid 458 through 475 removed outlier: 4.063A pdb=" N THR O 464 " --> pdb=" O MET O 460 " (cutoff:3.500A) Processing helix chain 'O' and resid 481 through 494 removed outlier: 3.701A pdb=" N ALA O 494 " --> pdb=" O THR O 490 " (cutoff:3.500A) Processing helix chain 'O' and resid 497 through 500 removed outlier: 3.882A pdb=" N PHE O 500 " --> pdb=" O PRO O 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 497 through 500' Processing helix chain 'O' and resid 501 through 524 Processing helix chain 'O' and resid 535 through 552 removed outlier: 3.889A pdb=" N LYS O 539 " --> pdb=" O HIS O 535 " (cutoff:3.500A) Processing helix chain 'O' and resid 554 through 563 Processing helix chain 'O' and resid 602 through 606 removed outlier: 3.754A pdb=" N ASP O 605 " --> pdb=" O ASN O 602 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 25 removed outlier: 3.746A pdb=" N ARG N 25 " --> pdb=" O ILE N 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 22 through 25' Processing helix chain 'N' and resid 26 through 31 Processing helix chain 'N' and resid 83 through 97 removed outlier: 3.603A pdb=" N LEU N 87 " --> pdb=" O ARG N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 125 removed outlier: 3.639A pdb=" N LEU N 124 " --> pdb=" O ARG N 121 " (cutoff:3.500A) Processing helix chain 'N' and resid 128 through 142 removed outlier: 3.893A pdb=" N TYR N 132 " --> pdb=" O GLN N 128 " (cutoff:3.500A) Processing helix chain 'N' and resid 143 through 157 removed outlier: 3.506A pdb=" N VAL N 153 " --> pdb=" O ALA N 149 " (cutoff:3.500A) Processing helix chain 'N' and resid 177 through 187 removed outlier: 3.627A pdb=" N GLU N 181 " --> pdb=" O THR N 177 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG N 185 " --> pdb=" O GLU N 181 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 131 through 132 removed outlier: 6.635A pdb=" N TYR K 131 " --> pdb=" O GLU K 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 199 through 201 removed outlier: 3.907A pdb=" N VAL K 199 " --> pdb=" O LYS K 275 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR K 277 " --> pdb=" O VAL K 199 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ILE K 312 " --> pdb=" O VAL K 338 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU K 337 " --> pdb=" O THR K 360 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 410 through 412 removed outlier: 6.121A pdb=" N LYS K 411 " --> pdb=" O VAL K 477 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 527 through 528 Processing sheet with id=AA5, first strand: chain 'O' and resid 527 through 528 550 hydrogen bonds defined for protein. 1608 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.46 Time building geometry restraints manager: 6.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3313 1.33 - 1.45: 3032 1.45 - 1.58: 7137 1.58 - 1.70: 5 1.70 - 1.82: 93 Bond restraints: 13580 Sorted by residual: bond pdb=" CA LYS O 55 " pdb=" C LYS O 55 " ideal model delta sigma weight residual 1.523 1.591 -0.068 1.56e-02 4.11e+03 1.88e+01 bond pdb=" CA ARG K 58 " pdb=" CB ARG K 58 " ideal model delta sigma weight residual 1.527 1.592 -0.066 1.75e-02 3.27e+03 1.40e+01 bond pdb=" C TYR L 173 " pdb=" N MET L 174 " ideal model delta sigma weight residual 1.331 1.272 0.059 1.63e-02 3.76e+03 1.31e+01 bond pdb=" CA ARG N 15 " pdb=" CB ARG N 15 " ideal model delta sigma weight residual 1.531 1.578 -0.047 1.52e-02 4.33e+03 9.72e+00 bond pdb=" CA TYR K 67 " pdb=" CB TYR K 67 " ideal model delta sigma weight residual 1.526 1.556 -0.030 1.09e-02 8.42e+03 7.47e+00 ... (remaining 13575 not shown) Histogram of bond angle deviations from ideal: 94.44 - 102.50: 57 102.50 - 110.57: 3431 110.57 - 118.63: 7029 118.63 - 126.69: 7649 126.69 - 134.75: 214 Bond angle restraints: 18380 Sorted by residual: angle pdb=" N ILE L 606 " pdb=" CA ILE L 606 " pdb=" C ILE L 606 " ideal model delta sigma weight residual 112.83 104.34 8.49 9.90e-01 1.02e+00 7.36e+01 angle pdb=" CB ARG L 465 " pdb=" CG ARG L 465 " pdb=" CD ARG L 465 " ideal model delta sigma weight residual 111.30 128.70 -17.40 2.30e+00 1.89e-01 5.72e+01 angle pdb=" C GLU L 98 " pdb=" N CYS L 99 " pdb=" CA CYS L 99 " ideal model delta sigma weight residual 122.65 110.82 11.83 1.60e+00 3.91e-01 5.47e+01 angle pdb=" C VAL N 18 " pdb=" N ASP N 19 " pdb=" CA ASP N 19 " ideal model delta sigma weight residual 121.54 133.51 -11.97 1.91e+00 2.74e-01 3.93e+01 angle pdb=" C ARG L 214 " pdb=" N CYS L 215 " pdb=" CA CYS L 215 " ideal model delta sigma weight residual 122.49 112.88 9.61 1.55e+00 4.16e-01 3.84e+01 ... (remaining 18375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.39: 6899 18.39 - 36.77: 1038 36.77 - 55.16: 172 55.16 - 73.55: 21 73.55 - 91.93: 16 Dihedral angle restraints: 8146 sinusoidal: 3359 harmonic: 4787 Sorted by residual: dihedral pdb=" CA ARG N 186 " pdb=" C ARG N 186 " pdb=" N GLU N 187 " pdb=" CA GLU N 187 " ideal model delta harmonic sigma weight residual 180.00 144.31 35.69 0 5.00e+00 4.00e-02 5.09e+01 dihedral pdb=" CA PHE K 9 " pdb=" C PHE K 9 " pdb=" N LEU K 10 " pdb=" CA LEU K 10 " ideal model delta harmonic sigma weight residual 180.00 144.54 35.46 0 5.00e+00 4.00e-02 5.03e+01 dihedral pdb=" CB CYS L 99 " pdb=" SG CYS L 99 " pdb=" SG CYS L 215 " pdb=" CB CYS L 215 " ideal model delta sinusoidal sigma weight residual 93.00 145.08 -52.08 1 1.00e+01 1.00e-02 3.70e+01 ... (remaining 8143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1602 0.093 - 0.185: 380 0.185 - 0.278: 47 0.278 - 0.370: 14 0.370 - 0.462: 1 Chirality restraints: 2044 Sorted by residual: chirality pdb=" CB VAL O 443 " pdb=" CA VAL O 443 " pdb=" CG1 VAL O 443 " pdb=" CG2 VAL O 443 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.35e+00 chirality pdb=" CG LEU L 289 " pdb=" CB LEU L 289 " pdb=" CD1 LEU L 289 " pdb=" CD2 LEU L 289 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CB ILE K 466 " pdb=" CA ILE K 466 " pdb=" CG1 ILE K 466 " pdb=" CG2 ILE K 466 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.00e+00 ... (remaining 2041 not shown) Planarity restraints: 2305 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 65 " -0.046 2.00e-02 2.50e+03 3.77e-02 3.56e+01 pdb=" CG TRP L 65 " 0.103 2.00e-02 2.50e+03 pdb=" CD1 TRP L 65 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP L 65 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP L 65 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP L 65 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP L 65 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 65 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 65 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP L 65 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU O 141 " 0.026 2.00e-02 2.50e+03 5.38e-02 2.90e+01 pdb=" CD GLU O 141 " -0.093 2.00e-02 2.50e+03 pdb=" OE1 GLU O 141 " 0.033 2.00e-02 2.50e+03 pdb=" OE2 GLU O 141 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP O 346 " -0.042 2.00e-02 2.50e+03 3.36e-02 2.82e+01 pdb=" CG TRP O 346 " 0.088 2.00e-02 2.50e+03 pdb=" CD1 TRP O 346 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP O 346 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP O 346 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP O 346 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP O 346 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP O 346 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP O 346 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP O 346 " -0.018 2.00e-02 2.50e+03 ... (remaining 2302 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1539 2.74 - 3.28: 13707 3.28 - 3.82: 22487 3.82 - 4.36: 25688 4.36 - 4.90: 41162 Nonbonded interactions: 104583 Sorted by model distance: nonbonded pdb=" OG SER L 393 " pdb=" OD1 ASN L 395 " model vdw 2.197 2.440 nonbonded pdb=" OG1 THR K 360 " pdb=" O LYS K 441 " model vdw 2.197 2.440 nonbonded pdb=" OE1 GLU L 69 " pdb=" OG1 THR L 73 " model vdw 2.225 2.440 nonbonded pdb=" O ASP O 300 " pdb=" OG SER O 304 " model vdw 2.230 2.440 nonbonded pdb=" O LYS K 60 " pdb=" NH1 ARG K 64 " model vdw 2.247 2.520 ... (remaining 104578 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 'L' and (resid 54 through 317 or (resid 318 through 319 and (name N or na \ me CA or name C or name O or name CB )) or resid 339 or (resid 340 and (name N o \ r name CA or name C or name O or name CB )) or resid 341 through 567 or resid 58 \ 9 through 608)) selection = (chain 'O' and (resid 54 through 86 or (resid 87 and (name N or name CA or name \ C or name O or name CB )) or resid 88 through 567 or resid 589 through 608)) } 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=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 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: 0.010 Extract box with map and model: 5.270 Check model and map are aligned: 0.180 Set scattering table: 0.140 Process input model: 36.700 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 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 : 0.009 0.082 13580 Z= 0.584 Angle : 1.806 18.409 18380 Z= 0.950 Chirality : 0.082 0.462 2044 Planarity : 0.010 0.096 2305 Dihedral : 17.449 91.931 5025 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 0.13 % Allowed : 3.17 % Favored : 96.69 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.78 (0.18), residues: 1579 helix: -2.31 (0.15), residues: 839 sheet: -1.85 (0.81), residues: 44 loop : -2.71 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.103 0.008 TRP L 65 HIS 0.023 0.003 HIS L 262 PHE 0.070 0.005 PHE K 356 TYR 0.054 0.005 TYR L 172 ARG 0.028 0.004 ARG K 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 1.662 Fit side-chains REVERT: K 369 TRP cc_start: 0.7807 (t-100) cc_final: 0.6971 (t-100) REVERT: L 226 MET cc_start: 0.7435 (mmm) cc_final: 0.7211 (tpt) REVERT: O 303 GLN cc_start: 0.9040 (tt0) cc_final: 0.8778 (tt0) outliers start: 2 outliers final: 0 residues processed: 98 average time/residue: 0.2044 time to fit residues: 31.8866 Evaluate side-chains 79 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 0.9980 chunk 119 optimal weight: 0.6980 chunk 66 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 123 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 143 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 289 ASN K 450 ASN ** L 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 444 ASN O 461 GLN ** O 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 96 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13580 Z= 0.189 Angle : 0.789 10.321 18380 Z= 0.405 Chirality : 0.046 0.225 2044 Planarity : 0.006 0.064 2305 Dihedral : 6.462 28.309 1747 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 1.42 % Allowed : 12.21 % Favored : 86.37 % 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: -2.78 (0.19), residues: 1579 helix: -1.22 (0.16), residues: 880 sheet: -0.73 (1.06), residues: 29 loop : -2.72 (0.21), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP L 65 HIS 0.005 0.001 HIS L 262 PHE 0.024 0.001 PHE L 167 TYR 0.020 0.002 TYR L 301 ARG 0.009 0.001 ARG L 146 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 90 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 50 LYS cc_start: 0.6673 (tptt) cc_final: 0.6400 (pptt) REVERT: K 369 TRP cc_start: 0.8013 (t-100) cc_final: 0.6715 (t-100) REVERT: L 226 MET cc_start: 0.7147 (mmm) cc_final: 0.6943 (tpt) REVERT: L 231 ILE cc_start: 0.8904 (tt) cc_final: 0.8651 (tp) REVERT: L 376 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8595 (mp0) REVERT: L 458 MET cc_start: 0.7059 (ptp) cc_final: 0.6784 (ptp) REVERT: O 119 MET cc_start: 0.8241 (ttt) cc_final: 0.7929 (tmm) REVERT: O 142 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8014 (pm20) REVERT: O 418 TYR cc_start: 0.7790 (OUTLIER) cc_final: 0.7312 (t80) outliers start: 21 outliers final: 11 residues processed: 104 average time/residue: 0.2087 time to fit residues: 34.7639 Evaluate side-chains 88 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain L residue 261 ILE Chi-restraints excluded: chain L residue 376 GLU Chi-restraints excluded: chain L residue 414 LEU Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain O residue 141 GLU Chi-restraints excluded: chain O residue 142 GLN Chi-restraints excluded: chain O residue 158 TYR Chi-restraints excluded: chain O residue 240 LEU Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 418 TYR Chi-restraints excluded: chain O residue 432 ILE Chi-restraints excluded: chain O residue 452 PHE Chi-restraints excluded: chain O residue 485 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 128 optimal weight: 7.9990 chunk 142 optimal weight: 0.0060 chunk 49 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 222 GLN ** L 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 598 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13580 Z= 0.175 Angle : 0.692 8.764 18380 Z= 0.355 Chirality : 0.044 0.219 2044 Planarity : 0.005 0.057 2305 Dihedral : 5.753 26.089 1747 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 3.10 % Allowed : 14.64 % Favored : 82.25 % 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: -2.05 (0.20), residues: 1579 helix: -0.60 (0.17), residues: 895 sheet: -0.69 (1.07), residues: 29 loop : -2.45 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 346 HIS 0.005 0.001 HIS L 262 PHE 0.019 0.001 PHE L 167 TYR 0.016 0.001 TYR K 53 ARG 0.006 0.001 ARG K 363 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 84 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 107 ASN cc_start: 0.6066 (OUTLIER) cc_final: 0.5508 (t0) REVERT: K 369 TRP cc_start: 0.8088 (t-100) cc_final: 0.7077 (t-100) REVERT: L 103 MET cc_start: 0.8080 (mtt) cc_final: 0.7733 (mtt) REVERT: L 231 ILE cc_start: 0.8930 (tt) cc_final: 0.8720 (tp) REVERT: L 232 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7071 (mtm180) REVERT: L 458 MET cc_start: 0.7023 (OUTLIER) cc_final: 0.6694 (ptp) REVERT: O 119 MET cc_start: 0.8311 (ttt) cc_final: 0.8008 (tmm) REVERT: O 158 TYR cc_start: 0.7075 (OUTLIER) cc_final: 0.4829 (t80) REVERT: O 418 TYR cc_start: 0.7730 (OUTLIER) cc_final: 0.7392 (t80) REVERT: O 460 MET cc_start: 0.8473 (tpt) cc_final: 0.8138 (tpt) outliers start: 46 outliers final: 23 residues processed: 120 average time/residue: 0.2301 time to fit residues: 42.4207 Evaluate side-chains 100 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 72 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain K residue 107 ASN Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain K residue 444 ASN Chi-restraints excluded: chain L residue 164 TRP Chi-restraints excluded: chain L residue 232 ARG Chi-restraints excluded: chain L residue 261 ILE Chi-restraints excluded: chain L residue 395 ASN Chi-restraints excluded: chain L residue 414 LEU Chi-restraints excluded: chain L residue 428 LEU Chi-restraints excluded: chain L residue 458 MET Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain O residue 141 GLU Chi-restraints excluded: chain O residue 142 GLN Chi-restraints excluded: chain O residue 143 TYR Chi-restraints excluded: chain O residue 158 TYR Chi-restraints excluded: chain O residue 240 LEU Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 357 GLN Chi-restraints excluded: chain O residue 381 GLN Chi-restraints excluded: chain O residue 418 TYR Chi-restraints excluded: chain O residue 452 PHE Chi-restraints excluded: chain O residue 485 LEU Chi-restraints excluded: chain O residue 507 LEU Chi-restraints excluded: chain O residue 544 ASP Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 130 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 0.0570 chunk 108 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 144 optimal weight: 0.0670 chunk 152 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 136 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 303 GLN O 484 GLN O 598 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13580 Z= 0.146 Angle : 0.646 9.078 18380 Z= 0.331 Chirality : 0.042 0.221 2044 Planarity : 0.004 0.051 2305 Dihedral : 5.297 25.773 1747 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.51 % Allowed : 16.80 % Favored : 79.69 % 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: -1.63 (0.21), residues: 1579 helix: -0.17 (0.18), residues: 878 sheet: -0.60 (1.06), residues: 29 loop : -2.37 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 71 HIS 0.005 0.001 HIS L 262 PHE 0.014 0.001 PHE L 167 TYR 0.013 0.001 TYR O 301 ARG 0.004 0.000 ARG O 232 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 83 time to evaluate : 1.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 107 ASN cc_start: 0.6186 (OUTLIER) cc_final: 0.5876 (t0) REVERT: K 369 TRP cc_start: 0.8231 (t-100) cc_final: 0.7762 (t-100) REVERT: L 103 MET cc_start: 0.8002 (mtt) cc_final: 0.7657 (mtt) REVERT: L 115 MET cc_start: 0.8834 (mmm) cc_final: 0.8462 (mmm) REVERT: L 232 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7044 (mtm180) REVERT: L 377 LEU cc_start: 0.9472 (mm) cc_final: 0.9202 (tt) REVERT: L 458 MET cc_start: 0.7016 (OUTLIER) cc_final: 0.6661 (ptp) REVERT: O 119 MET cc_start: 0.8252 (ttt) cc_final: 0.7951 (tmm) REVERT: O 158 TYR cc_start: 0.6907 (OUTLIER) cc_final: 0.4803 (t80) REVERT: O 354 ASP cc_start: 0.8459 (m-30) cc_final: 0.7811 (p0) REVERT: O 418 TYR cc_start: 0.7674 (OUTLIER) cc_final: 0.7380 (t80) REVERT: O 458 MET cc_start: 0.6712 (ptt) cc_final: 0.6490 (ptt) REVERT: O 460 MET cc_start: 0.8459 (tpt) cc_final: 0.8231 (tpt) outliers start: 52 outliers final: 28 residues processed: 128 average time/residue: 0.2331 time to fit residues: 46.1755 Evaluate side-chains 109 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 76 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain K residue 107 ASN Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 407 HIS Chi-restraints excluded: chain K residue 419 ASN Chi-restraints excluded: chain K residue 444 ASN Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 164 TRP Chi-restraints excluded: chain L residue 232 ARG Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 261 ILE Chi-restraints excluded: chain L residue 394 ASN Chi-restraints excluded: chain L residue 395 ASN Chi-restraints excluded: chain L residue 414 LEU Chi-restraints excluded: chain L residue 418 TYR Chi-restraints excluded: chain L residue 428 LEU Chi-restraints excluded: chain L residue 458 MET Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 595 GLU Chi-restraints excluded: chain O residue 65 TRP Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 141 GLU Chi-restraints excluded: chain O residue 142 GLN Chi-restraints excluded: chain O residue 143 TYR Chi-restraints excluded: chain O residue 158 TYR Chi-restraints excluded: chain O residue 215 CYS Chi-restraints excluded: chain O residue 240 LEU Chi-restraints excluded: chain O residue 357 GLN Chi-restraints excluded: chain O residue 381 GLN Chi-restraints excluded: chain O residue 418 TYR Chi-restraints excluded: chain O residue 452 PHE Chi-restraints excluded: chain O residue 485 LEU Chi-restraints excluded: chain N residue 79 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 113 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 0 optimal weight: 10.9990 chunk 77 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 598 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 13580 Z= 0.389 Angle : 0.808 9.977 18380 Z= 0.427 Chirality : 0.049 0.219 2044 Planarity : 0.005 0.050 2305 Dihedral : 6.313 27.141 1747 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 27.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 5.13 % Allowed : 19.37 % Favored : 75.51 % 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: -2.24 (0.20), residues: 1579 helix: -0.74 (0.17), residues: 876 sheet: -0.83 (0.95), residues: 24 loop : -2.51 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP N 190 HIS 0.006 0.002 HIS L 189 PHE 0.024 0.002 PHE K 387 TYR 0.032 0.002 TYR L 418 ARG 0.007 0.001 ARG K 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 71 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 128 ARG cc_start: 0.7061 (OUTLIER) cc_final: 0.6369 (ttp-110) REVERT: K 140 VAL cc_start: 0.9319 (OUTLIER) cc_final: 0.9074 (t) REVERT: K 303 TYR cc_start: 0.6021 (OUTLIER) cc_final: 0.4304 (t80) REVERT: L 232 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.6799 (mtp-110) REVERT: L 376 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8789 (mp0) REVERT: L 377 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9315 (tt) REVERT: L 394 ASN cc_start: 0.7426 (OUTLIER) cc_final: 0.7017 (p0) REVERT: L 458 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.7236 (ptt) REVERT: O 119 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8023 (tmm) REVERT: O 136 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8463 (mm) REVERT: O 183 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.6271 (m-80) REVERT: O 418 TYR cc_start: 0.7889 (OUTLIER) cc_final: 0.7452 (t80) outliers start: 76 outliers final: 41 residues processed: 135 average time/residue: 0.2410 time to fit residues: 49.4080 Evaluate side-chains 121 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 68 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain K residue 93 TRP Chi-restraints excluded: chain K residue 102 ASP Chi-restraints excluded: chain K residue 128 ARG Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 303 TYR Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain K residue 407 HIS Chi-restraints excluded: chain K residue 419 ASN Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 101 PHE Chi-restraints excluded: chain L residue 164 TRP Chi-restraints excluded: chain L residue 232 ARG Chi-restraints excluded: chain L residue 238 LEU Chi-restraints excluded: chain L residue 261 ILE Chi-restraints excluded: chain L residue 376 GLU Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 394 ASN Chi-restraints excluded: chain L residue 395 ASN Chi-restraints excluded: chain L residue 414 LEU Chi-restraints excluded: chain L residue 418 TYR Chi-restraints excluded: chain L residue 428 LEU Chi-restraints excluded: chain L residue 458 MET Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 595 GLU Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 105 TYR Chi-restraints excluded: chain O residue 109 ASP Chi-restraints excluded: chain O residue 119 MET Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 142 GLN Chi-restraints excluded: chain O residue 143 TYR Chi-restraints excluded: chain O residue 171 ILE Chi-restraints excluded: chain O residue 183 PHE Chi-restraints excluded: chain O residue 215 CYS Chi-restraints excluded: chain O residue 240 LEU Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 381 GLN Chi-restraints excluded: chain O residue 391 PHE Chi-restraints excluded: chain O residue 418 TYR Chi-restraints excluded: chain O residue 446 PHE Chi-restraints excluded: chain O residue 452 PHE Chi-restraints excluded: chain O residue 485 LEU Chi-restraints excluded: chain O residue 507 LEU Chi-restraints excluded: chain O residue 544 ASP Chi-restraints excluded: chain O residue 565 LEU Chi-restraints excluded: chain O residue 596 GLU Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 79 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 12 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 598 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13580 Z= 0.167 Angle : 0.665 10.669 18380 Z= 0.342 Chirality : 0.044 0.225 2044 Planarity : 0.004 0.051 2305 Dihedral : 5.476 25.350 1747 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 3.78 % Allowed : 22.06 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.21), residues: 1579 helix: -0.17 (0.18), residues: 880 sheet: 0.18 (1.26), residues: 19 loop : -2.33 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 346 HIS 0.005 0.001 HIS L 262 PHE 0.012 0.001 PHE N 102 TYR 0.025 0.001 TYR L 335 ARG 0.005 0.001 ARG O 232 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 83 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 369 TRP cc_start: 0.8272 (t-100) cc_final: 0.7658 (t-100) REVERT: L 115 MET cc_start: 0.8672 (mmm) cc_final: 0.8415 (mmm) REVERT: L 232 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7428 (mtm110) REVERT: L 376 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8706 (mp0) REVERT: L 394 ASN cc_start: 0.7332 (OUTLIER) cc_final: 0.6950 (p0) REVERT: L 458 MET cc_start: 0.7120 (OUTLIER) cc_final: 0.6776 (ptp) REVERT: O 119 MET cc_start: 0.8216 (ttt) cc_final: 0.7921 (tmm) REVERT: O 142 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8027 (pm20) REVERT: O 183 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.5915 (m-80) REVERT: O 418 TYR cc_start: 0.7750 (OUTLIER) cc_final: 0.7469 (t80) REVERT: O 460 MET cc_start: 0.8258 (tpt) cc_final: 0.7784 (tpt) REVERT: N 157 MET cc_start: 0.5567 (mtt) cc_final: 0.5216 (mmp) outliers start: 56 outliers final: 33 residues processed: 132 average time/residue: 0.2383 time to fit residues: 47.5893 Evaluate side-chains 113 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 73 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain K residue 93 TRP Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 407 HIS Chi-restraints excluded: chain K residue 419 ASN Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 164 TRP Chi-restraints excluded: chain L residue 232 ARG Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 261 ILE Chi-restraints excluded: chain L residue 376 GLU Chi-restraints excluded: chain L residue 394 ASN Chi-restraints excluded: chain L residue 395 ASN Chi-restraints excluded: chain L residue 414 LEU Chi-restraints excluded: chain L residue 418 TYR Chi-restraints excluded: chain L residue 428 LEU Chi-restraints excluded: chain L residue 458 MET Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 547 ILE Chi-restraints excluded: chain L residue 595 GLU Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 142 GLN Chi-restraints excluded: chain O residue 143 TYR Chi-restraints excluded: chain O residue 158 TYR Chi-restraints excluded: chain O residue 183 PHE Chi-restraints excluded: chain O residue 215 CYS Chi-restraints excluded: chain O residue 240 LEU Chi-restraints excluded: chain O residue 357 GLN Chi-restraints excluded: chain O residue 381 GLN Chi-restraints excluded: chain O residue 418 TYR Chi-restraints excluded: chain O residue 446 PHE Chi-restraints excluded: chain O residue 452 PHE Chi-restraints excluded: chain O residue 485 LEU Chi-restraints excluded: chain O residue 526 LEU Chi-restraints excluded: chain O residue 544 ASP Chi-restraints excluded: chain N residue 79 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 0.0070 chunk 17 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 86 optimal weight: 0.0170 chunk 128 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 152 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 chunk 70 optimal weight: 0.0070 overall best weight: 0.8058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 254 ASN O 598 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 13580 Z= 0.154 Angle : 0.669 16.305 18380 Z= 0.337 Chirality : 0.043 0.220 2044 Planarity : 0.004 0.049 2305 Dihedral : 5.116 25.107 1747 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 4.18 % Allowed : 22.47 % Favored : 73.35 % 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: -1.28 (0.21), residues: 1579 helix: 0.17 (0.18), residues: 874 sheet: -0.53 (1.05), residues: 28 loop : -2.27 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 346 HIS 0.005 0.001 HIS L 262 PHE 0.013 0.001 PHE L 167 TYR 0.028 0.001 TYR L 301 ARG 0.004 0.000 ARG O 232 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 80 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 115 MET cc_start: 0.8717 (mmm) cc_final: 0.8121 (mmm) REVERT: L 232 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.6949 (mtp-110) REVERT: L 376 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8642 (mp0) REVERT: L 458 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.6723 (ptp) REVERT: O 119 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7750 (tmm) REVERT: O 142 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7884 (pm20) REVERT: O 183 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.6040 (m-80) REVERT: O 418 TYR cc_start: 0.7671 (OUTLIER) cc_final: 0.7414 (t80) REVERT: O 598 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8278 (pp30) outliers start: 62 outliers final: 38 residues processed: 134 average time/residue: 0.2248 time to fit residues: 46.1006 Evaluate side-chains 119 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 73 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 407 HIS Chi-restraints excluded: chain K residue 419 ASN Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 164 TRP Chi-restraints excluded: chain L residue 232 ARG Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain L residue 341 THR Chi-restraints excluded: chain L residue 376 GLU Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 394 ASN Chi-restraints excluded: chain L residue 395 ASN Chi-restraints excluded: chain L residue 414 LEU Chi-restraints excluded: chain L residue 418 TYR Chi-restraints excluded: chain L residue 428 LEU Chi-restraints excluded: chain L residue 458 MET Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 547 ILE Chi-restraints excluded: chain L residue 595 GLU Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 119 MET Chi-restraints excluded: chain O residue 142 GLN Chi-restraints excluded: chain O residue 143 TYR Chi-restraints excluded: chain O residue 158 TYR Chi-restraints excluded: chain O residue 183 PHE Chi-restraints excluded: chain O residue 215 CYS Chi-restraints excluded: chain O residue 240 LEU Chi-restraints excluded: chain O residue 357 GLN Chi-restraints excluded: chain O residue 418 TYR Chi-restraints excluded: chain O residue 432 ILE Chi-restraints excluded: chain O residue 446 PHE Chi-restraints excluded: chain O residue 452 PHE Chi-restraints excluded: chain O residue 485 LEU Chi-restraints excluded: chain O residue 507 LEU Chi-restraints excluded: chain O residue 526 LEU Chi-restraints excluded: chain O residue 544 ASP Chi-restraints excluded: chain O residue 596 GLU Chi-restraints excluded: chain O residue 598 GLN Chi-restraints excluded: chain N residue 79 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 0.0040 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 598 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13580 Z= 0.195 Angle : 0.683 15.155 18380 Z= 0.347 Chirality : 0.044 0.274 2044 Planarity : 0.004 0.046 2305 Dihedral : 5.185 25.150 1747 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 4.05 % Allowed : 23.41 % Favored : 72.54 % 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: -1.29 (0.21), residues: 1579 helix: 0.15 (0.18), residues: 871 sheet: -0.64 (1.05), residues: 28 loop : -2.25 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP K 369 HIS 0.004 0.001 HIS K 108 PHE 0.011 0.001 PHE N 176 TYR 0.024 0.001 TYR L 335 ARG 0.004 0.000 ARG O 232 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 74 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 107 ASN cc_start: 0.5769 (OUTLIER) cc_final: 0.5478 (t0) REVERT: K 393 LYS cc_start: 0.7201 (OUTLIER) cc_final: 0.6732 (pttm) REVERT: L 232 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7065 (mtp-110) REVERT: L 376 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8706 (mp0) REVERT: L 394 ASN cc_start: 0.7399 (OUTLIER) cc_final: 0.7016 (p0) REVERT: L 458 MET cc_start: 0.7160 (OUTLIER) cc_final: 0.6820 (ptp) REVERT: O 119 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7789 (tmm) REVERT: O 142 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7875 (pm20) REVERT: O 183 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.6140 (m-80) REVERT: O 418 TYR cc_start: 0.7740 (OUTLIER) cc_final: 0.7427 (t80) REVERT: O 458 MET cc_start: 0.6566 (ptt) cc_final: 0.6343 (ptt) REVERT: O 460 MET cc_start: 0.8386 (tpt) cc_final: 0.8085 (tpt) outliers start: 60 outliers final: 41 residues processed: 126 average time/residue: 0.2245 time to fit residues: 43.8161 Evaluate side-chains 123 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 72 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain K residue 107 ASN Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 393 LYS Chi-restraints excluded: chain K residue 407 HIS Chi-restraints excluded: chain K residue 419 ASN Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 164 TRP Chi-restraints excluded: chain L residue 190 GLU Chi-restraints excluded: chain L residue 232 ARG Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 238 LEU Chi-restraints excluded: chain L residue 240 LEU Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain L residue 341 THR Chi-restraints excluded: chain L residue 376 GLU Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 394 ASN Chi-restraints excluded: chain L residue 395 ASN Chi-restraints excluded: chain L residue 414 LEU Chi-restraints excluded: chain L residue 418 TYR Chi-restraints excluded: chain L residue 428 LEU Chi-restraints excluded: chain L residue 458 MET Chi-restraints excluded: chain L residue 503 LYS Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 547 ILE Chi-restraints excluded: chain L residue 595 GLU Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 119 MET Chi-restraints excluded: chain O residue 142 GLN Chi-restraints excluded: chain O residue 143 TYR Chi-restraints excluded: chain O residue 158 TYR Chi-restraints excluded: chain O residue 183 PHE Chi-restraints excluded: chain O residue 215 CYS Chi-restraints excluded: chain O residue 240 LEU Chi-restraints excluded: chain O residue 357 GLN Chi-restraints excluded: chain O residue 418 TYR Chi-restraints excluded: chain O residue 432 ILE Chi-restraints excluded: chain O residue 446 PHE Chi-restraints excluded: chain O residue 452 PHE Chi-restraints excluded: chain O residue 485 LEU Chi-restraints excluded: chain O residue 507 LEU Chi-restraints excluded: chain O residue 526 LEU Chi-restraints excluded: chain O residue 544 ASP Chi-restraints excluded: chain O residue 596 GLU Chi-restraints excluded: chain N residue 79 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 141 optimal weight: 0.0070 chunk 85 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 111 optimal weight: 0.2980 chunk 43 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 150 optimal weight: 0.0980 overall best weight: 1.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 598 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13580 Z= 0.169 Angle : 0.668 14.290 18380 Z= 0.336 Chirality : 0.043 0.268 2044 Planarity : 0.004 0.047 2305 Dihedral : 5.062 25.139 1747 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.64 % Allowed : 24.49 % Favored : 71.86 % 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 (0.21), residues: 1579 helix: 0.26 (0.18), residues: 869 sheet: -0.60 (1.06), residues: 28 loop : -2.22 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP K 369 HIS 0.004 0.001 HIS L 262 PHE 0.012 0.001 PHE L 167 TYR 0.015 0.001 TYR O 301 ARG 0.004 0.000 ARG O 232 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 78 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 232 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7066 (mtp-110) REVERT: L 376 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8678 (mp0) REVERT: L 394 ASN cc_start: 0.7332 (OUTLIER) cc_final: 0.6944 (p0) REVERT: L 458 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.6887 (ptp) REVERT: O 119 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7789 (tmm) REVERT: O 142 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7818 (pm20) REVERT: O 183 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.6013 (m-80) REVERT: O 418 TYR cc_start: 0.7689 (OUTLIER) cc_final: 0.7445 (t80) REVERT: O 458 MET cc_start: 0.6504 (ptt) cc_final: 0.6293 (ptt) REVERT: O 598 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8239 (pp30) outliers start: 54 outliers final: 40 residues processed: 123 average time/residue: 0.2272 time to fit residues: 42.9224 Evaluate side-chains 125 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 76 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 334 LEU Chi-restraints excluded: chain K residue 407 HIS Chi-restraints excluded: chain K residue 419 ASN Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 164 TRP Chi-restraints excluded: chain L residue 190 GLU Chi-restraints excluded: chain L residue 232 ARG Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 238 LEU Chi-restraints excluded: chain L residue 240 LEU Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain L residue 341 THR Chi-restraints excluded: chain L residue 376 GLU Chi-restraints excluded: chain L residue 394 ASN Chi-restraints excluded: chain L residue 395 ASN Chi-restraints excluded: chain L residue 414 LEU Chi-restraints excluded: chain L residue 418 TYR Chi-restraints excluded: chain L residue 428 LEU Chi-restraints excluded: chain L residue 458 MET Chi-restraints excluded: chain L residue 503 LYS Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 547 ILE Chi-restraints excluded: chain L residue 595 GLU Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 119 MET Chi-restraints excluded: chain O residue 142 GLN Chi-restraints excluded: chain O residue 143 TYR Chi-restraints excluded: chain O residue 158 TYR Chi-restraints excluded: chain O residue 183 PHE Chi-restraints excluded: chain O residue 215 CYS Chi-restraints excluded: chain O residue 240 LEU Chi-restraints excluded: chain O residue 357 GLN Chi-restraints excluded: chain O residue 418 TYR Chi-restraints excluded: chain O residue 432 ILE Chi-restraints excluded: chain O residue 452 PHE Chi-restraints excluded: chain O residue 485 LEU Chi-restraints excluded: chain O residue 507 LEU Chi-restraints excluded: chain O residue 526 LEU Chi-restraints excluded: chain O residue 544 ASP Chi-restraints excluded: chain O residue 596 GLU Chi-restraints excluded: chain O residue 598 GLN Chi-restraints excluded: chain N residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 144 optimal weight: 0.9980 chunk 125 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 133 optimal weight: 0.9980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 598 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13580 Z= 0.197 Angle : 0.677 14.063 18380 Z= 0.342 Chirality : 0.044 0.266 2044 Planarity : 0.004 0.046 2305 Dihedral : 5.128 25.928 1747 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 3.91 % Allowed : 24.36 % Favored : 71.73 % 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: -1.27 (0.21), residues: 1579 helix: 0.14 (0.18), residues: 882 sheet: -0.72 (1.06), residues: 28 loop : -2.22 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP K 369 HIS 0.004 0.001 HIS K 108 PHE 0.012 0.001 PHE N 176 TYR 0.024 0.001 TYR L 335 ARG 0.004 0.000 ARG O 232 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 74 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 107 ASN cc_start: 0.5765 (OUTLIER) cc_final: 0.5490 (t0) REVERT: K 393 LYS cc_start: 0.7234 (OUTLIER) cc_final: 0.6608 (pttm) REVERT: L 204 MET cc_start: 0.7909 (mmp) cc_final: 0.7611 (mmm) REVERT: L 376 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8711 (mp0) REVERT: L 394 ASN cc_start: 0.7365 (OUTLIER) cc_final: 0.6978 (p0) REVERT: L 458 MET cc_start: 0.7180 (OUTLIER) cc_final: 0.6846 (ptp) REVERT: O 119 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7814 (tmm) REVERT: O 142 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7919 (pm20) REVERT: O 183 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.6075 (m-80) REVERT: O 418 TYR cc_start: 0.7738 (OUTLIER) cc_final: 0.7429 (t80) outliers start: 58 outliers final: 43 residues processed: 124 average time/residue: 0.2198 time to fit residues: 42.4561 Evaluate side-chains 126 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 74 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain K residue 107 ASN Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 199 VAL Chi-restraints excluded: chain K residue 334 LEU Chi-restraints excluded: chain K residue 393 LYS Chi-restraints excluded: chain K residue 407 HIS Chi-restraints excluded: chain K residue 419 ASN Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 164 TRP Chi-restraints excluded: chain L residue 190 GLU Chi-restraints excluded: chain L residue 232 ARG Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 238 LEU Chi-restraints excluded: chain L residue 240 LEU Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain L residue 341 THR Chi-restraints excluded: chain L residue 376 GLU Chi-restraints excluded: chain L residue 394 ASN Chi-restraints excluded: chain L residue 395 ASN Chi-restraints excluded: chain L residue 414 LEU Chi-restraints excluded: chain L residue 418 TYR Chi-restraints excluded: chain L residue 428 LEU Chi-restraints excluded: chain L residue 458 MET Chi-restraints excluded: chain L residue 503 LYS Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 547 ILE Chi-restraints excluded: chain L residue 595 GLU Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 119 MET Chi-restraints excluded: chain O residue 142 GLN Chi-restraints excluded: chain O residue 143 TYR Chi-restraints excluded: chain O residue 158 TYR Chi-restraints excluded: chain O residue 183 PHE Chi-restraints excluded: chain O residue 215 CYS Chi-restraints excluded: chain O residue 240 LEU Chi-restraints excluded: chain O residue 357 GLN Chi-restraints excluded: chain O residue 418 TYR Chi-restraints excluded: chain O residue 432 ILE Chi-restraints excluded: chain O residue 446 PHE Chi-restraints excluded: chain O residue 452 PHE Chi-restraints excluded: chain O residue 485 LEU Chi-restraints excluded: chain O residue 507 LEU Chi-restraints excluded: chain O residue 526 LEU Chi-restraints excluded: chain O residue 544 ASP Chi-restraints excluded: chain O residue 596 GLU Chi-restraints excluded: chain N residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 18 optimal weight: 0.0570 chunk 34 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 128 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 598 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.058669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.050265 restraints weight = 93603.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.051559 restraints weight = 50549.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.052441 restraints weight = 32739.573| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13580 Z= 0.168 Angle : 0.672 13.755 18380 Z= 0.337 Chirality : 0.043 0.256 2044 Planarity : 0.004 0.047 2305 Dihedral : 5.037 25.959 1747 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 3.71 % Allowed : 24.49 % Favored : 71.79 % 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: -1.11 (0.21), residues: 1579 helix: 0.27 (0.18), residues: 876 sheet: -0.70 (1.05), residues: 28 loop : -2.12 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP K 369 HIS 0.004 0.001 HIS K 108 PHE 0.012 0.001 PHE N 176 TYR 0.014 0.001 TYR O 301 ARG 0.004 0.000 ARG O 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2194.99 seconds wall clock time: 41 minutes 33.97 seconds (2493.97 seconds total)