Starting phenix.real_space_refine on Mon Mar 11 08:09:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d7r_30610/03_2024/7d7r_30610.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d7r_30610/03_2024/7d7r_30610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d7r_30610/03_2024/7d7r_30610.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d7r_30610/03_2024/7d7r_30610.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d7r_30610/03_2024/7d7r_30610.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d7r_30610/03_2024/7d7r_30610.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 4864 2.51 5 N 1368 2.21 5 O 1426 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 275": "OE1" <-> "OE2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A ARG 375": "NH1" <-> "NH2" Residue "A ASP 397": "OD1" <-> "OD2" Residue "A PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 440": "NH1" <-> "NH2" Residue "A ARG 452": "NH1" <-> "NH2" Residue "A TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 475": "NH1" <-> "NH2" Residue "A PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 552": "NH1" <-> "NH2" Residue "A GLU 571": "OE1" <-> "OE2" Residue "B GLU 275": "OE1" <-> "OE2" Residue "B ARG 276": "NH1" <-> "NH2" Residue "B TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 343": "NH1" <-> "NH2" Residue "B GLU 368": "OE1" <-> "OE2" Residue "B ARG 371": "NH1" <-> "NH2" Residue "B ARG 375": "NH1" <-> "NH2" Residue "B ASP 397": "OD1" <-> "OD2" Residue "B PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 440": "NH1" <-> "NH2" Residue "B ARG 452": "NH1" <-> "NH2" Residue "B TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 475": "NH1" <-> "NH2" Residue "B PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 552": "NH1" <-> "NH2" Residue "B GLU 571": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7680 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 3840 Classifications: {'peptide': 580} Incomplete info: {'truncation_to_alanine': 216} Link IDs: {'PTRANS': 12, 'TRANS': 567} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 773 Unresolved non-hydrogen angles: 992 Unresolved non-hydrogen dihedrals: 622 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 5, 'TYR:plan': 6, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 17, 'PHE:plan': 9, 'GLU:plan': 12, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 429 Chain: "B" Number of atoms: 3840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 3840 Classifications: {'peptide': 580} Incomplete info: {'truncation_to_alanine': 216} Link IDs: {'PTRANS': 12, 'TRANS': 567} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 773 Unresolved non-hydrogen angles: 992 Unresolved non-hydrogen dihedrals: 622 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 5, 'TYR:plan': 6, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 17, 'PHE:plan': 9, 'GLU:plan': 12, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 429 Time building chain proxies: 4.85, per 1000 atoms: 0.63 Number of scatterers: 7680 At special positions: 0 Unit cell: (86.32, 107.12, 134.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 1426 8.00 N 1368 7.00 C 4864 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: 3.03 Conformation dependent library (CDL) restraints added in 1.6 seconds 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 6 sheets defined 68.7% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 241 through 253 Processing helix chain 'A' and resid 261 through 297 removed outlier: 3.947A pdb=" N ARG A 276 " --> pdb=" O MET A 272 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) Proline residue: A 283 - end of helix Processing helix chain 'A' and resid 306 through 321 removed outlier: 4.207A pdb=" N LEU A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 353 removed outlier: 4.020A pdb=" N ARG A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 363 removed outlier: 3.970A pdb=" N GLY A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 390 removed outlier: 3.516A pdb=" N VAL A 369 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 373 " --> pdb=" O VAL A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 409 Processing helix chain 'A' and resid 412 through 459 removed outlier: 4.322A pdb=" N LYS A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE A 438 " --> pdb=" O TRP A 434 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASN A 459 " --> pdb=" O ASP A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 466 Processing helix chain 'A' and resid 471 through 523 removed outlier: 4.148A pdb=" N LEU A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 542 removed outlier: 3.613A pdb=" N PHE A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE A 537 " --> pdb=" O PHE A 533 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 549 Processing helix chain 'A' and resid 550 through 568 removed outlier: 3.740A pdb=" N GLN A 555 " --> pdb=" O TYR A 551 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASN A 563 " --> pdb=" O ILE A 559 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N MET A 564 " --> pdb=" O ASP A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 637 Processing helix chain 'A' and resid 659 through 664 Processing helix chain 'A' and resid 680 through 686 Processing helix chain 'A' and resid 692 through 704 Processing helix chain 'A' and resid 705 through 712 Processing helix chain 'A' and resid 728 through 744 Processing helix chain 'A' and resid 758 through 774 Processing helix chain 'A' and resid 807 through 815 Processing helix chain 'A' and resid 816 through 827 removed outlier: 4.106A pdb=" N ASP A 820 " --> pdb=" O GLY A 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 253 Processing helix chain 'B' and resid 261 through 297 removed outlier: 3.947A pdb=" N ARG B 276 " --> pdb=" O MET B 272 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B 277 " --> pdb=" O GLY B 273 " (cutoff:3.500A) Proline residue: B 283 - end of helix Processing helix chain 'B' and resid 306 through 321 removed outlier: 4.206A pdb=" N LEU B 315 " --> pdb=" O PHE B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 353 removed outlier: 4.021A pdb=" N ARG B 336 " --> pdb=" O PHE B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 363 removed outlier: 3.971A pdb=" N GLY B 363 " --> pdb=" O ARG B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 390 removed outlier: 3.516A pdb=" N VAL B 369 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA B 373 " --> pdb=" O VAL B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 409 Processing helix chain 'B' and resid 412 through 459 removed outlier: 4.322A pdb=" N LYS B 437 " --> pdb=" O GLU B 433 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE B 438 " --> pdb=" O TRP B 434 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASN B 459 " --> pdb=" O ASP B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 466 Processing helix chain 'B' and resid 471 through 523 removed outlier: 4.148A pdb=" N LEU B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 542 removed outlier: 3.613A pdb=" N PHE B 533 " --> pdb=" O ASP B 529 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE B 537 " --> pdb=" O PHE B 533 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE B 538 " --> pdb=" O GLY B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 549 Processing helix chain 'B' and resid 550 through 568 removed outlier: 3.740A pdb=" N GLN B 555 " --> pdb=" O TYR B 551 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASN B 563 " --> pdb=" O ILE B 559 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N MET B 564 " --> pdb=" O ASP B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 637 Processing helix chain 'B' and resid 659 through 664 Processing helix chain 'B' and resid 680 through 686 Processing helix chain 'B' and resid 692 through 704 Processing helix chain 'B' and resid 705 through 712 Processing helix chain 'B' and resid 728 through 744 Processing helix chain 'B' and resid 758 through 774 Processing helix chain 'B' and resid 807 through 815 Processing helix chain 'B' and resid 816 through 827 removed outlier: 4.105A pdb=" N ASP B 820 " --> pdb=" O GLY B 816 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 611 through 613 Processing sheet with id=AA2, first strand: chain 'A' and resid 666 through 669 removed outlier: 6.362A pdb=" N GLY A 667 " --> pdb=" O LEU A 749 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASP A 751 " --> pdb=" O GLY A 667 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL A 669 " --> pdb=" O ASP A 751 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ILE A 748 " --> pdb=" O ILE A 779 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N VAL A 781 " --> pdb=" O ILE A 748 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU A 750 " --> pdb=" O VAL A 781 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LEU A 619 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR A 618 " --> pdb=" O GLN A 793 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LEU A 795 " --> pdb=" O THR A 618 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ALA A 620 " --> pdb=" O LEU A 795 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ILE A 797 " --> pdb=" O ALA A 620 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL A 622 " --> pdb=" O ILE A 797 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE A 794 " --> pdb=" O ARG A 805 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ARG A 805 " --> pdb=" O ILE A 794 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL A 796 " --> pdb=" O VAL A 803 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 678 through 679 Processing sheet with id=AA4, first strand: chain 'B' and resid 611 through 613 Processing sheet with id=AA5, first strand: chain 'B' and resid 666 through 669 removed outlier: 6.363A pdb=" N GLY B 667 " --> pdb=" O LEU B 749 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ASP B 751 " --> pdb=" O GLY B 667 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL B 669 " --> pdb=" O ASP B 751 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ILE B 748 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N VAL B 781 " --> pdb=" O ILE B 748 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU B 750 " --> pdb=" O VAL B 781 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU B 619 " --> pdb=" O VAL B 780 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR B 618 " --> pdb=" O GLN B 793 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LEU B 795 " --> pdb=" O THR B 618 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ALA B 620 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ILE B 797 " --> pdb=" O ALA B 620 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B 622 " --> pdb=" O ILE B 797 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE B 794 " --> pdb=" O ARG B 805 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ARG B 805 " --> pdb=" O ILE B 794 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N VAL B 796 " --> pdb=" O VAL B 803 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 678 through 679 609 hydrogen bonds defined for protein. 1791 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2308 1.34 - 1.45: 1217 1.45 - 1.57: 4223 1.57 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 7786 Sorted by residual: bond pdb=" C PRO A 255 " pdb=" N ARG A 256 " ideal model delta sigma weight residual 1.325 1.270 0.055 1.41e-02 5.03e+03 1.54e+01 bond pdb=" C PRO B 255 " pdb=" N ARG B 256 " ideal model delta sigma weight residual 1.325 1.270 0.055 1.41e-02 5.03e+03 1.52e+01 bond pdb=" C ARG A 256 " pdb=" N GLY A 257 " ideal model delta sigma weight residual 1.331 1.363 -0.032 1.46e-02 4.69e+03 4.93e+00 bond pdb=" C ARG B 256 " pdb=" N GLY B 257 " ideal model delta sigma weight residual 1.331 1.363 -0.032 1.46e-02 4.69e+03 4.87e+00 bond pdb=" C ILE B 392 " pdb=" N PRO B 393 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.23e-02 6.61e+03 2.18e+00 ... (remaining 7781 not shown) Histogram of bond angle deviations from ideal: 99.40 - 106.33: 80 106.33 - 113.27: 4191 113.27 - 120.20: 2981 120.20 - 127.13: 3344 127.13 - 134.07: 46 Bond angle restraints: 10642 Sorted by residual: angle pdb=" N VAL B 282 " pdb=" CA VAL B 282 " pdb=" C VAL B 282 " ideal model delta sigma weight residual 108.88 117.15 -8.27 2.16e+00 2.14e-01 1.47e+01 angle pdb=" N VAL A 282 " pdb=" CA VAL A 282 " pdb=" C VAL A 282 " ideal model delta sigma weight residual 108.88 117.10 -8.22 2.16e+00 2.14e-01 1.45e+01 angle pdb=" C GLU B 593 " pdb=" N ASN B 594 " pdb=" CA ASN B 594 " ideal model delta sigma weight residual 122.82 128.22 -5.40 1.42e+00 4.96e-01 1.45e+01 angle pdb=" C GLU A 593 " pdb=" N ASN A 594 " pdb=" CA ASN A 594 " ideal model delta sigma weight residual 122.82 128.17 -5.35 1.42e+00 4.96e-01 1.42e+01 angle pdb=" N MET A 542 " pdb=" CA MET A 542 " pdb=" C MET A 542 " ideal model delta sigma weight residual 109.81 117.37 -7.56 2.21e+00 2.05e-01 1.17e+01 ... (remaining 10637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 4067 17.39 - 34.78: 346 34.78 - 52.17: 66 52.17 - 69.56: 19 69.56 - 86.94: 4 Dihedral angle restraints: 4502 sinusoidal: 1186 harmonic: 3316 Sorted by residual: dihedral pdb=" CA PRO A 713 " pdb=" C PRO A 713 " pdb=" N GLU A 714 " pdb=" CA GLU A 714 " ideal model delta harmonic sigma weight residual 180.00 -152.75 -27.25 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA PRO B 713 " pdb=" C PRO B 713 " pdb=" N GLU B 714 " pdb=" CA GLU B 714 " ideal model delta harmonic sigma weight residual 180.00 -152.75 -27.25 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA LEU B 568 " pdb=" C LEU B 568 " pdb=" N LYS B 569 " pdb=" CA LYS B 569 " ideal model delta harmonic sigma weight residual 180.00 -154.56 -25.44 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 4499 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 950 0.054 - 0.109: 288 0.109 - 0.163: 52 0.163 - 0.217: 8 0.217 - 0.271: 2 Chirality restraints: 1300 Sorted by residual: chirality pdb=" CA ASP A 799 " pdb=" N ASP A 799 " pdb=" C ASP A 799 " pdb=" CB ASP A 799 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA ASP B 799 " pdb=" N ASP B 799 " pdb=" C ASP B 799 " pdb=" CB ASP B 799 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CG LEU A 333 " pdb=" CB LEU A 333 " pdb=" CD1 LEU A 333 " pdb=" CD2 LEU A 333 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1297 not shown) Planarity restraints: 1394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 388 " 0.015 2.00e-02 2.50e+03 2.90e-02 8.40e+00 pdb=" C VAL B 388 " -0.050 2.00e-02 2.50e+03 pdb=" O VAL B 388 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE B 389 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 388 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.32e+00 pdb=" C VAL A 388 " 0.050 2.00e-02 2.50e+03 pdb=" O VAL A 388 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE A 389 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 542 " 0.047 5.00e-02 4.00e+02 7.02e-02 7.88e+00 pdb=" N PRO A 543 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 543 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 543 " 0.039 5.00e-02 4.00e+02 ... (remaining 1391 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2105 2.80 - 3.32: 7386 3.32 - 3.85: 12446 3.85 - 4.37: 13459 4.37 - 4.90: 22502 Nonbonded interactions: 57898 Sorted by model distance: nonbonded pdb=" OH TYR A 476 " pdb=" OE1 GLU B 346 " model vdw 2.270 2.440 nonbonded pdb=" OE1 GLN A 316 " pdb=" OG1 THR A 320 " model vdw 2.295 2.440 nonbonded pdb=" OE1 GLN B 316 " pdb=" OG1 THR B 320 " model vdw 2.296 2.440 nonbonded pdb=" O SER B 490 " pdb=" OG SER B 493 " model vdw 2.311 2.440 nonbonded pdb=" O SER A 490 " pdb=" OG SER A 493 " model vdw 2.311 2.440 ... (remaining 57893 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.860 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: 0.000 Extract box with map and model: 4.230 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.040 Find NCS groups from input model: 0.460 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6003 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 : 0.004 0.055 7786 Z= 0.282 Angle : 0.961 9.447 10642 Z= 0.529 Chirality : 0.054 0.271 1300 Planarity : 0.006 0.070 1394 Dihedral : 14.868 86.944 2374 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.65 % Favored : 96.18 % Rotamer: Outliers : 0.36 % Allowed : 10.95 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.19), residues: 1152 helix: -2.08 (0.14), residues: 758 sheet: -1.05 (0.58), residues: 82 loop : -3.22 (0.27), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 334 HIS 0.004 0.002 HIS B 352 PHE 0.032 0.002 PHE A 460 TYR 0.026 0.003 TYR B 541 ARG 0.006 0.001 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 227 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 LEU cc_start: 0.7870 (pp) cc_final: 0.7643 (pp) REVERT: A 328 ASN cc_start: 0.8140 (m-40) cc_final: 0.7351 (m-40) REVERT: A 330 ARG cc_start: 0.6843 (mtm-85) cc_final: 0.6589 (ttm110) REVERT: A 464 LYS cc_start: 0.7621 (mptt) cc_final: 0.7419 (pttt) REVERT: A 487 GLU cc_start: 0.7251 (tp30) cc_final: 0.6990 (tp30) REVERT: A 532 LEU cc_start: 0.8246 (tp) cc_final: 0.8001 (tp) REVERT: B 278 LEU cc_start: 0.7866 (pp) cc_final: 0.7640 (pp) REVERT: B 290 VAL cc_start: 0.7941 (m) cc_final: 0.7713 (t) REVERT: B 294 THR cc_start: 0.6162 (p) cc_final: 0.5504 (p) REVERT: B 328 ASN cc_start: 0.8051 (m-40) cc_final: 0.7296 (m-40) REVERT: B 464 LYS cc_start: 0.7803 (mptt) cc_final: 0.7558 (pttt) REVERT: B 519 PHE cc_start: 0.6365 (m-80) cc_final: 0.6156 (m-80) REVERT: B 525 LEU cc_start: 0.4824 (pt) cc_final: 0.4542 (mp) REVERT: B 532 LEU cc_start: 0.8210 (tp) cc_final: 0.7804 (tp) outliers start: 2 outliers final: 0 residues processed: 227 average time/residue: 0.2160 time to fit residues: 63.6118 Evaluate side-chains 152 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 46 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 105 optimal weight: 30.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 GLN ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN ** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6326 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 7786 Z= 0.360 Angle : 0.781 7.820 10642 Z= 0.436 Chirality : 0.046 0.171 1300 Planarity : 0.005 0.044 1394 Dihedral : 6.119 29.379 1226 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.47 % Favored : 94.18 % Rotamer: Outliers : 3.65 % Allowed : 22.08 % Favored : 74.27 % 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: -2.15 (0.22), residues: 1152 helix: -0.68 (0.17), residues: 784 sheet: -1.43 (0.51), residues: 82 loop : -3.23 (0.28), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 334 HIS 0.005 0.003 HIS A 361 PHE 0.030 0.004 PHE B 565 TYR 0.025 0.004 TYR B 541 ARG 0.007 0.001 ARG B 330 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 154 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 ASN cc_start: 0.7961 (m-40) cc_final: 0.7581 (m-40) REVERT: A 350 PHE cc_start: 0.8209 (t80) cc_final: 0.7960 (t80) REVERT: B 328 ASN cc_start: 0.7981 (m-40) cc_final: 0.7637 (m110) REVERT: B 350 PHE cc_start: 0.8313 (t80) cc_final: 0.8061 (t80) outliers start: 20 outliers final: 16 residues processed: 165 average time/residue: 0.1895 time to fit residues: 42.5751 Evaluate side-chains 155 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 139 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain B residue 309 TYR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 404 TYR Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 515 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 105 optimal weight: 40.0000 chunk 114 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 chunk 104 optimal weight: 40.0000 chunk 35 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6374 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7786 Z= 0.310 Angle : 0.756 9.227 10642 Z= 0.408 Chirality : 0.045 0.175 1300 Planarity : 0.005 0.070 1394 Dihedral : 5.972 29.859 1226 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.70 % Rotamer: Outliers : 6.39 % Allowed : 22.81 % Favored : 70.80 % 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: -1.66 (0.22), residues: 1152 helix: -0.16 (0.17), residues: 780 sheet: -2.04 (0.44), residues: 80 loop : -3.21 (0.29), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 334 HIS 0.007 0.003 HIS A 361 PHE 0.023 0.003 PHE A 565 TYR 0.025 0.003 TYR B 551 ARG 0.011 0.001 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 144 time to evaluate : 0.950 Fit side-chains REVERT: A 370 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7339 (tt) REVERT: B 350 PHE cc_start: 0.8354 (t80) cc_final: 0.8112 (t80) REVERT: B 462 THR cc_start: 0.6084 (p) cc_final: 0.5229 (p) REVERT: B 519 PHE cc_start: 0.6276 (m-80) cc_final: 0.6058 (m-80) outliers start: 35 outliers final: 17 residues processed: 166 average time/residue: 0.1736 time to fit residues: 39.9778 Evaluate side-chains 154 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 136 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 460 PHE Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain B residue 309 TYR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 515 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 20.0000 chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 40.0000 chunk 11 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 chunk 105 optimal weight: 30.0000 chunk 112 optimal weight: 40.0000 chunk 55 optimal weight: 10.0000 chunk 100 optimal weight: 30.0000 chunk 30 optimal weight: 0.0050 overall best weight: 5.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 HIS ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 ASN ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6468 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 7786 Z= 0.370 Angle : 0.840 8.826 10642 Z= 0.457 Chirality : 0.048 0.204 1300 Planarity : 0.006 0.085 1394 Dihedral : 6.377 32.119 1226 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 22.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.55 % Favored : 92.27 % Rotamer: Outliers : 7.30 % Allowed : 28.65 % Favored : 64.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.10 (0.22), residues: 1152 helix: -0.39 (0.17), residues: 772 sheet: -2.53 (0.45), residues: 80 loop : -3.54 (0.28), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 334 HIS 0.008 0.004 HIS A 361 PHE 0.021 0.003 PHE B 314 TYR 0.030 0.004 TYR A 551 ARG 0.005 0.001 ARG B 365 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 131 time to evaluate : 0.917 Fit side-chains REVERT: A 311 PHE cc_start: 0.2930 (OUTLIER) cc_final: -0.2855 (m-80) REVERT: A 424 TYR cc_start: 0.8211 (m-80) cc_final: 0.7944 (m-80) REVERT: B 424 TYR cc_start: 0.8204 (m-80) cc_final: 0.7911 (m-80) REVERT: B 545 ASN cc_start: 0.7986 (OUTLIER) cc_final: 0.7535 (p0) REVERT: B 570 GLU cc_start: 0.6125 (OUTLIER) cc_final: 0.5618 (mt-10) outliers start: 40 outliers final: 24 residues processed: 155 average time/residue: 0.1833 time to fit residues: 38.9175 Evaluate side-chains 148 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 121 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 460 PHE Chi-restraints excluded: chain A residue 466 TYR Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 309 TYR Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain B residue 570 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 20.0000 chunk 63 optimal weight: 0.9990 chunk 1 optimal weight: 0.2980 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 chunk 77 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 100 optimal weight: 30.0000 chunk 28 optimal weight: 0.0370 overall best weight: 1.0462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN A 539 GLN B 279 ASN ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN B 539 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7786 Z= 0.181 Angle : 0.697 10.097 10642 Z= 0.361 Chirality : 0.043 0.138 1300 Planarity : 0.003 0.036 1394 Dihedral : 5.293 25.997 1226 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.04 % Favored : 96.88 % Rotamer: Outliers : 4.56 % Allowed : 31.39 % Favored : 64.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.23), residues: 1152 helix: 0.34 (0.17), residues: 780 sheet: -1.80 (0.51), residues: 80 loop : -3.24 (0.31), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 412 HIS 0.003 0.001 HIS A 361 PHE 0.021 0.002 PHE B 460 TYR 0.020 0.002 TYR A 541 ARG 0.005 0.001 ARG B 330 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 150 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 PHE cc_start: 0.2794 (OUTLIER) cc_final: -0.1893 (m-80) REVERT: A 350 PHE cc_start: 0.8153 (t80) cc_final: 0.7918 (t80) REVERT: A 424 TYR cc_start: 0.7836 (m-80) cc_final: 0.7540 (m-80) REVERT: A 509 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8077 (tt) REVERT: A 545 ASN cc_start: 0.7675 (OUTLIER) cc_final: 0.7150 (p0) REVERT: B 290 VAL cc_start: 0.8241 (m) cc_final: 0.7980 (t) REVERT: B 311 PHE cc_start: 0.2992 (OUTLIER) cc_final: -0.1543 (m-80) REVERT: B 442 MET cc_start: 0.7777 (tpp) cc_final: 0.7509 (tpp) outliers start: 25 outliers final: 16 residues processed: 163 average time/residue: 0.1820 time to fit residues: 40.8482 Evaluate side-chains 151 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 311 PHE Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 564 MET Chi-restraints excluded: chain B residue 570 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 30.0000 chunk 100 optimal weight: 30.0000 chunk 22 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 27 optimal weight: 0.0670 chunk 112 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 51 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 58 optimal weight: 20.0000 chunk 108 optimal weight: 6.9990 overall best weight: 4.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 HIS ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6427 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7786 Z= 0.308 Angle : 0.780 11.263 10642 Z= 0.413 Chirality : 0.046 0.210 1300 Planarity : 0.005 0.057 1394 Dihedral : 5.683 27.463 1226 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.86 % Favored : 92.97 % Rotamer: Outliers : 6.02 % Allowed : 32.12 % Favored : 61.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.23), residues: 1152 helix: 0.15 (0.17), residues: 776 sheet: -1.41 (0.87), residues: 44 loop : -3.21 (0.29), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 334 HIS 0.005 0.002 HIS B 361 PHE 0.029 0.003 PHE A 418 TYR 0.027 0.003 TYR A 551 ARG 0.006 0.001 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 132 time to evaluate : 1.094 Fit side-chains REVERT: A 442 MET cc_start: 0.7733 (tpp) cc_final: 0.7082 (ttp) REVERT: A 545 ASN cc_start: 0.7699 (OUTLIER) cc_final: 0.7124 (p0) REVERT: B 424 TYR cc_start: 0.8097 (m-80) cc_final: 0.7780 (m-80) REVERT: B 442 MET cc_start: 0.7790 (tpp) cc_final: 0.7584 (tpp) REVERT: B 464 LYS cc_start: 0.8223 (mmtm) cc_final: 0.7840 (pttt) outliers start: 33 outliers final: 20 residues processed: 153 average time/residue: 0.1819 time to fit residues: 38.5264 Evaluate side-chains 152 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 309 TYR Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 361 HIS Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 515 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 20.0000 chunk 62 optimal weight: 0.9980 chunk 111 optimal weight: 20.0000 chunk 69 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6366 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7786 Z= 0.225 Angle : 0.734 9.777 10642 Z= 0.381 Chirality : 0.045 0.180 1300 Planarity : 0.004 0.054 1394 Dihedral : 5.367 26.391 1226 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.17 % Favored : 95.66 % Rotamer: Outliers : 5.84 % Allowed : 33.39 % Favored : 60.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.24), residues: 1152 helix: 0.39 (0.18), residues: 776 sheet: -1.12 (0.93), residues: 44 loop : -3.10 (0.29), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 412 HIS 0.015 0.003 HIS B 361 PHE 0.026 0.002 PHE A 418 TYR 0.019 0.002 TYR A 541 ARG 0.004 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 137 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: A 311 PHE cc_start: 0.2924 (OUTLIER) cc_final: -0.1698 (m-80) REVERT: A 509 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8079 (tt) REVERT: A 545 ASN cc_start: 0.7679 (OUTLIER) cc_final: 0.7195 (p0) REVERT: B 290 VAL cc_start: 0.8345 (m) cc_final: 0.8100 (t) REVERT: B 311 PHE cc_start: 0.2885 (OUTLIER) cc_final: -0.1504 (m-80) REVERT: B 354 HIS cc_start: 0.7281 (OUTLIER) cc_final: 0.7025 (m-70) REVERT: B 424 TYR cc_start: 0.8047 (m-80) cc_final: 0.7681 (m-80) REVERT: B 442 MET cc_start: 0.7752 (tpp) cc_final: 0.7494 (tpp) outliers start: 32 outliers final: 20 residues processed: 158 average time/residue: 0.1778 time to fit residues: 39.2225 Evaluate side-chains 156 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 311 PHE Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain B residue 361 HIS Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 515 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 55 optimal weight: 20.0000 chunk 10 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 101 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 97 optimal weight: 30.0000 chunk 104 optimal weight: 0.7980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 ASN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6300 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7786 Z= 0.190 Angle : 0.714 12.931 10642 Z= 0.362 Chirality : 0.044 0.195 1300 Planarity : 0.004 0.050 1394 Dihedral : 4.837 24.181 1226 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 6.20 % Allowed : 33.76 % Favored : 60.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.24), residues: 1152 helix: 0.88 (0.18), residues: 772 sheet: -0.92 (0.96), residues: 44 loop : -2.93 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 412 HIS 0.002 0.001 HIS A 354 PHE 0.027 0.002 PHE A 413 TYR 0.029 0.002 TYR B 465 ARG 0.003 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 150 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: A 311 PHE cc_start: 0.2862 (OUTLIER) cc_final: -0.1897 (m-80) REVERT: A 354 HIS cc_start: 0.7272 (OUTLIER) cc_final: 0.6757 (m-70) REVERT: A 502 ASN cc_start: 0.6281 (m-40) cc_final: 0.5554 (t0) REVERT: A 505 ILE cc_start: 0.7942 (mt) cc_final: 0.7572 (tp) REVERT: A 509 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7939 (tt) REVERT: A 545 ASN cc_start: 0.7496 (OUTLIER) cc_final: 0.7171 (p0) REVERT: B 290 VAL cc_start: 0.8265 (m) cc_final: 0.8046 (t) REVERT: B 311 PHE cc_start: 0.3077 (OUTLIER) cc_final: -0.1630 (m-10) REVERT: B 350 PHE cc_start: 0.8194 (t80) cc_final: 0.7899 (t80) REVERT: B 424 TYR cc_start: 0.7977 (m-80) cc_final: 0.7731 (m-80) REVERT: B 502 ASN cc_start: 0.6290 (m-40) cc_final: 0.5576 (t0) REVERT: B 505 ILE cc_start: 0.8113 (mt) cc_final: 0.7805 (tp) outliers start: 34 outliers final: 19 residues processed: 171 average time/residue: 0.1692 time to fit residues: 40.2476 Evaluate side-chains 164 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 140 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain B residue 311 PHE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 515 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 45 optimal weight: 20.0000 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 94 optimal weight: 20.0000 chunk 98 optimal weight: 9.9990 chunk 103 optimal weight: 20.0000 chunk 68 optimal weight: 0.0980 chunk 110 optimal weight: 40.0000 chunk 67 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 ASN A 459 ASN ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6261 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7786 Z= 0.177 Angle : 0.689 9.460 10642 Z= 0.350 Chirality : 0.043 0.194 1300 Planarity : 0.003 0.044 1394 Dihedral : 4.532 22.813 1226 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.38 % Allowed : 34.67 % Favored : 60.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.25), residues: 1152 helix: 1.11 (0.18), residues: 782 sheet: -0.84 (0.99), residues: 44 loop : -2.67 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 412 HIS 0.005 0.002 HIS B 354 PHE 0.028 0.002 PHE A 413 TYR 0.019 0.002 TYR B 465 ARG 0.007 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 152 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: A 290 VAL cc_start: 0.8259 (m) cc_final: 0.8009 (t) REVERT: A 311 PHE cc_start: 0.2892 (OUTLIER) cc_final: -0.1666 (m-80) REVERT: A 350 PHE cc_start: 0.8162 (t80) cc_final: 0.7671 (t80) REVERT: A 354 HIS cc_start: 0.7100 (OUTLIER) cc_final: 0.6657 (m-70) REVERT: A 502 ASN cc_start: 0.6173 (m-40) cc_final: 0.5657 (t0) REVERT: A 545 ASN cc_start: 0.7402 (OUTLIER) cc_final: 0.7060 (p0) REVERT: B 290 VAL cc_start: 0.8273 (m) cc_final: 0.8061 (t) REVERT: B 460 PHE cc_start: 0.5926 (OUTLIER) cc_final: 0.5399 (t80) REVERT: B 502 ASN cc_start: 0.6183 (m-40) cc_final: 0.5578 (t0) REVERT: B 505 ILE cc_start: 0.8146 (mt) cc_final: 0.7778 (tp) outliers start: 24 outliers final: 19 residues processed: 165 average time/residue: 0.1676 time to fit residues: 38.7369 Evaluate side-chains 164 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 141 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 460 PHE Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 515 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 40.0000 chunk 76 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 92 optimal weight: 40.0000 chunk 9 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 73 optimal weight: 0.8980 chunk 98 optimal weight: 0.1980 chunk 28 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6297 moved from start: 0.5098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7786 Z= 0.209 Angle : 0.744 12.912 10642 Z= 0.373 Chirality : 0.045 0.215 1300 Planarity : 0.003 0.039 1394 Dihedral : 4.577 23.059 1226 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.56 % Allowed : 35.40 % Favored : 60.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.25), residues: 1152 helix: 1.06 (0.18), residues: 782 sheet: -0.97 (0.99), residues: 44 loop : -2.70 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 412 HIS 0.004 0.002 HIS B 354 PHE 0.029 0.002 PHE A 413 TYR 0.057 0.002 TYR A 424 ARG 0.010 0.000 ARG B 330 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 144 time to evaluate : 0.877 Fit side-chains REVERT: A 290 VAL cc_start: 0.8294 (m) cc_final: 0.8006 (t) REVERT: A 311 PHE cc_start: 0.2731 (OUTLIER) cc_final: -0.1316 (m-10) REVERT: A 442 MET cc_start: 0.8004 (tpp) cc_final: 0.7762 (tpp) REVERT: A 502 ASN cc_start: 0.6218 (m-40) cc_final: 0.5528 (t0) REVERT: A 505 ILE cc_start: 0.7830 (mt) cc_final: 0.7368 (tp) REVERT: A 545 ASN cc_start: 0.7463 (OUTLIER) cc_final: 0.7114 (p0) REVERT: B 311 PHE cc_start: 0.2981 (OUTLIER) cc_final: -0.1763 (m-10) REVERT: B 502 ASN cc_start: 0.6296 (m-40) cc_final: 0.5597 (t0) REVERT: B 505 ILE cc_start: 0.7795 (mt) cc_final: 0.7487 (tp) outliers start: 25 outliers final: 19 residues processed: 160 average time/residue: 0.1725 time to fit residues: 38.5522 Evaluate side-chains 162 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 140 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 311 PHE Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 515 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 92 optimal weight: 40.0000 chunk 38 optimal weight: 30.0000 chunk 94 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 66 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 ASN ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.158980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.151714 restraints weight = 30357.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.153133 restraints weight = 19661.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.154124 restraints weight = 13501.987| |-----------------------------------------------------------------------------| r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6122 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7786 Z= 0.178 Angle : 0.713 9.735 10642 Z= 0.359 Chirality : 0.044 0.193 1300 Planarity : 0.003 0.043 1394 Dihedral : 4.314 21.512 1226 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.20 % Allowed : 35.58 % Favored : 60.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.25), residues: 1152 helix: 1.27 (0.18), residues: 778 sheet: -1.66 (0.72), residues: 60 loop : -2.37 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 412 HIS 0.004 0.002 HIS B 354 PHE 0.027 0.002 PHE A 413 TYR 0.017 0.002 TYR A 466 ARG 0.008 0.000 ARG B 330 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1628.29 seconds wall clock time: 30 minutes 8.55 seconds (1808.55 seconds total)