Starting phenix.real_space_refine on Fri Feb 16 03:59:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z38_14473/02_2024/7z38_14473_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z38_14473/02_2024/7z38_14473.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z38_14473/02_2024/7z38_14473.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z38_14473/02_2024/7z38_14473.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z38_14473/02_2024/7z38_14473_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z38_14473/02_2024/7z38_14473_updated.pdb" } resolution = 3.16 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= 0.003 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 7 5.49 5 Mg 2 5.21 5 S 74 5.16 5 C 9007 2.51 5 N 2423 2.21 5 O 2745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 70": "OE1" <-> "OE2" Residue "A PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 274": "OE1" <-> "OE2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A ASP 385": "OD1" <-> "OD2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 418": "OE1" <-> "OE2" Residue "A GLU 545": "OE1" <-> "OE2" Residue "A GLU 561": "OE1" <-> "OE2" Residue "A GLU 636": "OE1" <-> "OE2" Residue "B PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 61": "OD1" <-> "OD2" Residue "B ASP 66": "OD1" <-> "OD2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 188": "OD1" <-> "OD2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 421": "OE1" <-> "OE2" Residue "B ASP 422": "OD1" <-> "OD2" Residue "B GLU 424": "OE1" <-> "OE2" Residue "B ASP 444": "OD1" <-> "OD2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B ASP 529": "OD1" <-> "OD2" Residue "B TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 613": "OD1" <-> "OD2" Residue "C TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 457": "OD1" <-> "OD2" Residue "C PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 486": "OD1" <-> "OD2" Residue "C ASP 530": "OD1" <-> "OD2" Residue "C TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D GLU 99": "OE1" <-> "OE2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D GLU 109": "OE1" <-> "OE2" Residue "D ASP 139": "OD1" <-> "OD2" Residue "D PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14258 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5158 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 17, 'TRANS': 618} Chain breaks: 1 Chain: "B" Number of atoms: 5173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 5173 Classifications: {'peptide': 638} Link IDs: {'PTRANS': 17, 'TRANS': 620} Chain breaks: 1 Chain: "C" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1564 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 8, 'TRANS': 184} Chain breaks: 1 Chain: "D" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2299 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 4, 'TRANS': 268} 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: "B" 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: 7.38, per 1000 atoms: 0.52 Number of scatterers: 14258 At special positions: 0 Unit cell: (124.8, 118.976, 152.256, 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 74 16.00 P 7 15.00 Mg 2 11.99 O 2745 8.00 N 2423 7.00 C 9007 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: 5.47 Conformation dependent library (CDL) restraints added in 2.7 seconds 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3330 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 71 helices and 9 sheets defined 45.5% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.35 Creating SS restraints... Processing helix chain 'A' and resid 21 through 30 Processing helix chain 'A' and resid 36 through 60 removed outlier: 3.787A pdb=" N PHE A 39 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 40 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU A 57 " --> pdb=" O ILE A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 109 through 117 removed outlier: 3.848A pdb=" N LEU A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 138 Processing helix chain 'A' and resid 190 through 193 Processing helix chain 'A' and resid 195 through 204 Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 298 through 309 Processing helix chain 'A' and resid 346 through 348 No H-bonds generated for 'chain 'A' and resid 346 through 348' Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'A' and resid 398 through 419 removed outlier: 4.274A pdb=" N VAL A 409 " --> pdb=" O LYS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 443 removed outlier: 6.538A pdb=" N LYS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ASN A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 454 removed outlier: 3.744A pdb=" N GLU A 453 " --> pdb=" O ARG A 449 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU A 454 " --> pdb=" O ARG A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 475 Processing helix chain 'A' and resid 491 through 495 Processing helix chain 'A' and resid 501 through 505 Processing helix chain 'A' and resid 516 through 524 removed outlier: 3.651A pdb=" N GLN A 524 " --> pdb=" O CYS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 562 through 570 Processing helix chain 'A' and resid 600 through 607 Processing helix chain 'A' and resid 614 through 616 No H-bonds generated for 'chain 'A' and resid 614 through 616' Processing helix chain 'A' and resid 633 through 644 removed outlier: 3.615A pdb=" N ALA A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 665 Processing helix chain 'A' and resid 673 through 688 Processing helix chain 'B' and resid 21 through 30 Processing helix chain 'B' and resid 36 through 60 removed outlier: 3.545A pdb=" N LEU B 40 " --> pdb=" O GLU B 37 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR B 60 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 132 through 138 Processing helix chain 'B' and resid 190 through 193 Processing helix chain 'B' and resid 195 through 205 Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' Processing helix chain 'B' and resid 298 through 309 Processing helix chain 'B' and resid 346 through 348 No H-bonds generated for 'chain 'B' and resid 346 through 348' Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'B' and resid 400 through 420 Processing helix chain 'B' and resid 423 through 443 removed outlier: 3.992A pdb=" N LYS B 428 " --> pdb=" O GLU B 424 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA B 432 " --> pdb=" O LYS B 428 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LYS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ASN B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 454 removed outlier: 3.899A pdb=" N GLU B 453 " --> pdb=" O ARG B 449 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU B 454 " --> pdb=" O ARG B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 475 Processing helix chain 'B' and resid 491 through 495 Processing helix chain 'B' and resid 498 through 505 removed outlier: 3.577A pdb=" N GLU B 501 " --> pdb=" O ALA B 498 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ARG B 502 " --> pdb=" O PHE B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 524 removed outlier: 4.153A pdb=" N TYR B 520 " --> pdb=" O PRO B 516 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN B 524 " --> pdb=" O TYR B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 570 removed outlier: 5.362A pdb=" N ASN B 562 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU B 563 " --> pdb=" O LYS B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 608 removed outlier: 3.665A pdb=" N ALA B 608 " --> pdb=" O ARG B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 644 removed outlier: 3.659A pdb=" N LYS B 641 " --> pdb=" O THR B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 666 Processing helix chain 'B' and resid 673 through 688 Processing helix chain 'C' and resid 442 through 461 removed outlier: 3.660A pdb=" N ILE C 448 " --> pdb=" O GLN C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 473 No H-bonds generated for 'chain 'C' and resid 471 through 473' Processing helix chain 'C' and resid 514 through 518 Processing helix chain 'C' and resid 527 through 542 Processing helix chain 'C' and resid 554 through 563 removed outlier: 3.935A pdb=" N ILE C 558 " --> pdb=" O ARG C 554 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE C 559 " --> pdb=" O ASP C 555 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N MET C 560 " --> pdb=" O GLN C 556 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL C 561 " --> pdb=" O ILE C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 588 Processing helix chain 'C' and resid 599 through 611 removed outlier: 3.528A pdb=" N SER C 604 " --> pdb=" O PRO C 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 73 removed outlier: 4.154A pdb=" N ARG D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS D 33 " --> pdb=" O PHE D 29 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU D 38 " --> pdb=" O GLN D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 111 removed outlier: 3.776A pdb=" N GLU D 99 " --> pdb=" O GLU D 95 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN D 100 " --> pdb=" O ARG D 96 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS D 101 " --> pdb=" O SER D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 119 No H-bonds generated for 'chain 'D' and resid 116 through 119' Processing helix chain 'D' and resid 143 through 154 Processing helix chain 'D' and resid 156 through 164 Processing helix chain 'D' and resid 168 through 177 Processing helix chain 'D' and resid 179 through 181 No H-bonds generated for 'chain 'D' and resid 179 through 181' Processing helix chain 'D' and resid 184 through 200 Processing helix chain 'D' and resid 203 through 226 removed outlier: 3.892A pdb=" N GLN D 212 " --> pdb=" O GLN D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 242 removed outlier: 3.815A pdb=" N PHE D 234 " --> pdb=" O PRO D 230 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ARG D 235 " --> pdb=" O ARG D 231 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N GLN D 236 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE D 237 " --> pdb=" O CYS D 233 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE D 238 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR D 239 " --> pdb=" O ARG D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 273 Processing sheet with id= A, first strand: chain 'A' and resid 165 through 168 removed outlier: 7.108A pdb=" N HIS A 184 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL A 143 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE A 182 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL A 145 " --> pdb=" O LYS A 180 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LYS A 180 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N THR A 147 " --> pdb=" O GLY A 178 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLY A 178 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE A 75 " --> pdb=" O PRO A 212 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N THR A 214 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TYR A 216 " --> pdb=" O PRO A 77 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 217 " --> pdb=" O ILE A 277 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 360 through 363 removed outlier: 6.905A pdb=" N LEU A 355 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLY A 379 " --> pdb=" O LYS A 354 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N TYR A 356 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL A 381 " --> pdb=" O TYR A 356 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA A 317 " --> pdb=" O ILE A 335 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 533 through 535 removed outlier: 5.512A pdb=" N ILE A 483 " --> pdb=" O VAL A 534 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 577 through 580 removed outlier: 3.812A pdb=" N LYS A 577 " --> pdb=" O LYS A 624 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 83 through 88 removed outlier: 7.337A pdb=" N ILE B 75 " --> pdb=" O PRO B 212 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR B 214 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TYR B 216 " --> pdb=" O PRO B 77 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 217 " --> pdb=" O ILE B 277 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 165 through 168 removed outlier: 3.604A pdb=" N ARG B 168 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N HIS B 184 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL B 143 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE B 182 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL B 145 " --> pdb=" O LYS B 180 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LYS B 180 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N THR B 147 " --> pdb=" O GLY B 178 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLY B 178 " --> pdb=" O THR B 147 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 317 through 323 removed outlier: 3.856A pdb=" N ALA B 317 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET B 363 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N VAL B 357 " --> pdb=" O PHE B 361 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N PHE B 361 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 532 through 535 removed outlier: 6.333A pdb=" N VAL B 511 " --> pdb=" O ILE B 486 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 577 through 580 584 hydrogen bonds defined for protein. 1488 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: 4.26 Time building geometry restraints manager: 5.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4683 1.34 - 1.46: 2716 1.46 - 1.58: 6965 1.58 - 1.69: 11 1.69 - 1.81: 126 Bond restraints: 14501 Sorted by residual: bond pdb=" CB PRO A 79 " pdb=" CG PRO A 79 " ideal model delta sigma weight residual 1.492 1.619 -0.127 5.00e-02 4.00e+02 6.42e+00 bond pdb=" N VAL B 592 " pdb=" CA VAL B 592 " ideal model delta sigma weight residual 1.454 1.434 0.020 1.28e-02 6.10e+03 2.46e+00 bond pdb=" CG PRO A 79 " pdb=" CD PRO A 79 " ideal model delta sigma weight residual 1.503 1.556 -0.053 3.40e-02 8.65e+02 2.42e+00 bond pdb=" CG1 ILE B 591 " pdb=" CD1 ILE B 591 " ideal model delta sigma weight residual 1.513 1.458 0.055 3.90e-02 6.57e+02 2.01e+00 bond pdb=" CA HIS A 171 " pdb=" C HIS A 171 " ideal model delta sigma weight residual 1.523 1.541 -0.018 1.34e-02 5.57e+03 1.73e+00 ... (remaining 14496 not shown) Histogram of bond angle deviations from ideal: 98.17 - 106.59: 305 106.59 - 115.02: 8835 115.02 - 123.45: 10003 123.45 - 131.87: 324 131.87 - 140.30: 22 Bond angle restraints: 19489 Sorted by residual: angle pdb=" CA PRO A 79 " pdb=" N PRO A 79 " pdb=" CD PRO A 79 " ideal model delta sigma weight residual 112.00 102.43 9.57 1.40e+00 5.10e-01 4.68e+01 angle pdb=" C GLU D 142 " pdb=" CA GLU D 142 " pdb=" CB GLU D 142 " ideal model delta sigma weight residual 116.63 109.99 6.64 1.16e+00 7.43e-01 3.28e+01 angle pdb=" CA GLU D 142 " pdb=" C GLU D 142 " pdb=" N VAL D 143 " ideal model delta sigma weight residual 119.63 116.66 2.97 8.10e-01 1.52e+00 1.35e+01 angle pdb=" CA LYS A 349 " pdb=" CB LYS A 349 " pdb=" CG LYS A 349 " ideal model delta sigma weight residual 114.10 119.60 -5.50 2.00e+00 2.50e-01 7.55e+00 angle pdb=" C CYS C 424 " pdb=" N GLU C 425 " pdb=" CA GLU C 425 " ideal model delta sigma weight residual 121.54 126.76 -5.22 1.91e+00 2.74e-01 7.47e+00 ... (remaining 19484 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 7621 17.98 - 35.97: 1006 35.97 - 53.95: 261 53.95 - 71.94: 79 71.94 - 89.92: 39 Dihedral angle restraints: 9006 sinusoidal: 3881 harmonic: 5125 Sorted by residual: dihedral pdb=" CA LEU B 117 " pdb=" C LEU B 117 " pdb=" N GLN B 118 " pdb=" CA GLN B 118 " ideal model delta harmonic sigma weight residual 180.00 160.11 19.89 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ALA A 432 " pdb=" C ALA A 432 " pdb=" N PHE A 433 " pdb=" CA PHE A 433 " ideal model delta harmonic sigma weight residual -180.00 -162.49 -17.51 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ASP A 314 " pdb=" CB ASP A 314 " pdb=" CG ASP A 314 " pdb=" OD1 ASP A 314 " ideal model delta sinusoidal sigma weight residual -30.00 -88.45 58.45 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 9003 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1461 0.038 - 0.077: 523 0.077 - 0.115: 127 0.115 - 0.153: 23 0.153 - 0.191: 2 Chirality restraints: 2136 Sorted by residual: chirality pdb=" CA PRO A 79 " pdb=" N PRO A 79 " pdb=" C PRO A 79 " pdb=" CB PRO A 79 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" CG LEU C 603 " pdb=" CB LEU C 603 " pdb=" CD1 LEU C 603 " pdb=" CD2 LEU C 603 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.85e-01 chirality pdb=" CA ILE B 73 " pdb=" N ILE B 73 " pdb=" C ILE B 73 " pdb=" CB ILE B 73 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 2133 not shown) Planarity restraints: 2486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 78 " 0.066 5.00e-02 4.00e+02 9.44e-02 1.43e+01 pdb=" N PRO A 79 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO A 79 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 79 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 32 " 0.021 2.00e-02 2.50e+03 1.76e-02 5.39e+00 pdb=" CG PHE A 32 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 32 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 32 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 32 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 32 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 32 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 280 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.63e+00 pdb=" C GLU A 280 " -0.033 2.00e-02 2.50e+03 pdb=" O GLU A 280 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU A 281 " 0.011 2.00e-02 2.50e+03 ... (remaining 2483 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 203 2.65 - 3.21: 13318 3.21 - 3.77: 21950 3.77 - 4.34: 30648 4.34 - 4.90: 50811 Nonbonded interactions: 116930 Sorted by model distance: nonbonded pdb=" O ASN A 100 " pdb=" OG1 THR A 104 " model vdw 2.085 2.440 nonbonded pdb=" OH TYR B 520 " pdb=" OE1 GLN B 609 " model vdw 2.137 2.440 nonbonded pdb=" OD1 ASN B 46 " pdb="MG MG B 802 " model vdw 2.138 2.170 nonbonded pdb=" O GLY B 132 " pdb=" OG SER B 135 " model vdw 2.183 2.440 nonbonded pdb=" O GLU B 328 " pdb=" OG SER B 383 " model vdw 2.196 2.440 ... (remaining 116925 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 690 or resid 801 through 802)) selection = (chain 'B' and (resid 10 through 223 or resid 270 through 690 or resid 801 throu \ gh 802)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 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: 0.020 Extract box with map and model: 11.880 Check model and map are aligned: 0.240 Set scattering table: 0.120 Process input model: 39.480 Find NCS groups from input model: 0.680 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: 0.010 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 : 0.005 0.127 14501 Z= 0.314 Angle : 0.605 9.574 19489 Z= 0.332 Chirality : 0.042 0.191 2136 Planarity : 0.004 0.094 2486 Dihedral : 18.677 89.919 5676 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.86 % Favored : 94.08 % Rotamer: Outliers : 0.19 % Allowed : 23.11 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.21), residues: 1723 helix: 0.82 (0.19), residues: 809 sheet: -1.19 (0.36), residues: 213 loop : -1.50 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 157 HIS 0.004 0.001 HIS A 458 PHE 0.039 0.002 PHE A 32 TYR 0.025 0.002 TYR A 426 ARG 0.008 0.000 ARG A 449 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 177 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 472 TYR cc_start: 0.7759 (t80) cc_final: 0.7372 (t80) REVERT: D 216 MET cc_start: 0.5061 (mmm) cc_final: 0.4415 (ttt) outliers start: 3 outliers final: 3 residues processed: 177 average time/residue: 0.2900 time to fit residues: 73.1418 Evaluate side-chains 174 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 171 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 596 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 chunk 52 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.0606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14501 Z= 0.279 Angle : 0.535 6.802 19489 Z= 0.288 Chirality : 0.041 0.164 2136 Planarity : 0.004 0.042 2486 Dihedral : 6.484 71.259 1964 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.92 % Favored : 94.02 % Rotamer: Outliers : 3.37 % Allowed : 21.97 % Favored : 74.67 % 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 (0.20), residues: 1723 helix: 0.83 (0.19), residues: 792 sheet: -1.10 (0.36), residues: 209 loop : -1.48 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 157 HIS 0.004 0.001 HIS B 149 PHE 0.034 0.002 PHE A 32 TYR 0.018 0.002 TYR B 134 ARG 0.004 0.000 ARG B 506 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 184 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8197 (tt) REVERT: A 554 GLU cc_start: 0.7783 (tp30) cc_final: 0.7007 (mt-10) REVERT: B 137 TYR cc_start: 0.8760 (m-80) cc_final: 0.8237 (m-80) REVERT: B 472 TYR cc_start: 0.7720 (t80) cc_final: 0.6980 (t80) REVERT: C 478 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6006 (pp20) REVERT: D 12 VAL cc_start: 0.7913 (OUTLIER) cc_final: 0.7508 (t) REVERT: D 216 MET cc_start: 0.5174 (mmm) cc_final: 0.4517 (ttt) outliers start: 53 outliers final: 25 residues processed: 221 average time/residue: 0.2800 time to fit residues: 88.8103 Evaluate side-chains 201 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 173 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 14 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 0.9990 chunk 48 optimal weight: 0.0370 chunk 129 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 169 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 overall best weight: 0.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 GLN ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.0806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14501 Z= 0.261 Angle : 0.521 6.916 19489 Z= 0.279 Chirality : 0.041 0.154 2136 Planarity : 0.004 0.040 2486 Dihedral : 6.301 69.899 1962 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.92 % Favored : 94.02 % Rotamer: Outliers : 4.19 % Allowed : 22.16 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.20), residues: 1723 helix: 0.74 (0.19), residues: 794 sheet: -1.06 (0.36), residues: 204 loop : -1.46 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 157 HIS 0.003 0.001 HIS B 149 PHE 0.034 0.002 PHE A 32 TYR 0.018 0.002 TYR B 134 ARG 0.006 0.000 ARG D 36 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 178 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8134 (tt) REVERT: A 326 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.7259 (tm130) REVERT: A 531 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7368 (ptpp) REVERT: A 663 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8516 (mp) REVERT: B 123 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7669 (tp) REVERT: B 125 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.7501 (mmt) REVERT: B 137 TYR cc_start: 0.8831 (m-80) cc_final: 0.8260 (m-80) REVERT: B 308 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8451 (tp) REVERT: B 472 TYR cc_start: 0.7741 (t80) cc_final: 0.6972 (t80) REVERT: C 478 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6010 (pp20) REVERT: D 216 MET cc_start: 0.5280 (mmm) cc_final: 0.4672 (ttp) outliers start: 66 outliers final: 32 residues processed: 225 average time/residue: 0.2754 time to fit residues: 89.6870 Evaluate side-chains 209 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 169 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 460 HIS Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 128 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 30.0000 chunk 117 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 148 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14501 Z= 0.249 Angle : 0.518 7.834 19489 Z= 0.276 Chirality : 0.040 0.156 2136 Planarity : 0.004 0.041 2486 Dihedral : 6.131 69.864 1960 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.92 % Favored : 94.02 % Rotamer: Outliers : 4.70 % Allowed : 22.10 % Favored : 73.21 % 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: -0.59 (0.20), residues: 1723 helix: 0.74 (0.19), residues: 792 sheet: -1.05 (0.36), residues: 204 loop : -1.43 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 157 HIS 0.003 0.001 HIS B 149 PHE 0.032 0.002 PHE A 32 TYR 0.023 0.002 TYR A 426 ARG 0.004 0.000 ARG D 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 176 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8127 (tt) REVERT: A 326 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.7247 (tm130) REVERT: A 476 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.7710 (ttm) REVERT: A 531 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7393 (ptpp) REVERT: A 554 GLU cc_start: 0.7774 (tp30) cc_final: 0.6891 (mt-10) REVERT: A 663 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8356 (mp) REVERT: B 123 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7695 (tp) REVERT: B 125 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7445 (mmt) REVERT: B 137 TYR cc_start: 0.8857 (m-80) cc_final: 0.8308 (m-80) REVERT: B 308 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8456 (tp) REVERT: B 472 TYR cc_start: 0.7759 (t80) cc_final: 0.6972 (t80) REVERT: B 524 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7586 (mp10) REVERT: B 553 MET cc_start: 0.5796 (OUTLIER) cc_final: 0.5485 (mmm) REVERT: C 478 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6035 (pp20) REVERT: D 216 MET cc_start: 0.5203 (mmm) cc_final: 0.4691 (ttp) outliers start: 74 outliers final: 41 residues processed: 230 average time/residue: 0.3039 time to fit residues: 101.1019 Evaluate side-chains 220 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 168 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 524 GLN Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 460 HIS Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 128 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 GLN ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14501 Z= 0.262 Angle : 0.522 7.002 19489 Z= 0.277 Chirality : 0.041 0.174 2136 Planarity : 0.004 0.039 2486 Dihedral : 6.095 69.581 1960 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.98 % Favored : 93.96 % Rotamer: Outliers : 5.08 % Allowed : 21.90 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.20), residues: 1723 helix: 0.71 (0.19), residues: 792 sheet: -1.05 (0.36), residues: 204 loop : -1.42 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 157 HIS 0.003 0.001 HIS B 149 PHE 0.034 0.002 PHE A 32 TYR 0.025 0.002 TYR A 426 ARG 0.005 0.000 ARG D 36 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 175 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8135 (tt) REVERT: A 326 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.7250 (tm130) REVERT: A 476 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.7716 (ttm) REVERT: A 519 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6705 (mp0) REVERT: A 531 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7375 (ptpp) REVERT: A 554 GLU cc_start: 0.7797 (tp30) cc_final: 0.6926 (mt-10) REVERT: A 663 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8324 (mp) REVERT: B 123 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7715 (tp) REVERT: B 125 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.7461 (mmt) REVERT: B 137 TYR cc_start: 0.8892 (m-80) cc_final: 0.8283 (m-80) REVERT: B 308 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8460 (tp) REVERT: B 472 TYR cc_start: 0.7772 (t80) cc_final: 0.6954 (t80) REVERT: B 524 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7604 (mp10) REVERT: B 553 MET cc_start: 0.5831 (OUTLIER) cc_final: 0.5485 (mmm) REVERT: C 478 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6023 (pp20) REVERT: D 30 ARG cc_start: 0.8237 (mtm110) cc_final: 0.7890 (mtm-85) REVERT: D 216 MET cc_start: 0.5199 (mmm) cc_final: 0.4685 (ttp) REVERT: D 217 GLN cc_start: 0.4769 (mm-40) cc_final: 0.4341 (mt0) outliers start: 80 outliers final: 50 residues processed: 235 average time/residue: 0.2779 time to fit residues: 94.2930 Evaluate side-chains 225 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 163 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 519 GLU Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 682 ARG Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 524 GLN Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 631 ASP Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 460 HIS Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 206 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 0.8980 chunk 149 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 166 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 chunk 77 optimal weight: 0.0980 chunk 13 optimal weight: 2.9990 chunk 87 optimal weight: 0.2980 chunk 160 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14501 Z= 0.230 Angle : 0.509 6.976 19489 Z= 0.269 Chirality : 0.040 0.180 2136 Planarity : 0.004 0.040 2486 Dihedral : 5.894 69.556 1957 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.92 % Favored : 94.02 % Rotamer: Outliers : 4.83 % Allowed : 22.54 % Favored : 72.63 % 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: -0.57 (0.20), residues: 1723 helix: 0.76 (0.19), residues: 786 sheet: -1.03 (0.36), residues: 204 loop : -1.41 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 157 HIS 0.003 0.001 HIS A 442 PHE 0.032 0.002 PHE A 32 TYR 0.027 0.002 TYR A 426 ARG 0.006 0.000 ARG A 449 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 172 time to evaluate : 1.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8708 (OUTLIER) cc_final: 0.8449 (t80) REVERT: A 40 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8117 (tt) REVERT: A 326 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.7232 (tm130) REVERT: A 476 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.7673 (ttm) REVERT: A 519 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6654 (mp0) REVERT: A 531 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7390 (ptpp) REVERT: A 554 GLU cc_start: 0.7735 (tp30) cc_final: 0.6902 (mt-10) REVERT: A 663 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8315 (mp) REVERT: A 682 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.8130 (ptp90) REVERT: B 123 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7706 (tp) REVERT: B 125 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.7447 (mmt) REVERT: B 137 TYR cc_start: 0.8899 (m-80) cc_final: 0.8304 (m-80) REVERT: B 308 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8474 (tp) REVERT: B 472 TYR cc_start: 0.7733 (t80) cc_final: 0.6923 (t80) REVERT: B 524 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7600 (mp10) REVERT: B 553 MET cc_start: 0.5788 (OUTLIER) cc_final: 0.5458 (mmm) REVERT: C 478 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.5997 (pp20) REVERT: D 216 MET cc_start: 0.5198 (mmm) cc_final: 0.4764 (ttp) REVERT: D 217 GLN cc_start: 0.4872 (mm-40) cc_final: 0.4529 (mt0) outliers start: 76 outliers final: 46 residues processed: 227 average time/residue: 0.2876 time to fit residues: 93.6631 Evaluate side-chains 225 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 165 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 519 GLU Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 682 ARG Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 524 GLN Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 631 ASP Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 460 HIS Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 518 ARG Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 128 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 140 optimal weight: 0.0870 chunk 92 optimal weight: 2.9990 chunk 165 optimal weight: 20.0000 chunk 103 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 GLN ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14501 Z= 0.187 Angle : 0.488 6.738 19489 Z= 0.260 Chirality : 0.039 0.191 2136 Planarity : 0.004 0.039 2486 Dihedral : 5.726 67.770 1957 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.63 % Favored : 94.31 % Rotamer: Outliers : 4.32 % Allowed : 22.67 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.21), residues: 1723 helix: 0.84 (0.19), residues: 784 sheet: -0.98 (0.36), residues: 204 loop : -1.37 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 157 HIS 0.002 0.000 HIS A 442 PHE 0.028 0.001 PHE A 32 TYR 0.026 0.001 TYR A 426 ARG 0.006 0.000 ARG A 449 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 180 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.8373 (t80) REVERT: A 40 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8086 (tt) REVERT: A 326 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.7257 (tm130) REVERT: A 418 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7020 (mm-30) REVERT: A 476 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7628 (ttm) REVERT: A 531 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7336 (ptpp) REVERT: A 554 GLU cc_start: 0.7667 (tp30) cc_final: 0.6853 (mt-10) REVERT: A 663 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8346 (mp) REVERT: A 682 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.8101 (ptp90) REVERT: B 123 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7751 (tp) REVERT: B 137 TYR cc_start: 0.8865 (m-80) cc_final: 0.8272 (m-80) REVERT: B 389 ASN cc_start: 0.8650 (OUTLIER) cc_final: 0.8222 (m-40) REVERT: B 472 TYR cc_start: 0.7714 (t80) cc_final: 0.6971 (t80) REVERT: B 524 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7586 (mp10) REVERT: B 553 MET cc_start: 0.5760 (OUTLIER) cc_final: 0.5446 (mmm) REVERT: C 417 LEU cc_start: 0.6280 (OUTLIER) cc_final: 0.5724 (tt) REVERT: C 478 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6019 (pp20) REVERT: D 164 MET cc_start: 0.5596 (mmm) cc_final: 0.5256 (mmt) REVERT: D 216 MET cc_start: 0.5211 (mmm) cc_final: 0.4815 (ttp) REVERT: D 217 GLN cc_start: 0.5035 (mm-40) cc_final: 0.4688 (mt0) outliers start: 68 outliers final: 45 residues processed: 230 average time/residue: 0.2848 time to fit residues: 93.5680 Evaluate side-chains 228 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 170 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 682 ARG Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 389 ASN Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 524 GLN Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 631 ASP Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 460 HIS Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 518 ARG Chi-restraints excluded: chain D residue 14 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 112 optimal weight: 0.1980 chunk 81 optimal weight: 0.0980 chunk 15 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 158 optimal weight: 0.0040 chunk 144 optimal weight: 0.7980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14501 Z= 0.159 Angle : 0.488 7.160 19489 Z= 0.258 Chirality : 0.039 0.194 2136 Planarity : 0.004 0.041 2486 Dihedral : 5.560 63.636 1957 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.40 % Favored : 94.54 % Rotamer: Outliers : 3.94 % Allowed : 22.98 % Favored : 73.08 % 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: -0.38 (0.21), residues: 1723 helix: 0.90 (0.19), residues: 788 sheet: -0.87 (0.36), residues: 203 loop : -1.32 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 157 HIS 0.002 0.000 HIS A 625 PHE 0.024 0.001 PHE A 32 TYR 0.023 0.001 TYR A 426 ARG 0.007 0.000 ARG A 449 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 176 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.8260 (t80) REVERT: A 326 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.7236 (tm130) REVERT: A 418 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6999 (mm-30) REVERT: A 476 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7612 (ttm) REVERT: A 531 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7315 (ptpp) REVERT: A 554 GLU cc_start: 0.7638 (tp30) cc_final: 0.6906 (mt-10) REVERT: A 663 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8336 (mp) REVERT: A 682 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.8078 (ptp90) REVERT: B 137 TYR cc_start: 0.8834 (m-80) cc_final: 0.8224 (m-80) REVERT: B 389 ASN cc_start: 0.8627 (OUTLIER) cc_final: 0.8217 (m-40) REVERT: B 405 ARG cc_start: 0.7749 (ttp-170) cc_final: 0.7492 (ttm-80) REVERT: B 472 TYR cc_start: 0.7584 (t80) cc_final: 0.6822 (t80) REVERT: B 553 MET cc_start: 0.5780 (OUTLIER) cc_final: 0.5483 (mmm) REVERT: C 478 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6032 (pp20) REVERT: D 164 MET cc_start: 0.5587 (mmm) cc_final: 0.5201 (mmt) REVERT: D 216 MET cc_start: 0.5266 (mmm) cc_final: 0.4893 (ttp) REVERT: D 217 GLN cc_start: 0.5034 (mm-40) cc_final: 0.4734 (mt0) outliers start: 62 outliers final: 40 residues processed: 223 average time/residue: 0.2984 time to fit residues: 95.2354 Evaluate side-chains 220 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 171 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 682 ARG Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 389 ASN Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 631 ASP Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 460 HIS Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 518 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 20.0000 chunk 158 optimal weight: 0.0000 chunk 92 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 121 optimal weight: 0.0270 chunk 47 optimal weight: 0.7980 chunk 139 optimal weight: 6.9990 chunk 146 optimal weight: 0.6980 chunk 153 optimal weight: 30.0000 chunk 101 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 overall best weight: 0.4442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 GLN ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 14501 Z= 0.167 Angle : 0.491 6.846 19489 Z= 0.260 Chirality : 0.039 0.202 2136 Planarity : 0.004 0.040 2486 Dihedral : 5.507 62.307 1957 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.40 % Favored : 94.54 % Rotamer: Outliers : 3.81 % Allowed : 23.24 % Favored : 72.95 % 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: -0.36 (0.21), residues: 1723 helix: 0.92 (0.19), residues: 790 sheet: -0.79 (0.37), residues: 203 loop : -1.34 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 157 HIS 0.002 0.000 HIS A 442 PHE 0.023 0.001 PHE A 32 TYR 0.023 0.001 TYR A 426 ARG 0.007 0.000 ARG A 449 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 180 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.8303 (t80) REVERT: A 326 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.7253 (tm130) REVERT: A 418 GLU cc_start: 0.7269 (mm-30) cc_final: 0.6986 (mm-30) REVERT: A 476 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7586 (ttm) REVERT: A 531 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7305 (ptpp) REVERT: A 627 GLU cc_start: 0.7566 (tm-30) cc_final: 0.6943 (tt0) REVERT: A 682 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.8041 (ptp90) REVERT: B 85 THR cc_start: 0.8527 (OUTLIER) cc_final: 0.8147 (m) REVERT: B 123 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7903 (tp) REVERT: B 137 TYR cc_start: 0.8829 (m-80) cc_final: 0.8300 (m-80) REVERT: B 389 ASN cc_start: 0.8609 (OUTLIER) cc_final: 0.8193 (m-40) REVERT: B 405 ARG cc_start: 0.7743 (ttp-170) cc_final: 0.7496 (ttm-80) REVERT: B 472 TYR cc_start: 0.7592 (t80) cc_final: 0.6835 (t80) REVERT: B 553 MET cc_start: 0.5876 (OUTLIER) cc_final: 0.5497 (mmm) REVERT: C 478 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.5995 (pp20) REVERT: D 216 MET cc_start: 0.5223 (mmm) cc_final: 0.4862 (ttm) REVERT: D 217 GLN cc_start: 0.4972 (mm-40) cc_final: 0.4742 (mt0) outliers start: 60 outliers final: 39 residues processed: 224 average time/residue: 0.2847 time to fit residues: 91.4957 Evaluate side-chains 223 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 174 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 682 ARG Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 389 ASN Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 631 ASP Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 460 HIS Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain D residue 206 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 171 optimal weight: 8.9990 chunk 157 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 14501 Z= 0.338 Angle : 0.578 7.863 19489 Z= 0.304 Chirality : 0.042 0.197 2136 Planarity : 0.004 0.040 2486 Dihedral : 6.036 70.923 1957 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.92 % Favored : 94.02 % Rotamer: Outliers : 3.49 % Allowed : 23.68 % Favored : 72.83 % 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: -0.63 (0.20), residues: 1723 helix: 0.70 (0.19), residues: 797 sheet: -0.99 (0.36), residues: 208 loop : -1.49 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 157 HIS 0.004 0.001 HIS B 149 PHE 0.040 0.002 PHE A 32 TYR 0.027 0.002 TYR A 426 ARG 0.008 0.000 ARG A 449 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 164 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8173 (tt) REVERT: A 326 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.7204 (tm130) REVERT: A 476 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.7697 (ttm) REVERT: A 531 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7449 (ptpp) REVERT: A 554 GLU cc_start: 0.7934 (tp30) cc_final: 0.6878 (mt-10) REVERT: B 123 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.7813 (tp) REVERT: B 389 ASN cc_start: 0.8703 (OUTLIER) cc_final: 0.8248 (m-40) REVERT: B 524 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7618 (mp10) REVERT: B 553 MET cc_start: 0.5841 (OUTLIER) cc_final: 0.5461 (mmm) REVERT: C 478 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.5943 (pp20) REVERT: D 216 MET cc_start: 0.5229 (mmm) cc_final: 0.4777 (ttp) outliers start: 55 outliers final: 38 residues processed: 206 average time/residue: 0.2837 time to fit residues: 84.0179 Evaluate side-chains 208 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 161 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 682 ARG Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 389 ASN Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 524 GLN Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 631 ASP Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 460 HIS Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 518 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 136 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 140 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.202166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.147794 restraints weight = 15768.956| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.41 r_work: 0.3550 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 14501 Z= 0.235 Angle : 0.532 8.897 19489 Z= 0.280 Chirality : 0.040 0.186 2136 Planarity : 0.004 0.047 2486 Dihedral : 5.836 69.413 1957 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.51 % Favored : 94.43 % Rotamer: Outliers : 3.05 % Allowed : 24.00 % Favored : 72.95 % 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 (0.20), residues: 1723 helix: 0.80 (0.19), residues: 788 sheet: -1.00 (0.36), residues: 208 loop : -1.47 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 157 HIS 0.002 0.001 HIS B 149 PHE 0.035 0.002 PHE A 32 TYR 0.025 0.002 TYR A 426 ARG 0.014 0.000 ARG A 612 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3205.32 seconds wall clock time: 59 minutes 4.97 seconds (3544.97 seconds total)