Starting phenix.real_space_refine on Fri Feb 16 23:01:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpr_22420/02_2024/7jpr_22420_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpr_22420/02_2024/7jpr_22420.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/7jpr_22420/02_2024/7jpr_22420.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpr_22420/02_2024/7jpr_22420.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpr_22420/02_2024/7jpr_22420_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpr_22420/02_2024/7jpr_22420_neut_updated.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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 3 5.21 5 S 84 5.16 5 C 10721 2.51 5 N 2838 2.21 5 O 3082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 502": "OE1" <-> "OE2" Residue "A GLU 567": "OE1" <-> "OE2" Residue "A ARG 646": "NH1" <-> "NH2" Residue "A ASP 703": "OD1" <-> "OD2" Residue "A ARG 721": "NH1" <-> "NH2" Residue "A ASP 724": "OD1" <-> "OD2" Residue "A GLU 753": "OE1" <-> "OE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 774": "OE1" <-> "OE2" Residue "A PHE 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B GLU 358": "OE1" <-> "OE2" Residue "B ASP 361": "OD1" <-> "OD2" Residue "B GLU 382": "OE1" <-> "OE2" Residue "B ASP 383": "OD1" <-> "OD2" Residue "B GLU 456": "OE1" <-> "OE2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "B ASP 541": "OD1" <-> "OD2" Residue "B GLU 555": "OE1" <-> "OE2" Residue "C TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 45": "OE1" <-> "OE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 98": "NH1" <-> "NH2" Residue "C PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 350": "OE1" <-> "OE2" Residue "C PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 397": "OE1" <-> "OE2" Residue "C TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 451": "OE1" <-> "OE2" Residue "C GLU 484": "OE1" <-> "OE2" Residue "C PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C GLU 572": "OE1" <-> "OE2" Residue "C GLU 590": "OE1" <-> "OE2" Residue "C TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C ARG 680": "NH1" <-> "NH2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D GLU 86": "OE1" <-> "OE2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D GLU 121": "OE1" <-> "OE2" Residue "D PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 213": "NH1" <-> "NH2" Residue "D PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 247": "OE1" <-> "OE2" Residue "D GLU 258": "OE1" <-> "OE2" Residue "D GLU 264": "OE1" <-> "OE2" Residue "D GLU 304": "OE1" <-> "OE2" Residue "D ASP 337": "OD1" <-> "OD2" Residue "D GLU 341": "OE1" <-> "OE2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "D GLU 383": "OE1" <-> "OE2" Residue "E TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 93": "OE1" <-> "OE2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E ASP 132": "OD1" <-> "OD2" Residue "E PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 198": "OE1" <-> "OE2" Residue "E GLU 224": "OE1" <-> "OE2" Residue "E GLU 238": "OE1" <-> "OE2" Residue "E GLU 244": "OE1" <-> "OE2" Residue "E ARG 248": "NH1" <-> "NH2" Residue "E ARG 251": "NH1" <-> "NH2" Residue "E ARG 271": "NH1" <-> "NH2" Residue "E GLU 279": "OE1" <-> "OE2" Residue "E TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 414": "OD1" <-> "OD2" Residue "E PHE 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16737 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2795 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 12, 'TRANS': 339} Chain breaks: 3 Chain: "B" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2515 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 8, 'TRANS': 298} Chain: "C" Number of atoms: 4858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4858 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 24, 'TRANS': 568} Chain breaks: 8 Chain: "D" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3305 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 13, 'TRANS': 392} Chain breaks: 1 Chain: "E" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3168 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 369} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.48, per 1000 atoms: 0.51 Number of scatterers: 16737 At special positions: 0 Unit cell: (102.72, 131.61, 175.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 84 16.00 P 9 15.00 Mg 3 11.99 O 3082 8.00 N 2838 7.00 C 10721 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 6.16 Conformation dependent library (CDL) restraints added in 2.8 seconds 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3972 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 103 helices and 7 sheets defined 54.6% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.12 Creating SS restraints... Processing helix chain 'A' and resid 488 through 495 Processing helix chain 'A' and resid 508 through 522 removed outlier: 3.841A pdb=" N LYS A 521 " --> pdb=" O PHE A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 556 Processing helix chain 'A' and resid 576 through 587 removed outlier: 3.743A pdb=" N VAL A 579 " --> pdb=" O PRO A 576 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 587 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 604 Processing helix chain 'A' and resid 622 through 625 Processing helix chain 'A' and resid 632 through 638 Processing helix chain 'A' and resid 659 through 662 No H-bonds generated for 'chain 'A' and resid 659 through 662' Processing helix chain 'A' and resid 683 through 694 removed outlier: 3.525A pdb=" N LEU A 694 " --> pdb=" O LEU A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 715 Processing helix chain 'A' and resid 719 through 735 Processing helix chain 'A' and resid 748 through 758 Processing helix chain 'A' and resid 763 through 768 Processing helix chain 'A' and resid 772 through 788 Processing helix chain 'A' and resid 795 through 809 removed outlier: 3.640A pdb=" N ALA A 804 " --> pdb=" O SER A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 828 Processing helix chain 'A' and resid 851 through 859 removed outlier: 3.530A pdb=" N LYS A 859 " --> pdb=" O LEU A 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 275 Processing helix chain 'B' and resid 285 through 307 removed outlier: 3.568A pdb=" N GLN B 289 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LEU B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 293 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU B 297 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N PHE B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N HIS B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LYS B 300 " --> pdb=" O LYS B 296 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 329 Processing helix chain 'B' and resid 348 through 357 Processing helix chain 'B' and resid 369 through 382 Processing helix chain 'B' and resid 398 through 400 No H-bonds generated for 'chain 'B' and resid 398 through 400' Processing helix chain 'B' and resid 403 through 413 Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 474 through 482 Processing helix chain 'B' and resid 486 through 502 Processing helix chain 'B' and resid 513 through 522 Processing helix chain 'B' and resid 529 through 541 Processing helix chain 'B' and resid 563 through 571 Processing helix chain 'C' and resid 26 through 30 Processing helix chain 'C' and resid 37 through 85 removed outlier: 3.804A pdb=" N PHE C 44 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU C 45 " --> pdb=" O LYS C 41 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER C 82 " --> pdb=" O GLN C 78 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY C 83 " --> pdb=" O LYS C 79 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE C 84 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 128 removed outlier: 4.024A pdb=" N ASP C 115 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR C 117 " --> pdb=" O HIS C 114 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE C 118 " --> pdb=" O ASP C 115 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU C 123 " --> pdb=" O SER C 120 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN C 126 " --> pdb=" O GLU C 123 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN C 127 " --> pdb=" O ALA C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 158 removed outlier: 3.597A pdb=" N ILE C 152 " --> pdb=" O LEU C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 191 removed outlier: 3.564A pdb=" N TRP C 187 " --> pdb=" O SER C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'C' and resid 227 through 239 removed outlier: 3.631A pdb=" N ILE C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE C 235 " --> pdb=" O GLN C 231 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 262 removed outlier: 3.726A pdb=" N ILE C 259 " --> pdb=" O PRO C 256 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG C 261 " --> pdb=" O ILE C 258 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU C 262 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 270 removed outlier: 5.336A pdb=" N LEU C 270 " --> pdb=" O ALA C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 290 Processing helix chain 'C' and resid 304 through 312 Processing helix chain 'C' and resid 322 through 338 removed outlier: 3.526A pdb=" N LEU C 330 " --> pdb=" O LYS C 326 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU C 333 " --> pdb=" O GLN C 329 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE C 336 " --> pdb=" O LEU C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 344 removed outlier: 3.890A pdb=" N VAL C 343 " --> pdb=" O PRO C 340 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU C 344 " --> pdb=" O LEU C 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 340 through 344' Processing helix chain 'C' and resid 348 through 356 removed outlier: 3.899A pdb=" N ARG C 353 " --> pdb=" O PRO C 349 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG C 354 " --> pdb=" O GLU C 350 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE C 355 " --> pdb=" O ALA C 351 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN C 356 " --> pdb=" O LYS C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 367 Processing helix chain 'C' and resid 370 through 378 removed outlier: 3.535A pdb=" N ARG C 374 " --> pdb=" O PRO C 370 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU C 377 " --> pdb=" O ARG C 373 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS C 378 " --> pdb=" O ARG C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.595A pdb=" N LEU C 387 " --> pdb=" O LYS C 383 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR C 389 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 425 removed outlier: 3.634A pdb=" N THR C 398 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN C 399 " --> pdb=" O LYS C 395 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU C 400 " --> pdb=" O GLU C 396 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE C 413 " --> pdb=" O HIS C 409 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU C 414 " --> pdb=" O MET C 410 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL C 415 " --> pdb=" O ASN C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 443 removed outlier: 3.541A pdb=" N CYS C 440 " --> pdb=" O ARG C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 461 Processing helix chain 'C' and resid 465 through 481 removed outlier: 3.531A pdb=" N LYS C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE C 479 " --> pdb=" O CYS C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 499 removed outlier: 3.980A pdb=" N GLU C 495 " --> pdb=" O ALA C 491 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU C 496 " --> pdb=" O LYS C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 567 removed outlier: 3.642A pdb=" N GLU C 554 " --> pdb=" O GLU C 550 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN C 555 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL C 556 " --> pdb=" O LEU C 552 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG C 565 " --> pdb=" O ASP C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 580 No H-bonds generated for 'chain 'C' and resid 578 through 580' Processing helix chain 'C' and resid 585 through 591 Processing helix chain 'C' and resid 596 through 605 removed outlier: 3.616A pdb=" N HIS C 601 " --> pdb=" O ARG C 597 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU C 604 " --> pdb=" O LEU C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 609 No H-bonds generated for 'chain 'C' and resid 607 through 609' Processing helix chain 'C' and resid 629 through 637 removed outlier: 3.586A pdb=" N ALA C 633 " --> pdb=" O ASP C 629 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR C 634 " --> pdb=" O ILE C 630 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS C 637 " --> pdb=" O ALA C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 660 removed outlier: 3.636A pdb=" N VAL C 656 " --> pdb=" O ALA C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 676 through 690 removed outlier: 3.674A pdb=" N ARG C 683 " --> pdb=" O ALA C 679 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU C 688 " --> pdb=" O ALA C 684 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 28 Processing helix chain 'D' and resid 41 through 56 Processing helix chain 'D' and resid 73 through 85 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 107 through 117 Processing helix chain 'D' and resid 121 through 124 No H-bonds generated for 'chain 'D' and resid 121 through 124' Processing helix chain 'D' and resid 132 through 140 Processing helix chain 'D' and resid 161 through 165 Processing helix chain 'D' and resid 171 through 181 removed outlier: 4.110A pdb=" N ILE D 179 " --> pdb=" O ASN D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 201 No H-bonds generated for 'chain 'D' and resid 198 through 201' Processing helix chain 'D' and resid 204 through 209 Processing helix chain 'D' and resid 223 through 233 Processing helix chain 'D' and resid 243 through 257 Processing helix chain 'D' and resid 260 through 272 removed outlier: 3.745A pdb=" N VAL D 265 " --> pdb=" O SER D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 289 removed outlier: 4.615A pdb=" N ARG D 289 " --> pdb=" O LEU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 309 Processing helix chain 'D' and resid 313 through 320 removed outlier: 3.509A pdb=" N GLY D 320 " --> pdb=" O ASN D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 338 Processing helix chain 'D' and resid 346 through 358 Processing helix chain 'D' and resid 369 through 381 Processing helix chain 'D' and resid 408 through 416 Processing helix chain 'D' and resid 423 through 430 Processing helix chain 'E' and resid 13 through 22 Processing helix chain 'E' and resid 43 through 53 removed outlier: 4.019A pdb=" N THR E 47 " --> pdb=" O LYS E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 84 Processing helix chain 'E' and resid 99 through 109 Processing helix chain 'E' and resid 127 through 129 No H-bonds generated for 'chain 'E' and resid 127 through 129' Processing helix chain 'E' and resid 136 through 142 Processing helix chain 'E' and resid 144 through 148 Processing helix chain 'E' and resid 162 through 164 No H-bonds generated for 'chain 'E' and resid 162 through 164' Processing helix chain 'E' and resid 184 through 191 Processing helix chain 'E' and resid 201 through 215 Processing helix chain 'E' and resid 222 through 236 Proline residue: E 234 - end of helix Processing helix chain 'E' and resid 238 through 242 Processing helix chain 'E' and resid 250 through 267 Proline residue: E 259 - end of helix removed outlier: 4.404A pdb=" N GLN E 266 " --> pdb=" O LYS E 262 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR E 267 " --> pdb=" O LYS E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 283 Processing helix chain 'E' and resid 305 through 317 Processing helix chain 'E' and resid 321 through 328 removed outlier: 4.788A pdb=" N LYS E 325 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG E 326 " --> pdb=" O THR E 323 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE E 327 " --> pdb=" O ASP E 324 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE E 328 " --> pdb=" O LYS E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 369 removed outlier: 4.026A pdb=" N SER E 368 " --> pdb=" O ALA E 364 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE E 369 " --> pdb=" O ILE E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 387 removed outlier: 3.976A pdb=" N THR E 385 " --> pdb=" O PHE E 381 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER E 386 " --> pdb=" O SER E 382 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU E 387 " --> pdb=" O GLN E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 422 removed outlier: 3.516A pdb=" N ILE E 419 " --> pdb=" O PHE E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 431 No H-bonds generated for 'chain 'E' and resid 428 through 431' Processing sheet with id= A, first strand: chain 'A' and resid 674 through 677 removed outlier: 3.864A pdb=" N THR A 674 " --> pdb=" O CYS A 529 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER A 533 " --> pdb=" O MET A 676 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL A 649 " --> pdb=" O MET A 530 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ILE A 532 " --> pdb=" O VAL A 649 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ALA A 651 " --> pdb=" O ILE A 532 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 443 through 447 removed outlier: 6.467A pdb=" N ASN B 310 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N TYR B 446 " --> pdb=" O ASN B 310 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL B 312 " --> pdb=" O TYR B 446 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE B 311 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU B 388 " --> pdb=" O TYR B 419 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE B 421 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU B 390 " --> pdb=" O ILE B 421 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N SER B 423 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE B 392 " --> pdb=" O SER B 423 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE B 335 " --> pdb=" O PHE B 389 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N LEU B 391 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL B 337 " --> pdb=" O LEU B 391 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 271 through 276 removed outlier: 6.530A pdb=" N ILE C 100 " --> pdb=" O CYS C 272 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N GLU C 274 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N THR C 102 " --> pdb=" O GLU C 274 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N PHE C 276 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ALA C 104 " --> pdb=" O PHE C 276 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE C 252 " --> pdb=" O LEU C 105 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 213 through 216 removed outlier: 4.463A pdb=" N ARG D 213 " --> pdb=" O SER D 62 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU D 64 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE D 215 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN D 61 " --> pdb=" O ILE D 187 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL D 154 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N ILE D 190 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N PHE D 156 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N LEU D 192 " --> pdb=" O PHE D 156 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU D 158 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU D 95 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ILE D 157 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL D 97 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ASP D 159 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU D 99 " --> pdb=" O ASP D 159 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 385 through 387 Processing sheet with id= F, first strand: chain 'E' and resid 175 through 178 removed outlier: 8.336A pdb=" N ILE E 33 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL E 154 " --> pdb=" O ILE E 33 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ILE E 35 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N PHE E 156 " --> pdb=" O ILE E 35 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL E 120 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU E 155 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE E 122 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N LEU E 157 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU E 124 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP E 125 " --> pdb=" O VAL E 61 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 393 through 395 659 hydrogen bonds defined for protein. 1914 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: 4.40 Time building geometry restraints manager: 6.70 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: 4031 1.33 - 1.45: 3456 1.45 - 1.58: 9449 1.58 - 1.70: 15 1.70 - 1.82: 127 Bond restraints: 17078 Sorted by residual: bond pdb=" C4 ATP A 901 " pdb=" C5 ATP A 901 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.46e+01 bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.42e+01 bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.10e+01 bond pdb=" C5 ATP A 901 " pdb=" C6 ATP A 901 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 5.03e+01 bond pdb=" C5 ATP D 901 " pdb=" C6 ATP D 901 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.75e+01 ... (remaining 17073 not shown) Histogram of bond angle deviations from ideal: 97.23 - 105.02: 270 105.02 - 112.82: 8861 112.82 - 120.62: 8229 120.62 - 128.42: 5630 128.42 - 136.22: 127 Bond angle restraints: 23117 Sorted by residual: angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 117.71 22.16 1.00e+00 1.00e+00 4.91e+02 angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 120.25 19.62 1.00e+00 1.00e+00 3.85e+02 angle pdb=" PB ATP A 901 " pdb=" O3B ATP A 901 " pdb=" PG ATP A 901 " ideal model delta sigma weight residual 139.87 120.71 19.16 1.00e+00 1.00e+00 3.67e+02 angle pdb=" PA ATP E 501 " pdb=" O3A ATP E 501 " pdb=" PB ATP E 501 " ideal model delta sigma weight residual 136.83 119.68 17.15 1.00e+00 1.00e+00 2.94e+02 angle pdb=" PA ATP A 901 " pdb=" O3A ATP A 901 " pdb=" PB ATP A 901 " ideal model delta sigma weight residual 136.83 121.58 15.25 1.00e+00 1.00e+00 2.33e+02 ... (remaining 23112 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 9291 17.95 - 35.90: 885 35.90 - 53.86: 161 53.86 - 71.81: 42 71.81 - 89.76: 28 Dihedral angle restraints: 10407 sinusoidal: 4338 harmonic: 6069 Sorted by residual: dihedral pdb=" CA THR C 130 " pdb=" C THR C 130 " pdb=" N PRO C 131 " pdb=" CA PRO C 131 " ideal model delta harmonic sigma weight residual 180.00 155.95 24.05 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA ASP A 631 " pdb=" C ASP A 631 " pdb=" N ILE A 632 " pdb=" CA ILE A 632 " ideal model delta harmonic sigma weight residual 180.00 -156.17 -23.83 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA TYR D 339 " pdb=" C TYR D 339 " pdb=" N GLU D 340 " pdb=" CA GLU D 340 " ideal model delta harmonic sigma weight residual -180.00 -157.34 -22.66 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 10404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2182 0.079 - 0.158: 401 0.158 - 0.237: 44 0.237 - 0.316: 11 0.316 - 0.396: 3 Chirality restraints: 2641 Sorted by residual: chirality pdb=" CB THR B 448 " pdb=" CA THR B 448 " pdb=" OG1 THR B 448 " pdb=" CG2 THR B 448 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CB THR B 449 " pdb=" CA THR B 449 " pdb=" OG1 THR B 449 " pdb=" CG2 THR B 449 " both_signs ideal model delta sigma weight residual False 2.55 2.20 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CG LEU B 444 " pdb=" CB LEU B 444 " pdb=" CD1 LEU B 444 " pdb=" CD2 LEU B 444 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.61e+00 ... (remaining 2638 not shown) Planarity restraints: 2912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 404 " 0.083 5.00e-02 4.00e+02 1.24e-01 2.44e+01 pdb=" N PRO E 405 " -0.214 5.00e-02 4.00e+02 pdb=" CA PRO E 405 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO E 405 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 49 " 0.018 2.00e-02 2.50e+03 3.76e-02 1.42e+01 pdb=" CD GLU D 49 " -0.065 2.00e-02 2.50e+03 pdb=" OE1 GLU D 49 " 0.023 2.00e-02 2.50e+03 pdb=" OE2 GLU D 49 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 84 " 0.015 2.00e-02 2.50e+03 2.45e-02 1.05e+01 pdb=" CG PHE C 84 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE C 84 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE C 84 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 PHE C 84 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 84 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 84 " 0.001 2.00e-02 2.50e+03 ... (remaining 2909 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 128 2.62 - 3.19: 13892 3.19 - 3.76: 25890 3.76 - 4.33: 34109 4.33 - 4.90: 54472 Nonbonded interactions: 128491 Sorted by model distance: nonbonded pdb=" O1B ATP A 901 " pdb="MG MG A 902 " model vdw 2.048 2.170 nonbonded pdb=" O1G ATP D 901 " pdb="MG MG D 902 " model vdw 2.114 2.170 nonbonded pdb=" O3G ATP E 501 " pdb="MG MG E 502 " model vdw 2.147 2.170 nonbonded pdb=" O1B ATP E 501 " pdb="MG MG E 502 " model vdw 2.149 2.170 nonbonded pdb=" O3G ATP A 901 " pdb="MG MG A 902 " model vdw 2.155 2.170 ... (remaining 128486 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.640 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: 7.810 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 42.900 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 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 : 0.006 0.080 17078 Z= 0.418 Angle : 1.201 22.163 23117 Z= 0.719 Chirality : 0.062 0.396 2641 Planarity : 0.007 0.124 2912 Dihedral : 15.309 89.759 6435 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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: -2.74 (0.16), residues: 2005 helix: -1.82 (0.12), residues: 1160 sheet: 0.44 (0.39), residues: 166 loop : -2.10 (0.20), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP A 639 HIS 0.021 0.002 HIS C 81 PHE 0.056 0.004 PHE D 245 TYR 0.039 0.003 TYR C 408 ARG 0.019 0.002 ARG E 150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 1.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 516 ASN cc_start: 0.9413 (m-40) cc_final: 0.9144 (p0) REVERT: A 633 MET cc_start: 0.8281 (pmm) cc_final: 0.7978 (pmm) REVERT: A 852 ASP cc_start: 0.8530 (m-30) cc_final: 0.8002 (p0) REVERT: C 321 VAL cc_start: 0.9074 (m) cc_final: 0.8649 (t) REVERT: C 414 LEU cc_start: 0.9118 (mp) cc_final: 0.8850 (mp) REVERT: C 422 PHE cc_start: 0.7956 (m-80) cc_final: 0.7753 (m-80) REVERT: C 423 THR cc_start: 0.8482 (m) cc_final: 0.8281 (p) REVERT: D 174 TYR cc_start: 0.7652 (t80) cc_final: 0.7018 (t80) REVERT: D 281 MET cc_start: 0.7777 (tmm) cc_final: 0.7560 (tmm) REVERT: D 314 LYS cc_start: 0.8422 (mmtp) cc_final: 0.8015 (mttt) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.3014 time to fit residues: 124.5891 Evaluate side-chains 157 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 170 optimal weight: 8.9990 chunk 153 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 117 optimal weight: 0.4980 chunk 183 optimal weight: 4.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 HIS ** B 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN B 438 GLN ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 ASN ** C 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN C 703 HIS D 34 HIS ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 ASN D 233 GLN D 254 GLN D 263 GLN D 316 ASN ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 GLN D 400 GLN ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17078 Z= 0.272 Angle : 0.710 11.944 23117 Z= 0.357 Chirality : 0.042 0.157 2641 Planarity : 0.005 0.080 2912 Dihedral : 7.787 78.830 2296 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.92 % Allowed : 9.86 % Favored : 88.22 % 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: -1.12 (0.17), residues: 2005 helix: -0.40 (0.14), residues: 1178 sheet: 0.46 (0.38), residues: 173 loop : -1.52 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 445 HIS 0.006 0.001 HIS D 57 PHE 0.030 0.002 PHE C 693 TYR 0.023 0.002 TYR C 337 ARG 0.011 0.001 ARG D 359 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 154 time to evaluate : 2.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 516 ASN cc_start: 0.9410 (m-40) cc_final: 0.9129 (p0) REVERT: A 633 MET cc_start: 0.8564 (pmm) cc_final: 0.8252 (pmm) REVERT: C 140 ASP cc_start: 0.8767 (OUTLIER) cc_final: 0.8234 (p0) REVERT: C 260 HIS cc_start: 0.7693 (t-170) cc_final: 0.7155 (t-170) REVERT: C 261 ARG cc_start: 0.9100 (mmp-170) cc_final: 0.8524 (mmp-170) REVERT: C 394 LEU cc_start: 0.8332 (tp) cc_final: 0.8007 (mt) REVERT: C 469 MET cc_start: 0.7817 (ppp) cc_final: 0.7597 (ppp) REVERT: C 617 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8638 (pptt) REVERT: D 303 MET cc_start: 0.8720 (mtp) cc_final: 0.8494 (ptp) REVERT: D 314 LYS cc_start: 0.8426 (mmtp) cc_final: 0.7986 (mttt) REVERT: D 332 MET cc_start: 0.7316 (ttp) cc_final: 0.7074 (ttp) outliers start: 36 outliers final: 28 residues processed: 176 average time/residue: 0.2993 time to fit residues: 79.6650 Evaluate side-chains 163 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 133 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 698 LYS Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 617 LYS Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 371 ASP Chi-restraints excluded: chain E residue 410 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 183 optimal weight: 0.6980 chunk 198 optimal weight: 0.5980 chunk 163 optimal weight: 5.9990 chunk 182 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 825 HIS B 304 GLN ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 GLN ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 HIS D 316 ASN ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 GLN D 427 GLN ** E 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17078 Z= 0.171 Angle : 0.597 13.591 23117 Z= 0.296 Chirality : 0.039 0.156 2641 Planarity : 0.004 0.057 2912 Dihedral : 7.263 76.352 2296 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.03 % Allowed : 11.99 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.18), residues: 2005 helix: 0.38 (0.15), residues: 1178 sheet: 0.61 (0.38), residues: 174 loop : -1.38 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 433 HIS 0.004 0.001 HIS A 545 PHE 0.027 0.001 PHE C 693 TYR 0.016 0.001 TYR C 610 ARG 0.007 0.001 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 150 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 572 LYS cc_start: 0.8219 (pttm) cc_final: 0.7874 (ptpp) REVERT: A 633 MET cc_start: 0.8596 (pmm) cc_final: 0.8322 (pmm) REVERT: A 816 MET cc_start: 0.8048 (ptp) cc_final: 0.7795 (ptp) REVERT: A 852 ASP cc_start: 0.8598 (m-30) cc_final: 0.8189 (p0) REVERT: B 433 TRP cc_start: 0.6779 (p90) cc_final: 0.6422 (p90) REVERT: C 71 ASP cc_start: 0.8418 (m-30) cc_final: 0.8077 (m-30) REVERT: C 140 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.8014 (p0) REVERT: C 394 LEU cc_start: 0.8372 (tp) cc_final: 0.7979 (mt) REVERT: C 409 HIS cc_start: 0.8458 (OUTLIER) cc_final: 0.8144 (m-70) REVERT: C 422 PHE cc_start: 0.7971 (m-80) cc_final: 0.7746 (m-80) REVERT: C 634 TYR cc_start: 0.8218 (t80) cc_final: 0.7978 (t80) REVERT: D 51 LEU cc_start: 0.9500 (mt) cc_final: 0.9107 (pp) REVERT: D 314 LYS cc_start: 0.8386 (mmtp) cc_final: 0.7850 (mttt) REVERT: E 130 LEU cc_start: 0.9052 (mt) cc_final: 0.8806 (mt) outliers start: 38 outliers final: 26 residues processed: 176 average time/residue: 0.2850 time to fit residues: 77.8136 Evaluate side-chains 159 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 131 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 LYS Chi-restraints excluded: chain A residue 698 LYS Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 409 HIS Chi-restraints excluded: chain C residue 440 CYS Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 617 LYS Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 371 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 181 optimal weight: 2.9990 chunk 138 optimal weight: 9.9990 chunk 95 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 184 optimal weight: 3.9990 chunk 195 optimal weight: 0.0670 chunk 96 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 GLN C 365 ASN D 316 ASN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN ** E 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17078 Z= 0.236 Angle : 0.640 12.358 23117 Z= 0.319 Chirality : 0.040 0.220 2641 Planarity : 0.004 0.050 2912 Dihedral : 7.404 75.594 2296 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.88 % Allowed : 13.91 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.18), residues: 2005 helix: 0.51 (0.15), residues: 1178 sheet: 0.60 (0.39), residues: 175 loop : -1.33 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 445 HIS 0.030 0.001 HIS C 409 PHE 0.016 0.002 PHE E 328 TYR 0.017 0.002 TYR C 610 ARG 0.005 0.001 ARG D 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 133 time to evaluate : 2.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 572 LYS cc_start: 0.8397 (pttm) cc_final: 0.7907 (ptpp) REVERT: A 633 MET cc_start: 0.8783 (pmm) cc_final: 0.8454 (pmm) REVERT: A 816 MET cc_start: 0.8018 (ptp) cc_final: 0.7801 (ptp) REVERT: B 287 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8821 (pp) REVERT: C 29 TYR cc_start: 0.8037 (OUTLIER) cc_final: 0.7255 (m-80) REVERT: C 71 ASP cc_start: 0.8355 (m-30) cc_final: 0.8141 (m-30) REVERT: C 140 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.8123 (p0) REVERT: C 394 LEU cc_start: 0.8717 (tp) cc_final: 0.8359 (mt) REVERT: C 422 PHE cc_start: 0.8176 (m-80) cc_final: 0.7849 (m-80) REVERT: C 469 MET cc_start: 0.7987 (ppp) cc_final: 0.7764 (ppp) REVERT: C 634 TYR cc_start: 0.8469 (t80) cc_final: 0.8148 (t80) REVERT: D 314 LYS cc_start: 0.8441 (mmtp) cc_final: 0.7926 (mttt) REVERT: E 133 MET cc_start: 0.8376 (ttm) cc_final: 0.7418 (mmm) outliers start: 54 outliers final: 40 residues processed: 173 average time/residue: 0.2842 time to fit residues: 76.5134 Evaluate side-chains 168 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 125 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 LYS Chi-restraints excluded: chain A residue 698 LYS Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 409 HIS Chi-restraints excluded: chain C residue 440 CYS Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 617 LYS Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 371 ASP Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 410 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 162 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 145 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 166 optimal weight: 4.9990 chunk 134 optimal weight: 0.0470 chunk 0 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 chunk 175 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 overall best weight: 2.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 GLN ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 HIS D 36 ASN D 316 ASN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17078 Z= 0.190 Angle : 0.589 12.799 23117 Z= 0.291 Chirality : 0.040 0.175 2641 Planarity : 0.003 0.047 2912 Dihedral : 7.278 76.054 2296 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.20 % Allowed : 15.19 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.19), residues: 2005 helix: 0.83 (0.15), residues: 1173 sheet: 0.56 (0.39), residues: 177 loop : -1.32 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 433 HIS 0.009 0.001 HIS C 260 PHE 0.030 0.001 PHE D 353 TYR 0.014 0.001 TYR C 408 ARG 0.004 0.000 ARG D 205 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 133 time to evaluate : 2.111 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: A 633 MET cc_start: 0.8814 (pmm) cc_final: 0.8458 (pmm) REVERT: A 816 MET cc_start: 0.7796 (ptp) cc_final: 0.7298 (ptp) REVERT: A 852 ASP cc_start: 0.8564 (m-30) cc_final: 0.8199 (p0) REVERT: B 287 LEU cc_start: 0.9220 (mm) cc_final: 0.8826 (pp) REVERT: B 409 ILE cc_start: 0.8917 (mm) cc_final: 0.8645 (pt) REVERT: B 432 MET cc_start: 0.6983 (pmm) cc_final: 0.6738 (pmm) REVERT: C 29 TYR cc_start: 0.8016 (OUTLIER) cc_final: 0.7212 (m-80) REVERT: C 71 ASP cc_start: 0.8270 (m-30) cc_final: 0.8047 (m-30) REVERT: C 140 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.8178 (p0) REVERT: C 260 HIS cc_start: 0.8154 (t-170) cc_final: 0.7673 (t-170) REVERT: C 261 ARG cc_start: 0.9020 (mmp-170) cc_final: 0.8464 (mmp80) REVERT: C 394 LEU cc_start: 0.8803 (tp) cc_final: 0.8465 (mt) REVERT: C 409 HIS cc_start: 0.8491 (OUTLIER) cc_final: 0.7980 (m-70) REVERT: C 422 PHE cc_start: 0.8068 (m-80) cc_final: 0.7846 (m-80) REVERT: C 634 TYR cc_start: 0.8573 (t80) cc_final: 0.8270 (t80) REVERT: D 51 LEU cc_start: 0.9532 (mt) cc_final: 0.9048 (pp) REVERT: D 314 LYS cc_start: 0.8431 (mmtp) cc_final: 0.7912 (mttt) REVERT: D 359 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6808 (ppt90) REVERT: E 130 LEU cc_start: 0.9223 (mt) cc_final: 0.8780 (mp) REVERT: E 391 GLN cc_start: 0.8648 (mp10) cc_final: 0.8116 (mp10) outliers start: 60 outliers final: 41 residues processed: 179 average time/residue: 0.2763 time to fit residues: 76.7279 Evaluate side-chains 174 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 129 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 LYS Chi-restraints excluded: chain A residue 698 LYS Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 409 HIS Chi-restraints excluded: chain C residue 440 CYS Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 617 LYS Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 359 ARG Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 371 ASP Chi-restraints excluded: chain E residue 410 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 65 optimal weight: 0.0040 chunk 175 optimal weight: 8.9990 chunk 38 optimal weight: 0.0980 chunk 114 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 195 optimal weight: 8.9990 chunk 162 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 64 optimal weight: 30.0000 chunk 102 optimal weight: 6.9990 overall best weight: 4.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 GLN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 GLN ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 HIS D 316 ASN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 HIS ** D 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 HIS E 319 ASN ** E 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.5759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17078 Z= 0.321 Angle : 0.725 13.155 23117 Z= 0.363 Chirality : 0.043 0.181 2641 Planarity : 0.004 0.056 2912 Dihedral : 7.858 85.231 2296 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 24.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.73 % Allowed : 16.04 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.18), residues: 2005 helix: 0.24 (0.15), residues: 1173 sheet: 0.36 (0.39), residues: 165 loop : -1.44 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP B 433 HIS 0.024 0.002 HIS C 409 PHE 0.021 0.002 PHE D 132 TYR 0.022 0.002 TYR C 610 ARG 0.007 0.001 ARG B 327 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 129 time to evaluate : 2.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 816 MET cc_start: 0.7817 (ptp) cc_final: 0.7237 (ptp) REVERT: C 71 ASP cc_start: 0.8351 (m-30) cc_final: 0.8131 (m-30) REVERT: C 140 ASP cc_start: 0.8585 (OUTLIER) cc_final: 0.8148 (p0) REVERT: C 144 MET cc_start: 0.8505 (mmm) cc_final: 0.8225 (mmm) REVERT: C 394 LEU cc_start: 0.8966 (tp) cc_final: 0.8650 (mt) REVERT: C 469 MET cc_start: 0.8263 (ppp) cc_final: 0.8052 (ppp) REVERT: D 75 MET cc_start: 0.8590 (ptm) cc_final: 0.8195 (ptm) REVERT: D 76 LEU cc_start: 0.9261 (mm) cc_final: 0.9008 (tt) REVERT: D 314 LYS cc_start: 0.8470 (mmtp) cc_final: 0.7963 (mttt) REVERT: D 359 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.7155 (ppt90) REVERT: E 133 MET cc_start: 0.8519 (ttm) cc_final: 0.7569 (mmm) outliers start: 70 outliers final: 48 residues processed: 185 average time/residue: 0.3078 time to fit residues: 88.3107 Evaluate side-chains 174 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 124 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 698 LYS Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 443 TRP Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 181 MET Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 440 CYS Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 617 LYS Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 255 TYR Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 359 ARG Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 371 ASP Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 410 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 188 optimal weight: 0.7980 chunk 22 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 chunk 142 optimal weight: 8.9990 chunk 110 optimal weight: 0.0870 chunk 164 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 194 optimal weight: 0.3980 chunk 121 optimal weight: 3.9990 chunk 118 optimal weight: 0.0970 chunk 89 optimal weight: 4.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 HIS D 252 ASN D 316 ASN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.5564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17078 Z= 0.149 Angle : 0.621 12.678 23117 Z= 0.296 Chirality : 0.040 0.179 2641 Planarity : 0.003 0.044 2912 Dihedral : 7.114 81.549 2296 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.19 % Allowed : 17.70 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.19), residues: 2005 helix: 0.96 (0.15), residues: 1167 sheet: 0.62 (0.39), residues: 177 loop : -1.15 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP B 433 HIS 0.011 0.001 HIS C 260 PHE 0.014 0.001 PHE D 38 TYR 0.013 0.001 TYR E 269 ARG 0.004 0.000 ARG A 675 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 143 time to evaluate : 1.916 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: A 816 MET cc_start: 0.7703 (ptp) cc_final: 0.7258 (ptp) REVERT: A 852 ASP cc_start: 0.8528 (m-30) cc_final: 0.8232 (p0) REVERT: B 287 LEU cc_start: 0.9257 (mm) cc_final: 0.8864 (pp) REVERT: B 432 MET cc_start: 0.7320 (pmm) cc_final: 0.6712 (pmm) REVERT: C 24 LEU cc_start: 0.6303 (OUTLIER) cc_final: 0.5097 (mm) REVERT: C 71 ASP cc_start: 0.8197 (m-30) cc_final: 0.7945 (m-30) REVERT: C 140 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8243 (p0) REVERT: C 144 MET cc_start: 0.8558 (mmm) cc_final: 0.8272 (mmm) REVERT: C 261 ARG cc_start: 0.9006 (mmp-170) cc_final: 0.8570 (mmp80) REVERT: C 394 LEU cc_start: 0.8864 (tp) cc_final: 0.8541 (mt) REVERT: C 469 MET cc_start: 0.8135 (ppp) cc_final: 0.7932 (ppp) REVERT: D 75 MET cc_start: 0.8492 (ptm) cc_final: 0.8165 (ptm) REVERT: D 76 LEU cc_start: 0.9209 (mm) cc_final: 0.8962 (tt) REVERT: D 281 MET cc_start: 0.7746 (tmm) cc_final: 0.7424 (tmm) REVERT: D 314 LYS cc_start: 0.8344 (mmtp) cc_final: 0.7838 (mttt) REVERT: E 133 MET cc_start: 0.8289 (ttm) cc_final: 0.7476 (mmm) REVERT: E 391 GLN cc_start: 0.8598 (mp10) cc_final: 0.8035 (mp10) outliers start: 41 outliers final: 32 residues processed: 174 average time/residue: 0.2638 time to fit residues: 71.2418 Evaluate side-chains 167 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 133 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 LYS Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 617 LYS Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 371 ASP Chi-restraints excluded: chain E residue 410 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 120 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 123 optimal weight: 10.0000 chunk 132 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 153 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 ASN ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 GLN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.5680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17078 Z= 0.147 Angle : 0.600 14.481 23117 Z= 0.287 Chirality : 0.040 0.208 2641 Planarity : 0.003 0.045 2912 Dihedral : 6.983 79.726 2296 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.19 % Allowed : 18.23 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.19), residues: 2005 helix: 1.08 (0.15), residues: 1166 sheet: 0.74 (0.38), residues: 177 loop : -1.12 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP B 433 HIS 0.012 0.001 HIS C 260 PHE 0.042 0.001 PHE D 353 TYR 0.016 0.001 TYR C 634 ARG 0.004 0.000 ARG D 205 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 137 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 816 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7305 (ptp) REVERT: A 852 ASP cc_start: 0.8539 (m-30) cc_final: 0.8270 (p0) REVERT: B 287 LEU cc_start: 0.9224 (mm) cc_final: 0.8835 (pp) REVERT: C 24 LEU cc_start: 0.6017 (OUTLIER) cc_final: 0.4729 (mm) REVERT: C 71 ASP cc_start: 0.8216 (m-30) cc_final: 0.7983 (m-30) REVERT: C 140 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.8210 (p0) REVERT: C 144 MET cc_start: 0.8613 (mmm) cc_final: 0.8317 (mmm) REVERT: C 261 ARG cc_start: 0.9014 (mmp-170) cc_final: 0.8554 (mmp80) REVERT: C 394 LEU cc_start: 0.8947 (tp) cc_final: 0.8644 (mt) REVERT: C 469 MET cc_start: 0.8228 (ppp) cc_final: 0.7956 (ppp) REVERT: D 75 MET cc_start: 0.8442 (ptm) cc_final: 0.8082 (ptm) REVERT: D 76 LEU cc_start: 0.9216 (mm) cc_final: 0.8923 (tt) REVERT: D 281 MET cc_start: 0.7628 (tmm) cc_final: 0.7334 (tmm) REVERT: D 314 LYS cc_start: 0.8385 (mmtp) cc_final: 0.7857 (mttt) REVERT: E 133 MET cc_start: 0.8404 (ttm) cc_final: 0.7512 (mmm) REVERT: E 391 GLN cc_start: 0.8514 (mp10) cc_final: 0.7944 (mp10) outliers start: 41 outliers final: 32 residues processed: 168 average time/residue: 0.2785 time to fit residues: 72.6550 Evaluate side-chains 165 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 130 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 LYS Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 617 LYS Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 371 ASP Chi-restraints excluded: chain E residue 410 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 177 optimal weight: 1.9990 chunk 186 optimal weight: 10.0000 chunk 170 optimal weight: 0.7980 chunk 181 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 163 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 ASN ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 316 ASN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.6075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17078 Z= 0.220 Angle : 0.649 12.654 23117 Z= 0.315 Chirality : 0.041 0.208 2641 Planarity : 0.004 0.045 2912 Dihedral : 7.272 81.728 2296 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.35 % Allowed : 18.50 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.19), residues: 2005 helix: 0.94 (0.15), residues: 1175 sheet: 0.38 (0.39), residues: 183 loop : -1.19 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.003 TRP B 433 HIS 0.009 0.001 HIS C 260 PHE 0.017 0.001 PHE E 328 TYR 0.015 0.002 TYR C 634 ARG 0.005 0.001 ARG D 205 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 132 time to evaluate : 2.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 816 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.6900 (ptp) REVERT: A 852 ASP cc_start: 0.8596 (m-30) cc_final: 0.8272 (p0) REVERT: B 287 LEU cc_start: 0.9209 (mm) cc_final: 0.8829 (pp) REVERT: C 24 LEU cc_start: 0.6247 (OUTLIER) cc_final: 0.4978 (mm) REVERT: C 71 ASP cc_start: 0.8250 (m-30) cc_final: 0.8012 (m-30) REVERT: C 140 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.8223 (p0) REVERT: C 144 MET cc_start: 0.8601 (mmm) cc_final: 0.8301 (mmm) REVERT: C 261 ARG cc_start: 0.9046 (mmp-170) cc_final: 0.8568 (mmp80) REVERT: C 394 LEU cc_start: 0.8998 (tp) cc_final: 0.8702 (mt) REVERT: C 469 MET cc_start: 0.8249 (ppp) cc_final: 0.7966 (ppp) REVERT: D 75 MET cc_start: 0.8467 (ptm) cc_final: 0.8130 (ptm) REVERT: D 281 MET cc_start: 0.7616 (tmm) cc_final: 0.7288 (tmm) REVERT: D 314 LYS cc_start: 0.8450 (mmtp) cc_final: 0.7880 (mttt) REVERT: E 133 MET cc_start: 0.8353 (ttm) cc_final: 0.7613 (mmm) REVERT: E 391 GLN cc_start: 0.8693 (mp10) cc_final: 0.8201 (mp10) outliers start: 44 outliers final: 31 residues processed: 170 average time/residue: 0.2743 time to fit residues: 72.3747 Evaluate side-chains 163 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 129 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 LYS Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 617 LYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 371 ASP Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 410 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 119 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 chunk 117 optimal weight: 0.2980 chunk 91 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 201 optimal weight: 0.6980 chunk 185 optimal weight: 10.0000 chunk 160 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 123 optimal weight: 0.0980 chunk 98 optimal weight: 3.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 HIS ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.6023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17078 Z= 0.145 Angle : 0.627 13.572 23117 Z= 0.296 Chirality : 0.040 0.198 2641 Planarity : 0.003 0.044 2912 Dihedral : 6.928 76.644 2296 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.97 % Allowed : 18.71 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.19), residues: 2005 helix: 1.14 (0.15), residues: 1170 sheet: 0.77 (0.39), residues: 175 loop : -1.09 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP B 433 HIS 0.009 0.001 HIS C 260 PHE 0.015 0.001 PHE D 38 TYR 0.017 0.001 TYR C 634 ARG 0.003 0.000 ARG D 205 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 134 time to evaluate : 2.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 693 ARG cc_start: 0.7688 (mmt180) cc_final: 0.7405 (mmt180) REVERT: A 752 MET cc_start: 0.6605 (ppp) cc_final: 0.6366 (ppp) REVERT: A 852 ASP cc_start: 0.8442 (m-30) cc_final: 0.8207 (p0) REVERT: B 287 LEU cc_start: 0.9236 (mm) cc_final: 0.8850 (pp) REVERT: C 24 LEU cc_start: 0.6341 (OUTLIER) cc_final: 0.5192 (mm) REVERT: C 36 GLU cc_start: 0.0214 (OUTLIER) cc_final: -0.0047 (mp0) REVERT: C 71 ASP cc_start: 0.8186 (m-30) cc_final: 0.7956 (m-30) REVERT: C 140 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.8177 (p0) REVERT: C 144 MET cc_start: 0.8593 (mmm) cc_final: 0.8296 (mmm) REVERT: C 261 ARG cc_start: 0.9041 (mmp-170) cc_final: 0.8660 (mmp80) REVERT: C 394 LEU cc_start: 0.8966 (tp) cc_final: 0.8676 (mt) REVERT: C 469 MET cc_start: 0.8281 (ppp) cc_final: 0.8011 (ppp) REVERT: D 75 MET cc_start: 0.8417 (ptm) cc_final: 0.8105 (ptm) REVERT: D 281 MET cc_start: 0.7605 (tmm) cc_final: 0.7313 (tmm) REVERT: D 314 LYS cc_start: 0.8421 (mmtp) cc_final: 0.7901 (mttm) REVERT: E 133 MET cc_start: 0.8372 (ttm) cc_final: 0.8162 (ttm) REVERT: E 391 GLN cc_start: 0.8447 (mp10) cc_final: 0.7880 (mp10) outliers start: 37 outliers final: 31 residues processed: 162 average time/residue: 0.2738 time to fit residues: 69.0613 Evaluate side-chains 163 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 129 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 LYS Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 260 HIS Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 617 LYS Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 371 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 127 optimal weight: 3.9990 chunk 170 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 147 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 44 optimal weight: 0.8980 chunk 160 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 688 GLN ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.055784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.040647 restraints weight = 147811.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.041406 restraints weight = 107170.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.042043 restraints weight = 86220.131| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.6416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17078 Z= 0.255 Angle : 0.682 12.643 23117 Z= 0.334 Chirality : 0.042 0.214 2641 Planarity : 0.004 0.049 2912 Dihedral : 7.366 81.080 2296 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.29 % Allowed : 18.66 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.19), residues: 2005 helix: 0.86 (0.15), residues: 1181 sheet: 0.34 (0.39), residues: 183 loop : -1.20 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP B 433 HIS 0.026 0.001 HIS C 260 PHE 0.058 0.002 PHE C 422 TYR 0.015 0.002 TYR C 634 ARG 0.006 0.001 ARG C 261 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2934.77 seconds wall clock time: 55 minutes 7.33 seconds (3307.33 seconds total)