Starting phenix.real_space_refine on Wed Feb 14 12:05:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dny_30790/02_2024/7dny_30790.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dny_30790/02_2024/7dny_30790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dny_30790/02_2024/7dny_30790.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dny_30790/02_2024/7dny_30790.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dny_30790/02_2024/7dny_30790.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dny_30790/02_2024/7dny_30790.pdb" } resolution = 3.4 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= 0.009 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 34 5.16 5 C 5968 2.51 5 N 1557 2.21 5 O 1662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 529": "OD1" <-> "OD2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A PHE 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 604": "OE1" <-> "OE2" Residue "A PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 752": "OE1" <-> "OE2" Residue "A ASP 758": "OD1" <-> "OD2" Residue "B PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 365": "NH1" <-> "NH2" Residue "B GLU 433": "OE1" <-> "OE2" Residue "B ARG 435": "NH1" <-> "NH2" Residue "B GLU 446": "OE1" <-> "OE2" Residue "B TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 469": "OE1" <-> "OE2" Residue "B GLU 487": "OE1" <-> "OE2" Residue "B TYR 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B PHE 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 678": "OD1" <-> "OD2" Residue "B TYR 716": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 758": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9221 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4482 Classifications: {'peptide': 571} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 558} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4516 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 561} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 153 Unusual residues: {'HT9': 1, 'Y01': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.47, per 1000 atoms: 0.59 Number of scatterers: 9221 At special positions: 0 Unit cell: (68.88, 101.68, 137.104, 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 34 16.00 O 1662 8.00 N 1557 7.00 C 5968 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: 3.79 Conformation dependent library (CDL) restraints added in 1.8 seconds 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2110 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 8 sheets defined 72.2% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 258 through 295 removed outlier: 3.717A pdb=" N GLN A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) Proline residue: A 283 - end of helix removed outlier: 3.600A pdb=" N GLU A 295 " --> pdb=" O ASN A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 317 removed outlier: 4.463A pdb=" N TRP A 304 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 334 Processing helix chain 'A' and resid 334 through 355 removed outlier: 3.913A pdb=" N PHE A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 363 removed outlier: 3.605A pdb=" N GLY A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 390 removed outlier: 3.515A pdb=" N VAL A 369 " --> pdb=" O ARG A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 408 Processing helix chain 'A' and resid 410 through 459 removed outlier: 4.099A pdb=" N GLY A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA A 453 " --> pdb=" O THR A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 467 Processing helix chain 'A' and resid 468 through 522 Processing helix chain 'A' and resid 526 through 570 removed outlier: 4.155A pdb=" N TYR A 530 " --> pdb=" O GLN A 526 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) Proline residue: A 543 - end of helix removed outlier: 4.064A pdb=" N TRP A 546 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY A 548 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR A 549 " --> pdb=" O ASN A 545 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLN A 555 " --> pdb=" O TYR A 551 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N THR A 556 " --> pdb=" O ARG A 552 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 637 removed outlier: 4.062A pdb=" N LEU A 633 " --> pdb=" O LYS A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 664 removed outlier: 3.844A pdb=" N LEU A 662 " --> pdb=" O THR A 658 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 688 removed outlier: 3.720A pdb=" N GLY A 687 " --> pdb=" O ASN A 683 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ARG A 688 " --> pdb=" O ILE A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 703 Processing helix chain 'A' and resid 705 through 712 Processing helix chain 'A' and resid 714 through 718 removed outlier: 3.590A pdb=" N ARG A 717 " --> pdb=" O GLU A 714 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR A 718 " --> pdb=" O GLY A 715 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 714 through 718' Processing helix chain 'A' and resid 728 through 744 Processing helix chain 'A' and resid 758 through 773 Processing helix chain 'A' and resid 785 through 790 Processing helix chain 'A' and resid 807 through 815 Processing helix chain 'A' and resid 816 through 827 Processing helix chain 'B' and resid 258 through 295 removed outlier: 4.546A pdb=" N VAL B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Proline residue: B 283 - end of helix Processing helix chain 'B' and resid 298 through 316 removed outlier: 3.969A pdb=" N TRP B 304 " --> pdb=" O ASN B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 356 removed outlier: 4.515A pdb=" N ARG B 336 " --> pdb=" O PHE B 332 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N PHE B 340 " --> pdb=" O ARG B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 362 removed outlier: 3.620A pdb=" N HIS B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 408 removed outlier: 4.487A pdb=" N ILE B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ILE B 392 " --> pdb=" O VAL B 388 " (cutoff:3.500A) Proline residue: B 393 - end of helix Processing helix chain 'B' and resid 410 through 459 removed outlier: 3.545A pdb=" N GLY B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 466 Processing helix chain 'B' and resid 468 through 522 removed outlier: 4.196A pdb=" N LYS B 489 " --> pdb=" O GLY B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 542 removed outlier: 3.669A pdb=" N TYR B 530 " --> pdb=" O GLN B 526 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE B 538 " --> pdb=" O GLY B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 553 Processing helix chain 'B' and resid 553 through 570 removed outlier: 4.207A pdb=" N ASN B 557 " --> pdb=" O MET B 553 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU B 562 " --> pdb=" O PHE B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 637 Processing helix chain 'B' and resid 658 through 666 Processing helix chain 'B' and resid 680 through 685 Processing helix chain 'B' and resid 686 through 688 No H-bonds generated for 'chain 'B' and resid 686 through 688' Processing helix chain 'B' and resid 692 through 704 Processing helix chain 'B' and resid 705 through 712 Processing helix chain 'B' and resid 714 through 718 removed outlier: 3.730A pdb=" N ARG B 717 " --> pdb=" O GLU B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 744 Processing helix chain 'B' and resid 758 through 774 removed outlier: 3.759A pdb=" N ALA B 764 " --> pdb=" O SER B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 790 removed outlier: 3.553A pdb=" N ASN B 790 " --> pdb=" O SER B 786 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 815 Processing helix chain 'B' and resid 816 through 827 Processing sheet with id=AA1, first strand: chain 'A' and resid 606 through 607 removed outlier: 3.515A pdb=" N PHE A 597 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A 611 " --> pdb=" O PHE A 592 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 606 through 607 removed outlier: 3.515A pdb=" N PHE A 597 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N PHE A 592 " --> pdb=" O ARG A 648 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ARG A 648 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ASN A 594 " --> pdb=" O CYS A 646 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N CYS A 646 " --> pdb=" O ASN A 594 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 619 through 621 removed outlier: 6.900A pdb=" N LEU A 619 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 781 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 666 through 667 Processing sheet with id=AA5, first strand: chain 'A' and resid 795 through 798 removed outlier: 6.958A pdb=" N VAL A 796 " --> pdb=" O VAL A 803 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 595 through 597 removed outlier: 3.672A pdb=" N VAL B 595 " --> pdb=" O VAL B 609 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N PHE B 597 " --> pdb=" O GLN B 607 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N GLN B 607 " --> pdb=" O PHE B 597 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 619 through 620 Processing sheet with id=AA8, first strand: chain 'B' and resid 796 through 798 removed outlier: 7.321A pdb=" N VAL B 796 " --> pdb=" O VAL B 803 " (cutoff:3.500A) 615 hydrogen bonds defined for protein. 1818 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: 2.95 Time building geometry restraints manager: 4.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1549 1.32 - 1.45: 2494 1.45 - 1.57: 5313 1.57 - 1.70: 1 1.70 - 1.82: 56 Bond restraints: 9413 Sorted by residual: bond pdb=" N ILE A 747 " pdb=" CA ILE A 747 " ideal model delta sigma weight residual 1.456 1.496 -0.039 1.14e-02 7.69e+03 1.19e+01 bond pdb=" N THR B 320 " pdb=" CA THR B 320 " ideal model delta sigma weight residual 1.456 1.496 -0.039 1.23e-02 6.61e+03 1.03e+01 bond pdb=" N VAL B 527 " pdb=" CA VAL B 527 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.00e+01 bond pdb=" N ILE B 705 " pdb=" CA ILE B 705 " ideal model delta sigma weight residual 1.459 1.498 -0.040 1.25e-02 6.40e+03 1.00e+01 bond pdb=" N ALA A 744 " pdb=" CA ALA A 744 " ideal model delta sigma weight residual 1.457 1.485 -0.029 9.10e-03 1.21e+04 9.84e+00 ... (remaining 9408 not shown) Histogram of bond angle deviations from ideal: 94.60 - 102.52: 41 102.52 - 110.44: 2320 110.44 - 118.36: 5139 118.36 - 126.28: 5175 126.28 - 134.20: 132 Bond angle restraints: 12807 Sorted by residual: angle pdb=" CA GLY B 324 " pdb=" C GLY B 324 " pdb=" O GLY B 324 " ideal model delta sigma weight residual 122.37 118.09 4.28 7.30e-01 1.88e+00 3.43e+01 angle pdb=" C THR B 320 " pdb=" CA THR B 320 " pdb=" CB THR B 320 " ideal model delta sigma weight residual 110.06 117.37 -7.31 1.44e+00 4.82e-01 2.58e+01 angle pdb=" CB ARG A 452 " pdb=" CG ARG A 452 " pdb=" CD ARG A 452 " ideal model delta sigma weight residual 111.30 122.91 -11.61 2.30e+00 1.89e-01 2.55e+01 angle pdb=" N PHE B 409 " pdb=" CA PHE B 409 " pdb=" C PHE B 409 " ideal model delta sigma weight residual 109.18 102.13 7.05 1.42e+00 4.96e-01 2.47e+01 angle pdb=" CB MET A 442 " pdb=" CG MET A 442 " pdb=" SD MET A 442 " ideal model delta sigma weight residual 112.70 97.81 14.89 3.00e+00 1.11e-01 2.46e+01 ... (remaining 12802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 5107 17.66 - 35.32: 542 35.32 - 52.98: 97 52.98 - 70.63: 23 70.63 - 88.29: 12 Dihedral angle restraints: 5781 sinusoidal: 2487 harmonic: 3294 Sorted by residual: dihedral pdb=" CA ARG A 814 " pdb=" C ARG A 814 " pdb=" N GLY A 815 " pdb=" CA GLY A 815 " ideal model delta harmonic sigma weight residual 180.00 153.69 26.31 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA GLU A 591 " pdb=" C GLU A 591 " pdb=" N PHE A 592 " pdb=" CA PHE A 592 " ideal model delta harmonic sigma weight residual 180.00 154.23 25.77 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA LEU A 353 " pdb=" C LEU A 353 " pdb=" N HIS A 354 " pdb=" CA HIS A 354 " ideal model delta harmonic sigma weight residual 180.00 155.07 24.93 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 5778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1188 0.083 - 0.166: 254 0.166 - 0.249: 37 0.249 - 0.332: 7 0.332 - 0.416: 2 Chirality restraints: 1488 Sorted by residual: chirality pdb=" CB VAL B 696 " pdb=" CA VAL B 696 " pdb=" CG1 VAL B 696 " pdb=" CG2 VAL B 696 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.32e+00 chirality pdb=" CG LEU B 769 " pdb=" CB LEU B 769 " pdb=" CD1 LEU B 769 " pdb=" CD2 LEU B 769 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" CB VAL A 388 " pdb=" CA VAL A 388 " pdb=" CG1 VAL A 388 " pdb=" CG2 VAL A 388 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 1485 not shown) Planarity restraints: 1592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 HT9 A 904 " -0.065 2.00e-02 2.50e+03 1.85e-01 7.71e+02 pdb=" C11 HT9 A 904 " 0.080 2.00e-02 2.50e+03 pdb=" C12 HT9 A 904 " -0.045 2.00e-02 2.50e+03 pdb=" C13 HT9 A 904 " 0.062 2.00e-02 2.50e+03 pdb=" C14 HT9 A 904 " -0.262 2.00e-02 2.50e+03 pdb=" C20 HT9 A 904 " 0.144 2.00e-02 2.50e+03 pdb=" C21 HT9 A 904 " 0.313 2.00e-02 2.50e+03 pdb=" C35 HT9 A 904 " -0.312 2.00e-02 2.50e+03 pdb=" N3 HT9 A 904 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 299 " -0.037 2.00e-02 2.50e+03 3.06e-02 2.34e+01 pdb=" CG TRP A 299 " 0.078 2.00e-02 2.50e+03 pdb=" CD1 TRP A 299 " -0.039 2.00e-02 2.50e+03 pdb=" CD2 TRP A 299 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 299 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 299 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 299 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 299 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 299 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 299 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 542 " 0.060 5.00e-02 4.00e+02 9.03e-02 1.31e+01 pdb=" N PRO B 543 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO B 543 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 543 " 0.050 5.00e-02 4.00e+02 ... (remaining 1589 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 963 2.74 - 3.28: 9759 3.28 - 3.82: 16047 3.82 - 4.36: 18156 4.36 - 4.90: 29758 Nonbonded interactions: 74683 Sorted by model distance: nonbonded pdb=" O THR B 428 " pdb=" OG1 THR B 432 " model vdw 2.203 2.440 nonbonded pdb=" O ILE A 402 " pdb=" OG SER A 406 " model vdw 2.260 2.440 nonbonded pdb=" OG1 THR A 449 " pdb=" NH2 ARG A 452 " model vdw 2.303 2.520 nonbonded pdb=" OD1 ASN A 459 " pdb=" OG1 THR A 462 " model vdw 2.305 2.440 nonbonded pdb=" OE1 GLN B 701 " pdb=" OH TYR B 716 " model vdw 2.308 2.440 ... (remaining 74678 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 258 through 357 or (resid 358 through 359 and (name N or n \ ame CA or name C or name O or name CB )) or resid 360 through 463 or (resid 464 \ through 468 and (name N or name CA or name C or name O or name CB )) or resid 46 \ 9 through 828 or resid 901 through 902)) selection = (chain 'B' and (resid 258 through 465 or (resid 466 through 468 and (name N or n \ ame CA or name C or name O or name CB )) or resid 469 through 523 or (resid 524 \ and (name N or name CA or name C or name O or name CB )) or resid 525 or (resid \ 526 and (name N or name CA or name C or name O or name CB )) or resid 527 throug \ h 828 or resid 901 through 902)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 8.440 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.380 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.104 9413 Z= 0.583 Angle : 1.248 14.894 12807 Z= 0.742 Chirality : 0.071 0.416 1488 Planarity : 0.008 0.185 1592 Dihedral : 15.292 88.293 3671 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.04 % Allowed : 1.46 % Favored : 97.49 % Cbeta Deviations : 0.09 % 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: -1.83 (0.22), residues: 1142 helix: -0.53 (0.17), residues: 769 sheet: -2.07 (0.64), residues: 53 loop : -2.49 (0.28), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.005 TRP A 299 HIS 0.007 0.001 HIS B 352 PHE 0.051 0.004 PHE A 405 TYR 0.042 0.004 TYR A 465 ARG 0.023 0.001 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 153 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8188 (tm-30) REVERT: A 758 ASP cc_start: 0.8140 (m-30) cc_final: 0.7680 (t0) REVERT: B 309 TYR cc_start: 0.7549 (t80) cc_final: 0.7217 (t80) REVERT: B 370 LEU cc_start: 0.9107 (tp) cc_final: 0.8906 (tp) REVERT: B 422 SER cc_start: 0.7976 (m) cc_final: 0.7592 (p) REVERT: B 466 TYR cc_start: 0.7597 (m-80) cc_final: 0.7279 (m-80) REVERT: B 646 CYS cc_start: 0.8053 (m) cc_final: 0.7827 (m) REVERT: B 822 TRP cc_start: 0.8610 (t-100) cc_final: 0.8290 (t-100) outliers start: 10 outliers final: 2 residues processed: 161 average time/residue: 0.2322 time to fit residues: 50.4663 Evaluate side-chains 113 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 748 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 ASN ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9413 Z= 0.189 Angle : 0.648 7.260 12807 Z= 0.341 Chirality : 0.041 0.148 1488 Planarity : 0.005 0.071 1592 Dihedral : 8.167 59.165 1641 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.25 % Allowed : 10.55 % Favored : 88.19 % 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: -0.52 (0.24), residues: 1142 helix: 0.60 (0.18), residues: 776 sheet: -1.96 (0.67), residues: 53 loop : -2.36 (0.30), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 434 HIS 0.009 0.001 HIS A 354 PHE 0.021 0.002 PHE A 418 TYR 0.019 0.002 TYR A 483 ARG 0.006 0.000 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 143 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 TYR cc_start: 0.8310 (t80) cc_final: 0.7929 (t80) REVERT: A 388 VAL cc_start: 0.8412 (p) cc_final: 0.8181 (p) REVERT: A 478 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8220 (tm-30) REVERT: A 561 MET cc_start: 0.6995 (tmm) cc_final: 0.6775 (tmm) REVERT: A 758 ASP cc_start: 0.8069 (m-30) cc_final: 0.7626 (t0) REVERT: B 272 MET cc_start: 0.7981 (tmm) cc_final: 0.7779 (tmm) REVERT: B 309 TYR cc_start: 0.7304 (t80) cc_final: 0.7038 (t80) REVERT: B 370 LEU cc_start: 0.9141 (tp) cc_final: 0.8936 (tp) REVERT: B 422 SER cc_start: 0.7838 (m) cc_final: 0.7478 (p) REVERT: B 466 TYR cc_start: 0.7619 (m-80) cc_final: 0.7320 (m-80) REVERT: B 503 LEU cc_start: 0.8649 (tp) cc_final: 0.8393 (tp) REVERT: B 646 CYS cc_start: 0.7999 (m) cc_final: 0.7787 (m) REVERT: B 656 GLN cc_start: 0.8045 (mm110) cc_final: 0.7799 (mp10) REVERT: B 822 TRP cc_start: 0.8615 (t-100) cc_final: 0.8327 (t-100) outliers start: 12 outliers final: 7 residues processed: 152 average time/residue: 0.2097 time to fit residues: 44.5501 Evaluate side-chains 124 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 551 TYR Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 8.9990 chunk 32 optimal weight: 20.0000 chunk 86 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 92 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 chunk 83 optimal weight: 0.7980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 GLN ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9413 Z= 0.267 Angle : 0.647 8.373 12807 Z= 0.337 Chirality : 0.042 0.238 1488 Planarity : 0.004 0.054 1592 Dihedral : 7.707 59.738 1641 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.09 % Allowed : 14.52 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.24), residues: 1142 helix: 0.88 (0.18), residues: 771 sheet: -1.96 (0.67), residues: 53 loop : -2.16 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 434 HIS 0.012 0.001 HIS A 665 PHE 0.031 0.002 PHE A 418 TYR 0.032 0.002 TYR A 465 ARG 0.007 0.000 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 TYR cc_start: 0.8400 (t80) cc_final: 0.8038 (t80) REVERT: A 388 VAL cc_start: 0.8454 (p) cc_final: 0.8213 (p) REVERT: A 445 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.6727 (tm-30) REVERT: A 478 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8245 (tm-30) REVERT: A 483 TYR cc_start: 0.8728 (t80) cc_final: 0.8444 (t80) REVERT: A 518 TYR cc_start: 0.7917 (t80) cc_final: 0.7348 (t80) REVERT: A 561 MET cc_start: 0.7091 (tmm) cc_final: 0.6749 (tmm) REVERT: B 272 MET cc_start: 0.8091 (tmm) cc_final: 0.7826 (tmm) REVERT: B 309 TYR cc_start: 0.7563 (t80) cc_final: 0.7160 (t80) REVERT: B 370 LEU cc_start: 0.9163 (tp) cc_final: 0.8949 (tp) REVERT: B 466 TYR cc_start: 0.7652 (m-80) cc_final: 0.7392 (m-80) REVERT: B 503 LEU cc_start: 0.8716 (tp) cc_final: 0.8222 (tt) REVERT: B 646 CYS cc_start: 0.7983 (m) cc_final: 0.7772 (m) REVERT: B 697 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6443 (tt0) REVERT: B 822 TRP cc_start: 0.8612 (t-100) cc_final: 0.8315 (t-100) outliers start: 20 outliers final: 11 residues processed: 135 average time/residue: 0.2256 time to fit residues: 41.6635 Evaluate side-chains 130 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 445 GLN Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 551 TYR Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 434 TRP Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 697 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 0.0980 chunk 69 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 110 optimal weight: 0.3980 chunk 54 optimal weight: 3.9990 chunk 98 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9413 Z= 0.196 Angle : 0.606 8.920 12807 Z= 0.312 Chirality : 0.040 0.207 1488 Planarity : 0.004 0.047 1592 Dihedral : 7.072 59.026 1639 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.19 % Allowed : 17.24 % Favored : 80.56 % 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: 0.25 (0.25), residues: 1142 helix: 1.24 (0.19), residues: 766 sheet: -1.63 (0.74), residues: 46 loop : -2.17 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 434 HIS 0.008 0.001 HIS A 665 PHE 0.021 0.001 PHE A 418 TYR 0.034 0.002 TYR A 465 ARG 0.008 0.000 ARG B 723 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 125 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 TYR cc_start: 0.8358 (t80) cc_final: 0.8063 (t80) REVERT: A 388 VAL cc_start: 0.8450 (p) cc_final: 0.8222 (p) REVERT: A 478 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8269 (tm-30) REVERT: A 483 TYR cc_start: 0.8682 (t80) cc_final: 0.8462 (t80) REVERT: A 518 TYR cc_start: 0.7865 (t80) cc_final: 0.7288 (t80) REVERT: A 552 ARG cc_start: 0.8205 (ppt170) cc_final: 0.7472 (ttp80) REVERT: A 561 MET cc_start: 0.7021 (tmm) cc_final: 0.6686 (tmm) REVERT: A 758 ASP cc_start: 0.8025 (m-30) cc_final: 0.7601 (t0) REVERT: B 272 MET cc_start: 0.8093 (tmm) cc_final: 0.7834 (tmm) REVERT: B 275 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7910 (tm-30) REVERT: B 309 TYR cc_start: 0.7470 (t80) cc_final: 0.7112 (t80) REVERT: B 370 LEU cc_start: 0.9173 (tp) cc_final: 0.8959 (tp) REVERT: B 466 TYR cc_start: 0.7678 (m-80) cc_final: 0.7424 (m-80) REVERT: B 503 LEU cc_start: 0.8695 (tp) cc_final: 0.8445 (tp) REVERT: B 646 CYS cc_start: 0.7968 (m) cc_final: 0.7762 (m) REVERT: B 697 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6549 (tt0) REVERT: B 822 TRP cc_start: 0.8608 (t-100) cc_final: 0.8310 (t-100) outliers start: 21 outliers final: 14 residues processed: 141 average time/residue: 0.2327 time to fit residues: 44.6371 Evaluate side-chains 131 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 551 TYR Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain B residue 434 TRP Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 697 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 45 optimal weight: 10.0000 chunk 94 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 98 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 HIS A 445 GLN ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9413 Z= 0.170 Angle : 0.608 12.760 12807 Z= 0.306 Chirality : 0.039 0.171 1488 Planarity : 0.003 0.046 1592 Dihedral : 6.625 59.167 1639 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.61 % Allowed : 19.33 % Favored : 78.06 % 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: 0.52 (0.25), residues: 1142 helix: 1.50 (0.19), residues: 761 sheet: -1.88 (0.68), residues: 53 loop : -2.08 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 360 HIS 0.005 0.001 HIS A 665 PHE 0.015 0.001 PHE A 418 TYR 0.038 0.002 TYR A 465 ARG 0.010 0.000 ARG B 723 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 139 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 TYR cc_start: 0.8326 (t80) cc_final: 0.7993 (t80) REVERT: A 388 VAL cc_start: 0.8412 (p) cc_final: 0.8172 (p) REVERT: A 390 ASN cc_start: 0.7603 (m110) cc_final: 0.7400 (m-40) REVERT: A 445 GLN cc_start: 0.7110 (OUTLIER) cc_final: 0.6491 (tm-30) REVERT: A 478 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8278 (tm-30) REVERT: A 483 TYR cc_start: 0.8699 (t80) cc_final: 0.8366 (t80) REVERT: A 518 TYR cc_start: 0.7818 (t80) cc_final: 0.7292 (t80) REVERT: A 552 ARG cc_start: 0.8243 (ppt170) cc_final: 0.7462 (ttp80) REVERT: A 561 MET cc_start: 0.6974 (tmm) cc_final: 0.6739 (tmm) REVERT: A 743 LYS cc_start: 0.7859 (tptp) cc_final: 0.7590 (tppt) REVERT: A 758 ASP cc_start: 0.8028 (m-30) cc_final: 0.7614 (t0) REVERT: B 272 MET cc_start: 0.8054 (tmm) cc_final: 0.7842 (tmm) REVERT: B 309 TYR cc_start: 0.7439 (t80) cc_final: 0.7098 (t80) REVERT: B 370 LEU cc_start: 0.9162 (tp) cc_final: 0.8955 (tp) REVERT: B 466 TYR cc_start: 0.7677 (m-80) cc_final: 0.7441 (m-80) REVERT: B 503 LEU cc_start: 0.8688 (tp) cc_final: 0.8442 (tp) REVERT: B 646 CYS cc_start: 0.7952 (m) cc_final: 0.7743 (m) REVERT: B 697 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6579 (tt0) REVERT: B 766 GLN cc_start: 0.9278 (OUTLIER) cc_final: 0.9054 (mp10) REVERT: B 822 TRP cc_start: 0.8601 (t-100) cc_final: 0.8289 (t-100) outliers start: 25 outliers final: 15 residues processed: 156 average time/residue: 0.2220 time to fit residues: 47.5908 Evaluate side-chains 139 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 121 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 445 GLN Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 551 TYR Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain B residue 434 TRP Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 766 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 HIS ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9413 Z= 0.194 Angle : 0.635 15.041 12807 Z= 0.316 Chirality : 0.040 0.235 1488 Planarity : 0.003 0.044 1592 Dihedral : 6.515 59.538 1639 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.51 % Allowed : 20.38 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.25), residues: 1142 helix: 1.62 (0.19), residues: 761 sheet: -1.64 (0.73), residues: 46 loop : -2.06 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 360 HIS 0.004 0.001 HIS B 352 PHE 0.017 0.001 PHE A 418 TYR 0.032 0.001 TYR A 465 ARG 0.006 0.000 ARG B 723 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ASN cc_start: 0.7698 (m-40) cc_final: 0.7479 (m110) REVERT: A 386 TYR cc_start: 0.8322 (t80) cc_final: 0.8058 (t80) REVERT: A 388 VAL cc_start: 0.8433 (OUTLIER) cc_final: 0.8194 (p) REVERT: A 465 TYR cc_start: 0.8993 (m-80) cc_final: 0.8730 (m-80) REVERT: A 478 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8289 (tm-30) REVERT: A 518 TYR cc_start: 0.7802 (t80) cc_final: 0.7278 (t80) REVERT: A 552 ARG cc_start: 0.8186 (ppt170) cc_final: 0.7411 (ttp80) REVERT: A 561 MET cc_start: 0.7014 (tmm) cc_final: 0.6761 (tmm) REVERT: B 272 MET cc_start: 0.8143 (tmm) cc_final: 0.7906 (tmm) REVERT: B 275 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7939 (tm-30) REVERT: B 309 TYR cc_start: 0.7453 (t80) cc_final: 0.7132 (t80) REVERT: B 370 LEU cc_start: 0.9164 (tp) cc_final: 0.8955 (tp) REVERT: B 466 TYR cc_start: 0.7680 (m-80) cc_final: 0.7453 (m-80) REVERT: B 503 LEU cc_start: 0.8653 (tp) cc_final: 0.8404 (tp) REVERT: B 576 ASP cc_start: 0.8090 (t0) cc_final: 0.7888 (t0) REVERT: B 646 CYS cc_start: 0.7949 (m) cc_final: 0.7740 (m) REVERT: B 697 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6569 (tt0) REVERT: B 822 TRP cc_start: 0.8582 (t-100) cc_final: 0.8265 (t-100) outliers start: 24 outliers final: 15 residues processed: 150 average time/residue: 0.2293 time to fit residues: 47.0770 Evaluate side-chains 145 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 551 TYR Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain B residue 434 TRP Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 766 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 92 optimal weight: 50.0000 chunk 61 optimal weight: 0.7980 chunk 109 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9413 Z= 0.287 Angle : 0.681 13.833 12807 Z= 0.341 Chirality : 0.042 0.161 1488 Planarity : 0.004 0.044 1592 Dihedral : 6.697 59.096 1639 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.51 % Allowed : 21.63 % Favored : 75.86 % 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: 0.51 (0.25), residues: 1142 helix: 1.46 (0.18), residues: 762 sheet: -1.91 (0.68), residues: 53 loop : -1.99 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 360 HIS 0.003 0.001 HIS B 354 PHE 0.028 0.002 PHE A 418 TYR 0.028 0.002 TYR A 465 ARG 0.007 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 127 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 VAL cc_start: 0.8472 (OUTLIER) cc_final: 0.8236 (p) REVERT: A 478 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8268 (tm-30) REVERT: A 509 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8552 (tt) REVERT: A 518 TYR cc_start: 0.7854 (t80) cc_final: 0.7304 (t80) REVERT: A 552 ARG cc_start: 0.8282 (ppt170) cc_final: 0.7618 (ttp80) REVERT: A 561 MET cc_start: 0.6974 (tmm) cc_final: 0.6659 (tmm) REVERT: A 758 ASP cc_start: 0.8026 (m-30) cc_final: 0.7650 (t0) REVERT: B 272 MET cc_start: 0.8226 (tmm) cc_final: 0.7975 (tmm) REVERT: B 309 TYR cc_start: 0.7657 (t80) cc_final: 0.7249 (t80) REVERT: B 371 ARG cc_start: 0.8944 (tmm-80) cc_final: 0.8625 (ttp80) REVERT: B 466 TYR cc_start: 0.7689 (m-80) cc_final: 0.7465 (m-80) REVERT: B 503 LEU cc_start: 0.8703 (tp) cc_final: 0.8450 (tp) REVERT: B 576 ASP cc_start: 0.8194 (t0) cc_final: 0.7975 (t0) REVERT: B 646 CYS cc_start: 0.7891 (m) cc_final: 0.7662 (m) REVERT: B 672 ASP cc_start: 0.8930 (m-30) cc_final: 0.7796 (p0) REVERT: B 697 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6614 (tt0) REVERT: B 822 TRP cc_start: 0.8574 (t-100) cc_final: 0.8249 (t-100) outliers start: 24 outliers final: 15 residues processed: 145 average time/residue: 0.2363 time to fit residues: 46.4538 Evaluate side-chains 143 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 125 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain B residue 434 TRP Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 766 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 33 optimal weight: 20.0000 chunk 21 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9413 Z= 0.184 Angle : 0.653 14.789 12807 Z= 0.321 Chirality : 0.040 0.148 1488 Planarity : 0.003 0.044 1592 Dihedral : 6.407 58.500 1639 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.40 % Allowed : 21.84 % Favored : 75.76 % 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: 0.72 (0.25), residues: 1142 helix: 1.67 (0.19), residues: 762 sheet: -1.87 (0.68), residues: 53 loop : -2.04 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 360 HIS 0.003 0.001 HIS A 665 PHE 0.014 0.001 PHE A 418 TYR 0.029 0.002 TYR A 465 ARG 0.004 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 136 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ASN cc_start: 0.7801 (m-40) cc_final: 0.7573 (m110) REVERT: A 388 VAL cc_start: 0.8432 (OUTLIER) cc_final: 0.8195 (p) REVERT: A 478 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8270 (tm-30) REVERT: A 509 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8514 (tt) REVERT: A 518 TYR cc_start: 0.7780 (t80) cc_final: 0.7218 (t80) REVERT: A 561 MET cc_start: 0.7000 (tmm) cc_final: 0.6755 (tmm) REVERT: A 743 LYS cc_start: 0.7894 (tppt) cc_final: 0.7570 (tppt) REVERT: A 758 ASP cc_start: 0.8022 (m-30) cc_final: 0.7643 (t0) REVERT: B 272 MET cc_start: 0.8151 (tmm) cc_final: 0.7932 (tmm) REVERT: B 275 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7598 (tm-30) REVERT: B 309 TYR cc_start: 0.7490 (t80) cc_final: 0.7139 (t80) REVERT: B 371 ARG cc_start: 0.8963 (tmm-80) cc_final: 0.8606 (ttp80) REVERT: B 466 TYR cc_start: 0.7663 (m-80) cc_final: 0.7444 (m-80) REVERT: B 503 LEU cc_start: 0.8690 (tp) cc_final: 0.8451 (tp) REVERT: B 576 ASP cc_start: 0.8136 (t0) cc_final: 0.7927 (t0) REVERT: B 646 CYS cc_start: 0.7911 (m) cc_final: 0.7694 (m) REVERT: B 672 ASP cc_start: 0.8903 (m-30) cc_final: 0.7816 (p0) REVERT: B 697 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6561 (tt0) REVERT: B 822 TRP cc_start: 0.8548 (t-100) cc_final: 0.8206 (t-100) outliers start: 23 outliers final: 15 residues processed: 151 average time/residue: 0.2360 time to fit residues: 48.3066 Evaluate side-chains 144 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain B residue 434 TRP Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 766 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 20.0000 chunk 102 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 31 optimal weight: 0.0770 chunk 92 optimal weight: 40.0000 chunk 67 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 HIS ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9413 Z= 0.215 Angle : 0.668 14.820 12807 Z= 0.329 Chirality : 0.041 0.320 1488 Planarity : 0.003 0.046 1592 Dihedral : 6.355 58.694 1639 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.51 % Allowed : 22.47 % Favored : 75.03 % 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: 0.69 (0.25), residues: 1142 helix: 1.64 (0.19), residues: 761 sheet: -1.84 (0.69), residues: 53 loop : -2.03 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 360 HIS 0.003 0.001 HIS A 665 PHE 0.018 0.001 PHE A 418 TYR 0.034 0.002 TYR A 483 ARG 0.006 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 135 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ASN cc_start: 0.7850 (m-40) cc_final: 0.7622 (m110) REVERT: A 388 VAL cc_start: 0.8462 (OUTLIER) cc_final: 0.8232 (p) REVERT: A 478 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8274 (tm-30) REVERT: A 500 THR cc_start: 0.8259 (m) cc_final: 0.8055 (m) REVERT: A 509 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8513 (tt) REVERT: A 518 TYR cc_start: 0.7786 (t80) cc_final: 0.7228 (t80) REVERT: A 561 MET cc_start: 0.6995 (tmm) cc_final: 0.6739 (tmm) REVERT: A 758 ASP cc_start: 0.8016 (m-30) cc_final: 0.7646 (t0) REVERT: B 272 MET cc_start: 0.8202 (tmm) cc_final: 0.7952 (tmm) REVERT: B 275 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7668 (tm-30) REVERT: B 309 TYR cc_start: 0.7535 (t80) cc_final: 0.7170 (t80) REVERT: B 371 ARG cc_start: 0.8953 (tmm-80) cc_final: 0.8604 (ttp80) REVERT: B 466 TYR cc_start: 0.7699 (m-80) cc_final: 0.7462 (m-80) REVERT: B 503 LEU cc_start: 0.8695 (tp) cc_final: 0.8452 (tp) REVERT: B 576 ASP cc_start: 0.8139 (t0) cc_final: 0.7937 (t0) REVERT: B 646 CYS cc_start: 0.7907 (m) cc_final: 0.7692 (m) REVERT: B 672 ASP cc_start: 0.8901 (m-30) cc_final: 0.7839 (p0) REVERT: B 697 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6449 (tt0) REVERT: B 822 TRP cc_start: 0.8538 (t-100) cc_final: 0.8194 (t-100) outliers start: 24 outliers final: 17 residues processed: 153 average time/residue: 0.2320 time to fit residues: 48.1865 Evaluate side-chains 147 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 551 TYR Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain B residue 434 TRP Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 766 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 20.0000 chunk 75 optimal weight: 0.7980 chunk 113 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS A 354 HIS ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 HIS ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9413 Z= 0.188 Angle : 0.686 15.177 12807 Z= 0.333 Chirality : 0.041 0.203 1488 Planarity : 0.003 0.047 1592 Dihedral : 6.227 59.250 1639 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.19 % Allowed : 22.57 % Favored : 75.24 % 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: 0.80 (0.25), residues: 1142 helix: 1.71 (0.19), residues: 761 sheet: -1.79 (0.70), residues: 53 loop : -1.96 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 360 HIS 0.003 0.001 HIS A 665 PHE 0.014 0.001 PHE A 418 TYR 0.038 0.002 TYR A 465 ARG 0.007 0.000 ARG A 439 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 135 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ASN cc_start: 0.7790 (m-40) cc_final: 0.7575 (m110) REVERT: A 388 VAL cc_start: 0.8428 (OUTLIER) cc_final: 0.8181 (p) REVERT: A 478 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8298 (tm-30) REVERT: A 500 THR cc_start: 0.8239 (m) cc_final: 0.8026 (m) REVERT: A 509 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8500 (tt) REVERT: A 518 TYR cc_start: 0.7756 (t80) cc_final: 0.7208 (t80) REVERT: A 561 MET cc_start: 0.7040 (tmm) cc_final: 0.6799 (tmm) REVERT: A 743 LYS cc_start: 0.7904 (tppt) cc_final: 0.7514 (tppt) REVERT: A 758 ASP cc_start: 0.8008 (m-30) cc_final: 0.7635 (t0) REVERT: B 275 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7900 (tm-30) REVERT: B 309 TYR cc_start: 0.7472 (t80) cc_final: 0.7134 (t80) REVERT: B 371 ARG cc_start: 0.8930 (tmm-80) cc_final: 0.8594 (ttp80) REVERT: B 466 TYR cc_start: 0.7712 (m-80) cc_final: 0.7496 (m-80) REVERT: B 503 LEU cc_start: 0.8695 (tp) cc_final: 0.8464 (tp) REVERT: B 576 ASP cc_start: 0.8105 (t0) cc_final: 0.7904 (t0) REVERT: B 672 ASP cc_start: 0.8868 (m-30) cc_final: 0.7846 (p0) REVERT: B 822 TRP cc_start: 0.8509 (t-100) cc_final: 0.8166 (t-100) outliers start: 21 outliers final: 14 residues processed: 150 average time/residue: 0.2264 time to fit residues: 46.6494 Evaluate side-chains 149 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 133 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 551 TYR Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain B residue 434 TRP Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 766 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.4980 chunk 13 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 5 optimal weight: 0.4980 chunk 65 optimal weight: 0.0050 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS A 354 HIS ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 HIS ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 GLN B 783 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5272 r_free = 0.5272 target = 0.231711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.162875 restraints weight = 17825.024| |-----------------------------------------------------------------------------| r_work (start): 0.4533 rms_B_bonded: 3.56 r_work: 0.4391 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.4391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4311 r_free = 0.4311 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4310 r_free = 0.4310 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.4310 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9413 Z= 0.175 Angle : 0.690 15.485 12807 Z= 0.334 Chirality : 0.040 0.154 1488 Planarity : 0.003 0.045 1592 Dihedral : 6.062 59.201 1637 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.88 % Allowed : 23.09 % Favored : 75.03 % 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: 0.90 (0.25), residues: 1142 helix: 1.80 (0.19), residues: 762 sheet: -1.54 (0.72), residues: 52 loop : -2.02 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 360 HIS 0.003 0.001 HIS A 665 PHE 0.011 0.001 PHE A 418 TYR 0.023 0.001 TYR A 483 ARG 0.007 0.000 ARG A 439 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2320.77 seconds wall clock time: 42 minutes 50.64 seconds (2570.64 seconds total)