Starting phenix.real_space_refine on Thu Feb 15 12:27:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kuk_9578/02_2024/6kuk_9578_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kuk_9578/02_2024/6kuk_9578.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kuk_9578/02_2024/6kuk_9578.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kuk_9578/02_2024/6kuk_9578.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kuk_9578/02_2024/6kuk_9578_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kuk_9578/02_2024/6kuk_9578_neut.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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: 5 Type Number sf(0) Gaussians P 23 5.49 5 S 109 5.16 5 C 7695 2.51 5 N 2091 2.21 5 O 2326 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 212": "NH1" <-> "NH2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A ARG 281": "NH1" <-> "NH2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A ARG 361": "NH1" <-> "NH2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "A PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 138": "NH1" <-> "NH2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 428": "NH1" <-> "NH2" Residue "B ARG 435": "NH1" <-> "NH2" Residue "B TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 573": "NH1" <-> "NH2" Residue "B ARG 629": "NH1" <-> "NH2" Residue "B PHE 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 676": "NH1" <-> "NH2" Residue "B ARG 741": "NH1" <-> "NH2" Residue "B ARG 750": "NH1" <-> "NH2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "C ARG 133": "NH1" <-> "NH2" Residue "C ARG 150": "NH1" <-> "NH2" Residue "C ARG 223": "NH1" <-> "NH2" Residue "C ARG 235": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12244 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4176 Classifications: {'peptide': 511} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 489} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5568 Classifications: {'peptide': 701} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 25, 'TRANS': 675} Chain breaks: 4 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2006 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 11, 'TRANS': 237} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "R" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 163 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 5} Chain: "V" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 331 Classifications: {'RNA': 15} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 10, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 11} Time building chain proxies: 7.38, per 1000 atoms: 0.60 Number of scatterers: 12244 At special positions: 0 Unit cell: (111.52, 110.16, 110.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 109 16.00 P 23 15.00 O 2326 8.00 N 2091 7.00 C 7695 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: 5.64 Conformation dependent library (CDL) restraints added in 2.2 seconds 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2766 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 12 sheets defined 47.5% alpha, 7.8% beta 7 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 3.70 Creating SS restraints... Processing helix chain 'A' and resid 191 through 198 removed outlier: 3.774A pdb=" N ALA A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 217 removed outlier: 3.661A pdb=" N THR A 217 " --> pdb=" O THR A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 234 removed outlier: 4.103A pdb=" N SER A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 295 Processing helix chain 'A' and resid 296 through 300 removed outlier: 3.710A pdb=" N PHE A 299 " --> pdb=" O ASN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 328 removed outlier: 3.577A pdb=" N ASP A 328 " --> pdb=" O ARG A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 381 through 390 Processing helix chain 'A' and resid 416 through 432 Processing helix chain 'A' and resid 434 through 457 removed outlier: 3.719A pdb=" N ARG A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE A 457 " --> pdb=" O GLU A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 589 removed outlier: 3.758A pdb=" N MET A 574 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 575 " --> pdb=" O ILE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 637 Processing helix chain 'A' and resid 639 through 661 removed outlier: 3.831A pdb=" N GLU A 643 " --> pdb=" O ASP A 639 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP A 661 " --> pdb=" O GLN A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 678 Processing helix chain 'A' and resid 684 through 703 Processing helix chain 'B' and resid 4 through 11 removed outlier: 3.838A pdb=" N LEU B 7 " --> pdb=" O ASN B 4 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU B 8 " --> pdb=" O PRO B 5 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN B 11 " --> pdb=" O LEU B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 22 removed outlier: 3.843A pdb=" N TYR B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 removed outlier: 3.909A pdb=" N SER B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 99 Processing helix chain 'B' and resid 104 through 118 Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 141 through 157 Processing helix chain 'B' and resid 164 through 178 removed outlier: 3.658A pdb=" N TYR B 168 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TRP B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 250 through 268 Processing helix chain 'B' and resid 281 through 293 removed outlier: 3.944A pdb=" N LYS B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 314 removed outlier: 3.579A pdb=" N GLU B 313 " --> pdb=" O LYS B 310 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N CYS B 314 " --> pdb=" O TRP B 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 310 through 314' Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.822A pdb=" N TYR B 320 " --> pdb=" O GLN B 316 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 Processing helix chain 'B' and resid 341 through 347 Processing helix chain 'B' and resid 378 through 382 removed outlier: 3.605A pdb=" N LEU B 381 " --> pdb=" O ARG B 378 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET B 382 " --> pdb=" O LYS B 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 378 through 382' Processing helix chain 'B' and resid 383 through 391 removed outlier: 3.705A pdb=" N ARG B 387 " --> pdb=" O ASN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 397 Processing helix chain 'B' and resid 416 through 425 removed outlier: 3.539A pdb=" N PHE B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 475 Processing helix chain 'B' and resid 510 through 514 Processing helix chain 'B' and resid 523 through 537 Processing helix chain 'B' and resid 541 through 561 Processing helix chain 'B' and resid 573 through 580 removed outlier: 3.711A pdb=" N ILE B 577 " --> pdb=" O ARG B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 584 Processing helix chain 'B' and resid 586 through 590 removed outlier: 3.717A pdb=" N GLY B 589 " --> pdb=" O ASN B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 595 Processing helix chain 'B' and resid 608 through 614 Processing helix chain 'B' and resid 618 through 626 Processing helix chain 'B' and resid 675 through 696 removed outlier: 3.741A pdb=" N ALA B 679 " --> pdb=" O MET B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 728 removed outlier: 3.574A pdb=" N ASN B 728 " --> pdb=" O THR B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 752 Processing helix chain 'C' and resid 3 through 15 removed outlier: 3.577A pdb=" N THR C 15 " --> pdb=" O TYR C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 37 removed outlier: 4.001A pdb=" N THR C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS C 37 " --> pdb=" O THR C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 56 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 99 through 109 Processing helix chain 'C' and resid 114 through 122 removed outlier: 3.720A pdb=" N TYR C 122 " --> pdb=" O ILE C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 134 removed outlier: 3.726A pdb=" N GLU C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 172 removed outlier: 3.690A pdb=" N GLU C 168 " --> pdb=" O LYS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 179 removed outlier: 4.391A pdb=" N GLU C 178 " --> pdb=" O PHE C 175 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA C 179 " --> pdb=" O GLU C 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 175 through 179' Processing helix chain 'C' and resid 186 through 197 Processing helix chain 'C' and resid 206 through 215 removed outlier: 4.078A pdb=" N ALA C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 236 Processing helix chain 'C' and resid 238 through 243 removed outlier: 4.085A pdb=" N GLY C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 240 through 241 Processing sheet with id=AA2, first strand: chain 'A' and resid 275 through 276 removed outlier: 3.690A pdb=" N LYS A 275 " --> pdb=" O ASP A 478 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP A 478 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 350 through 353 removed outlier: 5.656A pdb=" N LYS A 350 " --> pdb=" O GLU B 367 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL B 369 " --> pdb=" O LYS A 350 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE A 352 " --> pdb=" O VAL B 369 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 463 through 466 removed outlier: 6.533A pdb=" N LYS A 544 " --> pdb=" O THR A 525 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N THR A 525 " --> pdb=" O LYS A 544 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU A 546 " --> pdb=" O ALA A 523 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 602 through 604 Processing sheet with id=AA6, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AA7, first strand: chain 'B' and resid 131 through 133 Processing sheet with id=AA8, first strand: chain 'B' and resid 181 through 185 Processing sheet with id=AA9, first strand: chain 'B' and resid 242 through 245 removed outlier: 7.680A pdb=" N ILE B 226 " --> pdb=" O LYS B 352 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 491 through 492 Processing sheet with id=AB2, first strand: chain 'B' and resid 663 through 664 removed outlier: 4.706A pdb=" N ARG B 663 " --> pdb=" O MET C 62 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 149 through 153 506 hydrogen bonds defined for protein. 1410 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 19 hydrogen bonds 38 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 4.11 Time building geometry restraints manager: 6.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3496 1.33 - 1.46: 2456 1.46 - 1.58: 6357 1.58 - 1.70: 44 1.70 - 1.82: 181 Bond restraints: 12534 Sorted by residual: bond pdb=" CA ILE B 730 " pdb=" C ILE B 730 " ideal model delta sigma weight residual 1.523 1.461 0.062 1.27e-02 6.20e+03 2.41e+01 bond pdb=" N ILE B 731 " pdb=" CA ILE B 731 " ideal model delta sigma weight residual 1.459 1.423 0.036 1.25e-02 6.40e+03 8.35e+00 bond pdb=" N ILE B 730 " pdb=" CA ILE B 730 " ideal model delta sigma weight residual 1.459 1.430 0.029 1.25e-02 6.40e+03 5.24e+00 bond pdb=" C LEU B 510 " pdb=" N PRO B 511 " ideal model delta sigma weight residual 1.337 1.357 -0.021 1.11e-02 8.12e+03 3.55e+00 bond pdb=" CG1 ILE A 447 " pdb=" CD1 ILE A 447 " ideal model delta sigma weight residual 1.513 1.443 0.070 3.90e-02 6.57e+02 3.24e+00 ... (remaining 12529 not shown) Histogram of bond angle deviations from ideal: 97.89 - 105.12: 354 105.12 - 112.36: 6092 112.36 - 119.60: 4621 119.60 - 126.83: 5677 126.83 - 134.07: 204 Bond angle restraints: 16948 Sorted by residual: angle pdb=" N ILE B 393 " pdb=" CA ILE B 393 " pdb=" C ILE B 393 " ideal model delta sigma weight residual 113.20 105.82 7.38 9.60e-01 1.09e+00 5.90e+01 angle pdb=" CA LYS A 488 " pdb=" CB LYS A 488 " pdb=" CG LYS A 488 " ideal model delta sigma weight residual 114.10 122.85 -8.75 2.00e+00 2.50e-01 1.92e+01 angle pdb=" N GLY B 441 " pdb=" CA GLY B 441 " pdb=" C GLY B 441 " ideal model delta sigma weight residual 110.58 116.42 -5.84 1.35e+00 5.49e-01 1.87e+01 angle pdb=" O ILE B 730 " pdb=" C ILE B 730 " pdb=" N ILE B 731 " ideal model delta sigma weight residual 122.57 127.75 -5.18 1.25e+00 6.40e-01 1.72e+01 angle pdb=" C THR B 515 " pdb=" CA THR B 515 " pdb=" CB THR B 515 " ideal model delta sigma weight residual 110.44 104.10 6.34 1.68e+00 3.54e-01 1.42e+01 ... (remaining 16943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.63: 7170 15.63 - 31.26: 391 31.26 - 46.89: 102 46.89 - 62.51: 27 62.51 - 78.14: 25 Dihedral angle restraints: 7715 sinusoidal: 3455 harmonic: 4260 Sorted by residual: dihedral pdb=" CA ILE C 186 " pdb=" C ILE C 186 " pdb=" N GLN C 187 " pdb=" CA GLN C 187 " ideal model delta harmonic sigma weight residual 180.00 -151.88 -28.12 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA ASN B 728 " pdb=" C ASN B 728 " pdb=" N GLY B 729 " pdb=" CA GLY B 729 " ideal model delta harmonic sigma weight residual -180.00 -154.49 -25.51 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA ILE A 604 " pdb=" C ILE A 604 " pdb=" N ALA A 605 " pdb=" CA ALA A 605 " ideal model delta harmonic sigma weight residual 180.00 155.00 25.00 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 7712 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1476 0.072 - 0.143: 347 0.143 - 0.214: 28 0.214 - 0.286: 3 0.286 - 0.357: 1 Chirality restraints: 1855 Sorted by residual: chirality pdb=" CB ILE B 304 " pdb=" CA ILE B 304 " pdb=" CG1 ILE B 304 " pdb=" CG2 ILE B 304 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CB ILE B 72 " pdb=" CA ILE B 72 " pdb=" CG1 ILE B 72 " pdb=" CG2 ILE B 72 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB ILE C 249 " pdb=" CA ILE C 249 " pdb=" CG1 ILE C 249 " pdb=" CG2 ILE C 249 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 1852 not shown) Planarity restraints: 2068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 386 " -0.020 2.00e-02 2.50e+03 1.70e-02 7.19e+00 pdb=" CG TRP A 386 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP A 386 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP A 386 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 386 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 386 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A 386 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 386 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 386 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 386 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN C 155 " -0.040 5.00e-02 4.00e+02 6.11e-02 5.98e+00 pdb=" N PRO C 156 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO C 156 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 156 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 731 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.08e+00 pdb=" C ILE B 731 " -0.039 2.00e-02 2.50e+03 pdb=" O ILE B 731 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY B 732 " 0.013 2.00e-02 2.50e+03 ... (remaining 2065 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1419 2.74 - 3.28: 11176 3.28 - 3.82: 18742 3.82 - 4.36: 22829 4.36 - 4.90: 38857 Nonbonded interactions: 93023 Sorted by model distance: nonbonded pdb=" OE2 GLU A 408 " pdb=" NH2 ARG B 557 " model vdw 2.201 2.520 nonbonded pdb=" OH TYR B 49 " pdb=" NZ LYS B 310 " model vdw 2.221 2.520 nonbonded pdb=" OD2 ASP B 615 " pdb=" NZ LYS C 129 " model vdw 2.235 2.520 nonbonded pdb=" O ALA B 152 " pdb=" OG1 THR B 156 " model vdw 2.269 2.440 nonbonded pdb=" OE1 GLN A 649 " pdb=" OH TYR B 6 " model vdw 2.269 2.440 ... (remaining 93018 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.970 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 38.810 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 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 : 0.008 0.074 12534 Z= 0.503 Angle : 1.025 10.708 16948 Z= 0.565 Chirality : 0.059 0.357 1855 Planarity : 0.007 0.061 2068 Dihedral : 11.980 78.142 4949 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.61 % Favored : 91.19 % Rotamer: Outliers : 0.47 % Allowed : 3.04 % Favored : 96.49 % 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: -4.88 (0.16), residues: 1441 helix: -3.38 (0.12), residues: 646 sheet: -2.14 (0.46), residues: 126 loop : -3.25 (0.19), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP A 386 HIS 0.012 0.003 HIS A 451 PHE 0.033 0.004 PHE B 122 TYR 0.033 0.003 TYR B 38 ARG 0.009 0.001 ARG B 573 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 450 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 LYS cc_start: 0.8426 (tmmt) cc_final: 0.7937 (tmmt) REVERT: A 277 HIS cc_start: 0.6382 (t70) cc_final: 0.6097 (t-90) REVERT: A 278 ASP cc_start: 0.7021 (t0) cc_final: 0.6750 (t0) REVERT: A 290 ASP cc_start: 0.7697 (m-30) cc_final: 0.7345 (m-30) REVERT: A 364 GLU cc_start: 0.7887 (mp0) cc_final: 0.7495 (mp0) REVERT: A 367 GLN cc_start: 0.6979 (pt0) cc_final: 0.6774 (mt0) REVERT: A 495 ASP cc_start: 0.7719 (m-30) cc_final: 0.7335 (p0) REVERT: A 650 LYS cc_start: 0.7918 (mtmm) cc_final: 0.7697 (pttp) REVERT: B 47 TYR cc_start: 0.8098 (m-10) cc_final: 0.7856 (m-10) REVERT: B 140 MET cc_start: 0.7415 (mtt) cc_final: 0.7012 (mtt) REVERT: B 147 GLN cc_start: 0.8495 (tp-100) cc_final: 0.7534 (tm-30) REVERT: B 182 LYS cc_start: 0.7447 (mtmt) cc_final: 0.6930 (mtmm) REVERT: B 410 MET cc_start: 0.5452 (mtp) cc_final: 0.5174 (mtp) REVERT: B 490 LEU cc_start: 0.8707 (tp) cc_final: 0.8451 (tp) REVERT: B 515 THR cc_start: 0.6793 (p) cc_final: 0.6548 (t) REVERT: B 560 TYR cc_start: 0.7239 (m-80) cc_final: 0.6870 (m-80) REVERT: B 578 ARG cc_start: 0.5434 (OUTLIER) cc_final: 0.5185 (mtp180) REVERT: B 685 TYR cc_start: 0.7535 (m-10) cc_final: 0.6901 (m-80) REVERT: C 18 LYS cc_start: 0.7199 (mttt) cc_final: 0.6863 (tppt) REVERT: C 65 ARG cc_start: 0.7065 (ttt90) cc_final: 0.6785 (ttm-80) REVERT: C 80 ILE cc_start: 0.5637 (mt) cc_final: 0.4733 (mt) REVERT: C 213 MET cc_start: 0.5011 (ptm) cc_final: 0.4581 (ptm) outliers start: 6 outliers final: 1 residues processed: 454 average time/residue: 0.2956 time to fit residues: 181.2726 Evaluate side-chains 293 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 291 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 578 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 6.9990 chunk 110 optimal weight: 0.0970 chunk 61 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 85 optimal weight: 0.0010 chunk 132 optimal weight: 0.9980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 HIS ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 GLN A 640 ASN A 647 ASN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B 154 GLN B 303 ASN B 477 ASN C 148 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12534 Z= 0.181 Angle : 0.648 17.064 16948 Z= 0.330 Chirality : 0.042 0.176 1855 Planarity : 0.005 0.056 2068 Dihedral : 11.717 75.747 1930 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.18 % Favored : 93.75 % Rotamer: Outliers : 3.20 % Allowed : 10.29 % Favored : 86.52 % 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: -3.00 (0.19), residues: 1441 helix: -1.19 (0.18), residues: 658 sheet: -1.46 (0.49), residues: 117 loop : -2.95 (0.20), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 386 HIS 0.003 0.001 HIS A 490 PHE 0.029 0.001 PHE B 108 TYR 0.014 0.001 TYR B 692 ARG 0.007 0.001 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 341 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8052 (pt) REVERT: A 231 ASP cc_start: 0.9207 (t70) cc_final: 0.8789 (t70) REVERT: A 277 HIS cc_start: 0.6381 (t70) cc_final: 0.6135 (t-90) REVERT: A 290 ASP cc_start: 0.7738 (m-30) cc_final: 0.7318 (m-30) REVERT: A 318 LEU cc_start: 0.8610 (tp) cc_final: 0.8370 (tp) REVERT: A 367 GLN cc_start: 0.7002 (pt0) cc_final: 0.6605 (mt0) REVERT: A 416 MET cc_start: 0.8421 (ppp) cc_final: 0.7758 (ppp) REVERT: A 442 LYS cc_start: 0.9104 (tttt) cc_final: 0.8714 (tttm) REVERT: A 650 LYS cc_start: 0.7862 (mtmm) cc_final: 0.7630 (ptpp) REVERT: A 653 LEU cc_start: 0.8728 (mm) cc_final: 0.8467 (mt) REVERT: B 98 GLU cc_start: 0.7012 (tp30) cc_final: 0.6671 (tp30) REVERT: B 147 GLN cc_start: 0.8544 (tp40) cc_final: 0.7379 (tm-30) REVERT: B 182 LYS cc_start: 0.7276 (mtmt) cc_final: 0.6915 (mtmm) REVERT: B 262 GLN cc_start: 0.8349 (tt0) cc_final: 0.7894 (tm-30) REVERT: B 515 THR cc_start: 0.6681 (p) cc_final: 0.6457 (t) REVERT: B 560 TYR cc_start: 0.7250 (m-80) cc_final: 0.6860 (m-80) REVERT: B 587 LYS cc_start: 0.7470 (mttt) cc_final: 0.7152 (mttt) REVERT: C 18 LYS cc_start: 0.7114 (mttt) cc_final: 0.6786 (tppt) REVERT: C 51 MET cc_start: 0.7240 (tpp) cc_final: 0.6380 (tpp) REVERT: C 65 ARG cc_start: 0.7211 (ttt90) cc_final: 0.7005 (ttm-80) REVERT: C 213 MET cc_start: 0.4971 (ptm) cc_final: 0.4549 (ptm) outliers start: 41 outliers final: 24 residues processed: 363 average time/residue: 0.2716 time to fit residues: 136.2429 Evaluate side-chains 303 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 278 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 692 ASP Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 743 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 249 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 110 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN B 312 ASN B 477 ASN C 141 ASN C 217 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12534 Z= 0.184 Angle : 0.615 16.233 16948 Z= 0.308 Chirality : 0.041 0.153 1855 Planarity : 0.004 0.047 2068 Dihedral : 11.433 74.201 1926 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.87 % Favored : 93.06 % Rotamer: Outliers : 3.20 % Allowed : 13.87 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.21), residues: 1441 helix: -0.34 (0.19), residues: 669 sheet: -0.99 (0.50), residues: 122 loop : -2.72 (0.21), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 386 HIS 0.004 0.001 HIS A 451 PHE 0.021 0.001 PHE B 108 TYR 0.010 0.001 TYR B 560 ARG 0.006 0.001 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 308 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.9153 (t70) cc_final: 0.8604 (t70) REVERT: A 235 ARG cc_start: 0.8734 (tpp-160) cc_final: 0.8406 (tpp-160) REVERT: A 290 ASP cc_start: 0.7744 (m-30) cc_final: 0.7362 (m-30) REVERT: A 328 ASP cc_start: 0.7869 (t0) cc_final: 0.7584 (t0) REVERT: A 367 GLN cc_start: 0.6877 (pt0) cc_final: 0.6524 (mt0) REVERT: A 416 MET cc_start: 0.8325 (ppp) cc_final: 0.7953 (ppp) REVERT: A 442 LYS cc_start: 0.9127 (tttt) cc_final: 0.8881 (tttm) REVERT: A 555 MET cc_start: 0.8135 (mmt) cc_final: 0.7869 (mtp) REVERT: A 650 LYS cc_start: 0.7693 (mtmm) cc_final: 0.7437 (pttp) REVERT: A 653 LEU cc_start: 0.8675 (mm) cc_final: 0.8407 (mp) REVERT: B 95 GLU cc_start: 0.7080 (mt-10) cc_final: 0.6350 (mm-30) REVERT: B 147 GLN cc_start: 0.8705 (tp40) cc_final: 0.7554 (tm-30) REVERT: B 182 LYS cc_start: 0.7078 (mtmt) cc_final: 0.6476 (mtmm) REVERT: B 262 GLN cc_start: 0.8412 (tt0) cc_final: 0.8149 (tt0) REVERT: B 313 GLU cc_start: 0.8322 (mm-30) cc_final: 0.8070 (mm-30) REVERT: B 320 TYR cc_start: 0.7811 (m-80) cc_final: 0.7426 (m-80) REVERT: B 461 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7138 (tt0) REVERT: B 490 LEU cc_start: 0.8357 (tp) cc_final: 0.8089 (tp) REVERT: B 515 THR cc_start: 0.6628 (p) cc_final: 0.6364 (t) REVERT: B 560 TYR cc_start: 0.7269 (m-80) cc_final: 0.6835 (m-80) REVERT: B 587 LYS cc_start: 0.7596 (mttt) cc_final: 0.7300 (mttt) REVERT: C 18 LYS cc_start: 0.7132 (mttt) cc_final: 0.6781 (tppt) REVERT: C 51 MET cc_start: 0.7265 (tpp) cc_final: 0.6302 (tpp) REVERT: C 55 MET cc_start: 0.4342 (mmp) cc_final: 0.3817 (mmm) REVERT: C 171 MET cc_start: 0.8148 (mmm) cc_final: 0.7233 (mtm) REVERT: C 213 MET cc_start: 0.5072 (ptm) cc_final: 0.4560 (ptm) REVERT: C 247 TRP cc_start: 0.8424 (p-90) cc_final: 0.8200 (p-90) outliers start: 41 outliers final: 28 residues processed: 328 average time/residue: 0.2741 time to fit residues: 127.3389 Evaluate side-chains 296 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 268 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 401 CYS Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 249 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 2.9990 chunk 99 optimal weight: 0.0010 chunk 68 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 63 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 126 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12534 Z= 0.176 Angle : 0.598 16.843 16948 Z= 0.298 Chirality : 0.041 0.167 1855 Planarity : 0.004 0.047 2068 Dihedral : 11.322 73.733 1926 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.66 % Favored : 93.27 % Rotamer: Outliers : 3.59 % Allowed : 14.34 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.21), residues: 1441 helix: 0.05 (0.20), residues: 675 sheet: -0.95 (0.50), residues: 124 loop : -2.59 (0.22), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 386 HIS 0.004 0.001 HIS A 451 PHE 0.036 0.001 PHE B 108 TYR 0.011 0.001 TYR B 560 ARG 0.007 0.000 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 276 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.9030 (t70) cc_final: 0.8694 (t70) REVERT: A 290 ASP cc_start: 0.7845 (m-30) cc_final: 0.7443 (m-30) REVERT: A 367 GLN cc_start: 0.6836 (pt0) cc_final: 0.6505 (mt0) REVERT: A 416 MET cc_start: 0.8234 (ppp) cc_final: 0.7850 (ppp) REVERT: A 555 MET cc_start: 0.8133 (mmt) cc_final: 0.7901 (mtp) REVERT: A 656 LEU cc_start: 0.8825 (tt) cc_final: 0.8270 (tp) REVERT: B 1 MET cc_start: 0.8109 (tmm) cc_final: 0.7872 (tmm) REVERT: B 14 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8262 (tp) REVERT: B 95 GLU cc_start: 0.7297 (mt-10) cc_final: 0.6733 (mm-30) REVERT: B 182 LYS cc_start: 0.6909 (mtmt) cc_final: 0.6650 (mttp) REVERT: B 313 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8033 (mm-30) REVERT: B 320 TYR cc_start: 0.7835 (m-80) cc_final: 0.7456 (m-80) REVERT: B 461 GLU cc_start: 0.7346 (mt-10) cc_final: 0.7136 (tt0) REVERT: B 515 THR cc_start: 0.6609 (p) cc_final: 0.6367 (t) REVERT: B 560 TYR cc_start: 0.7210 (m-80) cc_final: 0.6831 (m-80) REVERT: B 587 LYS cc_start: 0.7668 (mttt) cc_final: 0.7419 (mttt) REVERT: C 18 LYS cc_start: 0.7114 (mttt) cc_final: 0.6773 (tppt) REVERT: C 51 MET cc_start: 0.7329 (tpp) cc_final: 0.6474 (tpp) REVERT: C 55 MET cc_start: 0.4359 (mmp) cc_final: 0.3922 (mmm) REVERT: C 171 MET cc_start: 0.8112 (mmm) cc_final: 0.7276 (mtm) REVERT: C 213 MET cc_start: 0.5067 (ptm) cc_final: 0.4576 (ptm) REVERT: C 247 TRP cc_start: 0.8450 (p-90) cc_final: 0.8159 (p-90) outliers start: 46 outliers final: 35 residues processed: 305 average time/residue: 0.2491 time to fit residues: 107.8565 Evaluate side-chains 296 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 260 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 401 CYS Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 743 ILE Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 249 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 0.0870 chunk 126 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN B 672 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12534 Z= 0.267 Angle : 0.655 16.952 16948 Z= 0.328 Chirality : 0.043 0.153 1855 Planarity : 0.004 0.046 2068 Dihedral : 11.358 73.549 1926 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.26 % Favored : 91.67 % Rotamer: Outliers : 4.44 % Allowed : 16.45 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.21), residues: 1441 helix: 0.10 (0.20), residues: 672 sheet: -1.19 (0.51), residues: 119 loop : -2.59 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 386 HIS 0.006 0.001 HIS A 451 PHE 0.031 0.002 PHE B 108 TYR 0.013 0.001 TYR B 22 ARG 0.004 0.001 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 269 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.9017 (t70) cc_final: 0.8411 (t70) REVERT: A 328 ASP cc_start: 0.7990 (t0) cc_final: 0.7632 (t70) REVERT: A 367 GLN cc_start: 0.6892 (pt0) cc_final: 0.6594 (mt0) REVERT: A 650 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7840 (ptpp) REVERT: A 709 PHE cc_start: 0.7104 (OUTLIER) cc_final: 0.6838 (m-10) REVERT: B 1 MET cc_start: 0.8164 (tmm) cc_final: 0.7884 (tmm) REVERT: B 95 GLU cc_start: 0.7449 (mt-10) cc_final: 0.6933 (mm-30) REVERT: B 147 GLN cc_start: 0.8747 (tp40) cc_final: 0.8228 (tp40) REVERT: B 151 ASP cc_start: 0.7475 (m-30) cc_final: 0.7101 (m-30) REVERT: B 222 ARG cc_start: 0.7834 (ttm170) cc_final: 0.7473 (mmm-85) REVERT: B 320 TYR cc_start: 0.7872 (m-10) cc_final: 0.7336 (m-80) REVERT: B 515 THR cc_start: 0.6908 (p) cc_final: 0.6637 (t) REVERT: B 560 TYR cc_start: 0.7145 (m-80) cc_final: 0.6730 (m-80) REVERT: B 587 LYS cc_start: 0.7735 (mttt) cc_final: 0.7455 (mttt) REVERT: C 18 LYS cc_start: 0.7605 (mttt) cc_final: 0.7185 (tppt) REVERT: C 51 MET cc_start: 0.7529 (tpp) cc_final: 0.6634 (tpp) REVERT: C 55 MET cc_start: 0.4776 (mmp) cc_final: 0.4356 (mmm) REVERT: C 213 MET cc_start: 0.5074 (ptm) cc_final: 0.4624 (ptm) REVERT: C 232 ARG cc_start: 0.7933 (mtm-85) cc_final: 0.7691 (mtm-85) outliers start: 57 outliers final: 42 residues processed: 303 average time/residue: 0.2393 time to fit residues: 103.8351 Evaluate side-chains 294 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 250 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 650 LYS Chi-restraints excluded: chain A residue 709 PHE Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 401 CYS Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 505 ASN Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 743 ILE Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 249 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 0.6980 chunk 127 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 82 optimal weight: 0.1980 chunk 34 optimal weight: 0.0010 chunk 141 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 GLN C 217 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12534 Z= 0.163 Angle : 0.598 17.437 16948 Z= 0.294 Chirality : 0.041 0.153 1855 Planarity : 0.004 0.046 2068 Dihedral : 11.206 73.661 1926 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.04 % Favored : 93.89 % Rotamer: Outliers : 3.20 % Allowed : 17.69 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.22), residues: 1441 helix: 0.37 (0.20), residues: 678 sheet: -0.95 (0.52), residues: 117 loop : -2.45 (0.22), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 247 HIS 0.003 0.001 HIS A 490 PHE 0.022 0.001 PHE A 292 TYR 0.011 0.001 TYR B 560 ARG 0.004 0.000 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 270 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8869 (t70) cc_final: 0.8511 (t70) REVERT: A 367 GLN cc_start: 0.7016 (pt0) cc_final: 0.6643 (mt0) REVERT: A 555 MET cc_start: 0.8108 (mmt) cc_final: 0.7783 (mtp) REVERT: A 601 ARG cc_start: 0.8519 (mmt180) cc_final: 0.8145 (mmm160) REVERT: B 1 MET cc_start: 0.8101 (tmm) cc_final: 0.7852 (tmm) REVERT: B 14 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8329 (tp) REVERT: B 47 TYR cc_start: 0.7959 (m-10) cc_final: 0.7417 (m-10) REVERT: B 95 GLU cc_start: 0.7307 (mt-10) cc_final: 0.6734 (mm-30) REVERT: B 151 ASP cc_start: 0.7300 (m-30) cc_final: 0.6963 (m-30) REVERT: B 165 MET cc_start: 0.7698 (mmm) cc_final: 0.7266 (mmm) REVERT: B 320 TYR cc_start: 0.7898 (m-10) cc_final: 0.7418 (m-80) REVERT: B 334 LEU cc_start: 0.8945 (tp) cc_final: 0.8659 (tp) REVERT: B 382 MET cc_start: 0.7516 (mtp) cc_final: 0.7212 (ttm) REVERT: B 461 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6994 (tp30) REVERT: B 515 THR cc_start: 0.6709 (p) cc_final: 0.6500 (t) REVERT: B 560 TYR cc_start: 0.7197 (m-80) cc_final: 0.6845 (m-80) REVERT: B 587 LYS cc_start: 0.7702 (mttt) cc_final: 0.7447 (mttt) REVERT: C 18 LYS cc_start: 0.7550 (mttt) cc_final: 0.7140 (tppt) REVERT: C 51 MET cc_start: 0.7605 (tpp) cc_final: 0.6948 (tpp) REVERT: C 55 MET cc_start: 0.4531 (mmp) cc_final: 0.4237 (mmm) REVERT: C 171 MET cc_start: 0.8347 (mmm) cc_final: 0.7561 (mtm) REVERT: C 213 MET cc_start: 0.5084 (ptm) cc_final: 0.4631 (ptm) outliers start: 41 outliers final: 31 residues processed: 296 average time/residue: 0.2586 time to fit residues: 108.1094 Evaluate side-chains 291 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 259 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 505 ASN Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 743 ILE Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 249 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 140 optimal weight: 0.4980 chunk 88 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 64 optimal weight: 0.1980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 HIS ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12534 Z= 0.172 Angle : 0.611 17.600 16948 Z= 0.301 Chirality : 0.041 0.158 1855 Planarity : 0.003 0.046 2068 Dihedral : 11.209 73.628 1926 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.01 % Favored : 92.92 % Rotamer: Outliers : 3.35 % Allowed : 18.47 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.22), residues: 1441 helix: 0.47 (0.20), residues: 678 sheet: -0.46 (0.54), residues: 107 loop : -2.42 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP A 388 HIS 0.003 0.001 HIS A 451 PHE 0.020 0.001 PHE C 212 TYR 0.015 0.001 TYR B 38 ARG 0.011 0.000 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 264 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8847 (t70) cc_final: 0.8373 (t70) REVERT: A 292 PHE cc_start: 0.7244 (t80) cc_final: 0.6447 (t80) REVERT: A 328 ASP cc_start: 0.8016 (t0) cc_final: 0.7631 (t0) REVERT: A 367 GLN cc_start: 0.7127 (pt0) cc_final: 0.6647 (mt0) REVERT: A 601 ARG cc_start: 0.8521 (mmt180) cc_final: 0.7963 (mtp85) REVERT: B 1 MET cc_start: 0.8091 (tmm) cc_final: 0.7855 (tmm) REVERT: B 47 TYR cc_start: 0.7870 (m-10) cc_final: 0.7360 (m-10) REVERT: B 95 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6700 (mm-30) REVERT: B 165 MET cc_start: 0.7814 (mmm) cc_final: 0.7409 (mmm) REVERT: B 301 MET cc_start: 0.8721 (tmm) cc_final: 0.8478 (tmm) REVERT: B 320 TYR cc_start: 0.7936 (m-10) cc_final: 0.6820 (m-80) REVERT: B 334 LEU cc_start: 0.8952 (tp) cc_final: 0.8673 (tp) REVERT: B 382 MET cc_start: 0.7716 (mtp) cc_final: 0.7406 (ttm) REVERT: B 461 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6986 (tp30) REVERT: B 560 TYR cc_start: 0.7038 (m-80) cc_final: 0.6762 (m-80) REVERT: B 587 LYS cc_start: 0.7638 (mttt) cc_final: 0.7425 (mttt) REVERT: C 18 LYS cc_start: 0.7542 (mttt) cc_final: 0.7145 (tppt) REVERT: C 51 MET cc_start: 0.7616 (tpp) cc_final: 0.7073 (tpp) REVERT: C 131 ARG cc_start: 0.8172 (mtm110) cc_final: 0.7643 (mtm-85) REVERT: C 171 MET cc_start: 0.8309 (mmm) cc_final: 0.7552 (mtm) REVERT: C 213 MET cc_start: 0.5113 (ptm) cc_final: 0.4664 (ptm) outliers start: 43 outliers final: 35 residues processed: 291 average time/residue: 0.2389 time to fit residues: 99.0774 Evaluate side-chains 284 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 248 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 505 ASN Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 743 ILE Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 249 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 89 optimal weight: 0.1980 chunk 95 optimal weight: 0.7980 chunk 69 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 110 optimal weight: 0.0060 chunk 128 optimal weight: 9.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN B 672 ASN C 217 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12534 Z= 0.165 Angle : 0.609 17.821 16948 Z= 0.300 Chirality : 0.041 0.154 1855 Planarity : 0.003 0.045 2068 Dihedral : 11.168 73.663 1926 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.04 % Favored : 93.89 % Rotamer: Outliers : 3.35 % Allowed : 18.94 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.22), residues: 1441 helix: 0.54 (0.20), residues: 686 sheet: -0.43 (0.54), residues: 107 loop : -2.44 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.002 TRP A 388 HIS 0.003 0.001 HIS A 451 PHE 0.018 0.001 PHE B 108 TYR 0.019 0.001 TYR C 11 ARG 0.009 0.000 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 263 time to evaluate : 1.333 Fit side-chains revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8827 (t70) cc_final: 0.8462 (t70) REVERT: A 328 ASP cc_start: 0.8003 (t0) cc_final: 0.7611 (t0) REVERT: A 367 GLN cc_start: 0.7107 (pt0) cc_final: 0.6636 (mt0) REVERT: A 601 ARG cc_start: 0.8504 (mmt180) cc_final: 0.7976 (mtp85) REVERT: B 1 MET cc_start: 0.8157 (tmm) cc_final: 0.7914 (tmm) REVERT: B 47 TYR cc_start: 0.7850 (m-10) cc_final: 0.7364 (m-10) REVERT: B 95 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6588 (mm-30) REVERT: B 165 MET cc_start: 0.7813 (mmm) cc_final: 0.7369 (mmm) REVERT: B 301 MET cc_start: 0.8724 (tmm) cc_final: 0.8468 (tmm) REVERT: B 320 TYR cc_start: 0.7909 (m-10) cc_final: 0.6955 (m-80) REVERT: B 334 LEU cc_start: 0.8936 (tp) cc_final: 0.8671 (tp) REVERT: B 461 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6831 (tp30) REVERT: B 560 TYR cc_start: 0.7075 (m-80) cc_final: 0.6812 (m-80) REVERT: B 587 LYS cc_start: 0.7613 (mttt) cc_final: 0.7300 (mttt) REVERT: B 751 LEU cc_start: 0.8681 (tp) cc_final: 0.8199 (pp) REVERT: C 18 LYS cc_start: 0.7545 (mttt) cc_final: 0.7127 (tppt) REVERT: C 51 MET cc_start: 0.7619 (tpp) cc_final: 0.6930 (tpp) REVERT: C 55 MET cc_start: 0.4391 (mmp) cc_final: 0.3755 (mmm) REVERT: C 131 ARG cc_start: 0.8231 (mtm110) cc_final: 0.7714 (mtm-85) REVERT: C 171 MET cc_start: 0.8167 (mmm) cc_final: 0.7433 (mtm) REVERT: C 213 MET cc_start: 0.5096 (ptm) cc_final: 0.4657 (ptm) outliers start: 43 outliers final: 31 residues processed: 294 average time/residue: 0.2474 time to fit residues: 103.5771 Evaluate side-chains 289 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 257 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 505 ASN Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 249 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12534 Z= 0.314 Angle : 0.716 17.255 16948 Z= 0.356 Chirality : 0.045 0.160 1855 Planarity : 0.004 0.059 2068 Dihedral : 11.327 73.479 1926 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.16 % Favored : 90.77 % Rotamer: Outliers : 3.66 % Allowed : 18.55 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.22), residues: 1441 helix: 0.45 (0.20), residues: 666 sheet: -1.01 (0.51), residues: 115 loop : -2.44 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.003 TRP A 388 HIS 0.005 0.001 HIS A 451 PHE 0.023 0.002 PHE B 122 TYR 0.019 0.002 TYR C 11 ARG 0.007 0.001 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 252 time to evaluate : 1.399 Fit side-chains revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8856 (t70) cc_final: 0.8360 (t70) REVERT: A 367 GLN cc_start: 0.6753 (pt0) cc_final: 0.6426 (mt0) REVERT: A 416 MET cc_start: 0.8215 (ppp) cc_final: 0.7924 (ppp) REVERT: A 497 MET cc_start: 0.7382 (mmm) cc_final: 0.7075 (mmt) REVERT: A 601 ARG cc_start: 0.8514 (mmt180) cc_final: 0.7895 (mmm160) REVERT: B 1 MET cc_start: 0.8081 (tmm) cc_final: 0.7724 (tmm) REVERT: B 95 GLU cc_start: 0.7445 (mt-10) cc_final: 0.6886 (mm-30) REVERT: B 151 ASP cc_start: 0.7367 (m-30) cc_final: 0.6983 (m-30) REVERT: B 320 TYR cc_start: 0.8000 (m-10) cc_final: 0.7266 (m-80) REVERT: B 374 LYS cc_start: 0.7705 (mmtt) cc_final: 0.7297 (mmtp) REVERT: B 408 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.7341 (ttm) REVERT: B 560 TYR cc_start: 0.7265 (m-80) cc_final: 0.6983 (m-80) REVERT: C 18 LYS cc_start: 0.7718 (mttt) cc_final: 0.7138 (tppt) REVERT: C 38 TRP cc_start: 0.7220 (OUTLIER) cc_final: 0.6395 (m100) REVERT: C 51 MET cc_start: 0.7681 (tpp) cc_final: 0.6973 (tpp) REVERT: C 131 ARG cc_start: 0.8374 (mtm110) cc_final: 0.7955 (mtm-85) REVERT: C 155 GLN cc_start: 0.6838 (OUTLIER) cc_final: 0.6517 (tp-100) REVERT: C 171 MET cc_start: 0.8284 (mmm) cc_final: 0.7579 (mtm) REVERT: C 213 MET cc_start: 0.5280 (ptm) cc_final: 0.4833 (ptm) outliers start: 47 outliers final: 37 residues processed: 282 average time/residue: 0.2440 time to fit residues: 99.3110 Evaluate side-chains 281 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 241 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 401 CYS Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 505 ASN Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 38 TRP Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 249 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 96 optimal weight: 0.4980 chunk 145 optimal weight: 5.9990 chunk 133 optimal weight: 0.6980 chunk 115 optimal weight: 0.0370 chunk 12 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12534 Z= 0.170 Angle : 0.640 18.056 16948 Z= 0.314 Chirality : 0.041 0.164 1855 Planarity : 0.004 0.061 2068 Dihedral : 11.195 73.629 1926 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.32 % Favored : 93.62 % Rotamer: Outliers : 2.34 % Allowed : 20.34 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.22), residues: 1441 helix: 0.51 (0.20), residues: 685 sheet: -0.46 (0.53), residues: 107 loop : -2.37 (0.22), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP A 388 HIS 0.003 0.001 HIS A 490 PHE 0.019 0.001 PHE A 457 TYR 0.018 0.001 TYR C 11 ARG 0.007 0.000 ARG C 131 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 266 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8794 (t70) cc_final: 0.8417 (t70) REVERT: A 328 ASP cc_start: 0.7936 (t0) cc_final: 0.7526 (t0) REVERT: A 367 GLN cc_start: 0.7059 (pt0) cc_final: 0.6587 (mt0) REVERT: A 412 CYS cc_start: 0.8414 (p) cc_final: 0.7492 (m) REVERT: A 421 LYS cc_start: 0.6988 (tttm) cc_final: 0.6425 (tppp) REVERT: A 514 LYS cc_start: 0.8039 (tttt) cc_final: 0.7602 (ttpt) REVERT: A 601 ARG cc_start: 0.8496 (mmt180) cc_final: 0.7920 (mmm160) REVERT: B 47 TYR cc_start: 0.7863 (m-10) cc_final: 0.7529 (m-10) REVERT: B 95 GLU cc_start: 0.7436 (mt-10) cc_final: 0.6873 (mm-30) REVERT: B 98 GLU cc_start: 0.7506 (tp30) cc_final: 0.6986 (tm-30) REVERT: B 320 TYR cc_start: 0.7859 (m-10) cc_final: 0.7283 (m-80) REVERT: B 334 LEU cc_start: 0.9001 (tp) cc_final: 0.8666 (tp) REVERT: B 408 MET cc_start: 0.7467 (ttp) cc_final: 0.7240 (ttm) REVERT: B 560 TYR cc_start: 0.7035 (m-80) cc_final: 0.6834 (m-80) REVERT: C 18 LYS cc_start: 0.7742 (mttt) cc_final: 0.7166 (tppt) REVERT: C 51 MET cc_start: 0.7595 (tpp) cc_final: 0.6886 (tpp) REVERT: C 55 MET cc_start: 0.4187 (mmp) cc_final: 0.3651 (mmm) REVERT: C 131 ARG cc_start: 0.8315 (mtm110) cc_final: 0.7894 (mtm-85) REVERT: C 171 MET cc_start: 0.8146 (mmm) cc_final: 0.7417 (mtm) REVERT: C 213 MET cc_start: 0.5012 (ptm) cc_final: 0.4591 (ptm) outliers start: 30 outliers final: 28 residues processed: 285 average time/residue: 0.2335 time to fit residues: 95.8247 Evaluate side-chains 283 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 255 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 505 ASN Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 249 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 0.0000 chunk 35 optimal weight: 0.9980 chunk 106 optimal weight: 0.1980 chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 0.2980 chunk 116 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN B 519 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.175211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.146065 restraints weight = 18460.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.148922 restraints weight = 11399.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.150830 restraints weight = 8209.868| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.4829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12534 Z= 0.165 Angle : 0.627 17.994 16948 Z= 0.306 Chirality : 0.041 0.203 1855 Planarity : 0.004 0.050 2068 Dihedral : 11.138 73.625 1926 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.59 % Favored : 93.34 % Rotamer: Outliers : 2.34 % Allowed : 20.19 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.22), residues: 1441 helix: 0.56 (0.20), residues: 685 sheet: -0.40 (0.55), residues: 103 loop : -2.35 (0.22), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 388 HIS 0.003 0.000 HIS A 451 PHE 0.038 0.001 PHE A 292 TYR 0.018 0.001 TYR C 11 ARG 0.007 0.000 ARG C 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2856.54 seconds wall clock time: 52 minutes 36.10 seconds (3156.10 seconds total)