Starting phenix.real_space_refine on Fri Mar 15 04:31:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7i_9934/03_2024/6k7i_9934.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7i_9934/03_2024/6k7i_9934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7i_9934/03_2024/6k7i_9934.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7i_9934/03_2024/6k7i_9934.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7i_9934/03_2024/6k7i_9934.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7i_9934/03_2024/6k7i_9934.pdb" } resolution = 3.22 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 56 5.16 5 C 6857 2.51 5 N 1753 2.21 5 O 1921 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 98": "NH1" <-> "NH2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 168": "OD1" <-> "OD2" Residue "A ASP 208": "OD1" <-> "OD2" Residue "A TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 478": "OE1" <-> "OE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 601": "OE1" <-> "OE2" Residue "A TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 786": "OD1" <-> "OD2" Residue "A ASP 816": "OD1" <-> "OD2" Residue "A TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 863": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 908": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 926": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 950": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 962": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 968": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 972": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 991": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1031": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C ARG 162": "NH1" <-> "NH2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 225": "OE1" <-> "OE2" Residue "C ARG 290": "NH1" <-> "NH2" Residue "C TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10590 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7853 Classifications: {'peptide': 986} Link IDs: {'PTRANS': 30, 'TRANS': 955} Chain breaks: 3 Chain: "C" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2604 Classifications: {'peptide': 324} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 299} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ACP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'NAG': 2, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.34, per 1000 atoms: 0.60 Number of scatterers: 10590 At special positions: 0 Unit cell: (72.21, 112.88, 168.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 P 3 15.00 O 1921 8.00 N 1753 7.00 C 6857 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.02 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.04 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 Links applied ALPHA1-4 " NAG B 2 " - " MAN B 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN C 180 " " NAG C 401 " - " ASN C 294 " " NAG C 402 " - " ASN C 107 " Time building additional restraints: 4.17 Conformation dependent library (CDL) restraints added in 2.0 seconds 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2466 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 9 sheets defined 47.8% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 60 through 62 No H-bonds generated for 'chain 'A' and resid 60 through 62' Processing helix chain 'A' and resid 63 through 74 Processing helix chain 'A' and resid 75 through 88 removed outlier: 3.628A pdb=" N SER A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 129 Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.525A pdb=" N ALA A 179 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET A 180 " --> pdb=" O PRO A 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 176 through 180' Processing helix chain 'A' and resid 208 through 214 Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 288 through 323 Processing helix chain 'A' and resid 339 through 352 Processing helix chain 'A' and resid 353 through 355 No H-bonds generated for 'chain 'A' and resid 353 through 355' Processing helix chain 'A' and resid 358 through 377 Processing helix chain 'A' and resid 393 through 401 removed outlier: 4.213A pdb=" N LEU A 396 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N GLU A 398 " --> pdb=" O ASN A 395 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 400 " --> pdb=" O ASN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 455 Processing helix chain 'A' and resid 458 through 472 removed outlier: 4.361A pdb=" N GLU A 464 " --> pdb=" O PRO A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 502 Processing helix chain 'A' and resid 559 through 567 removed outlier: 3.850A pdb=" N ARG A 566 " --> pdb=" O VAL A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 585 Processing helix chain 'A' and resid 600 through 617 removed outlier: 4.617A pdb=" N SER A 617 " --> pdb=" O ARG A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 623 removed outlier: 3.575A pdb=" N LEU A 622 " --> pdb=" O GLN A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 631 Processing helix chain 'A' and resid 651 through 662 Processing helix chain 'A' and resid 673 through 681 removed outlier: 4.490A pdb=" N ASN A 679 " --> pdb=" O GLU A 675 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY A 681 " --> pdb=" O ALA A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 738 Processing helix chain 'A' and resid 742 through 751 Processing helix chain 'A' and resid 762 through 777 removed outlier: 3.585A pdb=" N GLN A 776 " --> pdb=" O MET A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 797 Processing helix chain 'A' and resid 809 through 815 Processing helix chain 'A' and resid 823 through 833 removed outlier: 4.349A pdb=" N ASN A 827 " --> pdb=" O LYS A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 856 removed outlier: 4.092A pdb=" N ASN A 838 " --> pdb=" O ALA A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 866 removed outlier: 3.699A pdb=" N TRP A 860 " --> pdb=" O ILE A 856 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL A 864 " --> pdb=" O TRP A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 879 Processing helix chain 'A' and resid 887 through 896 removed outlier: 4.185A pdb=" N LEU A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 908 Processing helix chain 'A' and resid 910 through 918 removed outlier: 3.650A pdb=" N THR A 914 " --> pdb=" O GLU A 910 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN A 916 " --> pdb=" O TYR A 912 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 917 " --> pdb=" O LYS A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 948 Proline residue: A 944 - end of helix Processing helix chain 'A' and resid 961 through 985 removed outlier: 4.419A pdb=" N LEU A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 972 " --> pdb=" O PHE A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1011 Processing helix chain 'A' and resid 1025 through 1033 Processing helix chain 'A' and resid 1035 through 1061 removed outlier: 4.066A pdb=" N LEU A1041 " --> pdb=" O TRP A1037 " (cutoff:3.500A) Proline residue: A1044 - end of helix removed outlier: 4.942A pdb=" N LEU A1050 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ASP A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 74 Proline residue: C 52 - end of helix removed outlier: 3.520A pdb=" N PHE C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE C 56 " --> pdb=" O PRO C 52 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU C 59 " --> pdb=" O PHE C 55 " (cutoff:3.500A) Proline residue: C 63 - end of helix Processing helix chain 'C' and resid 89 through 95 removed outlier: 4.002A pdb=" N LYS C 93 " --> pdb=" O PRO C 90 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU C 95 " --> pdb=" O ASN C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 136 Processing helix chain 'C' and resid 139 through 144 Processing helix chain 'C' and resid 146 through 152 Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 222 through 227 Processing helix chain 'C' and resid 239 through 243 Processing helix chain 'C' and resid 254 through 262 Processing helix chain 'C' and resid 323 through 350 Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 144 through 147 removed outlier: 3.639A pdb=" N GLU A 144 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLN A 136 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR A 169 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA4, first strand: chain 'A' and resid 390 through 391 removed outlier: 6.554A pdb=" N THR A 781 " --> pdb=" O VAL A 799 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N VAL A 801 " --> pdb=" O THR A 781 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ALA A 783 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ILE A 803 " --> pdb=" O ALA A 783 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLY A 785 " --> pdb=" O ILE A 803 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL A 780 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LYS A 404 " --> pdb=" O LYS A 665 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N TRP A 667 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE A 406 " --> pdb=" O TRP A 667 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE A 666 " --> pdb=" O VAL A 756 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N CYS A 758 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE A 668 " --> pdb=" O CYS A 758 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU A 727 " --> pdb=" O ILE A 757 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE A 694 " --> pdb=" O ILE A 728 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 415 through 425 removed outlier: 6.101A pdb=" N VAL A 418 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LYS A 647 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA A 643 " --> pdb=" O LYS A 422 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N CYS A 424 " --> pdb=" O ALA A 641 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ALA A 641 " --> pdb=" O CYS A 424 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LEU A 638 " --> pdb=" O VAL A 596 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL A 596 " --> pdb=" O LEU A 638 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY A 640 " --> pdb=" O PHE A 594 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 592 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 544 " --> pdb=" O ASN A 530 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASN A 530 " --> pdb=" O ILE A 544 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 507 through 509 removed outlier: 6.621A pdb=" N PHE A 507 " --> pdb=" O ILE A 517 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ILE A 517 " --> pdb=" O PHE A 507 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 509 " --> pdb=" O VAL A 515 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 81 removed outlier: 5.715A pdb=" N TYR C 122 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LEU C 272 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU C 124 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ARG C 270 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 102 through 103 removed outlier: 4.473A pdb=" N CYS C 102 " --> pdb=" O TYR C 297 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 108 through 110 removed outlier: 3.503A pdb=" N PHE C 108 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) 461 hydrogen bonds defined for protein. 1329 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: 3.03 Time building geometry restraints manager: 4.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1784 1.32 - 1.44: 2914 1.44 - 1.57: 6050 1.57 - 1.69: 6 1.69 - 1.82: 87 Bond restraints: 10841 Sorted by residual: bond pdb=" O2B ACP A1201 " pdb=" PB ACP A1201 " ideal model delta sigma weight residual 1.507 1.614 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" O3A ACP A1201 " pdb=" PB ACP A1201 " ideal model delta sigma weight residual 1.698 1.603 0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C4 ACP A1201 " pdb=" C5 ACP A1201 " ideal model delta sigma weight residual 1.386 1.469 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" O3G ACP A1201 " pdb=" PG ACP A1201 " ideal model delta sigma weight residual 1.532 1.607 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C5 ACP A1201 " pdb=" C6 ACP A1201 " ideal model delta sigma weight residual 1.407 1.479 -0.072 2.00e-02 2.50e+03 1.29e+01 ... (remaining 10836 not shown) Histogram of bond angle deviations from ideal: 96.55 - 104.49: 185 104.49 - 112.43: 5345 112.43 - 120.37: 5065 120.37 - 128.31: 4015 128.31 - 136.25: 112 Bond angle restraints: 14722 Sorted by residual: angle pdb=" C LEU A 687 " pdb=" N LYS A 688 " pdb=" CA LYS A 688 " ideal model delta sigma weight residual 121.54 134.13 -12.59 1.91e+00 2.74e-01 4.34e+01 angle pdb=" C SER A 175 " pdb=" N GLU A 176 " pdb=" CA GLU A 176 " ideal model delta sigma weight residual 120.97 135.49 -14.52 2.84e+00 1.24e-01 2.61e+01 angle pdb=" C PRO A 384 " pdb=" N THR A 385 " pdb=" CA THR A 385 " ideal model delta sigma weight residual 121.54 131.22 -9.68 1.91e+00 2.74e-01 2.57e+01 angle pdb=" C LYS A 688 " pdb=" N LYS A 689 " pdb=" CA LYS A 689 " ideal model delta sigma weight residual 121.54 130.84 -9.30 1.91e+00 2.74e-01 2.37e+01 angle pdb=" C ALA A 57 " pdb=" N LYS A 58 " pdb=" CA LYS A 58 " ideal model delta sigma weight residual 121.54 130.66 -9.12 1.91e+00 2.74e-01 2.28e+01 ... (remaining 14717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.47: 6025 22.47 - 44.94: 486 44.94 - 67.40: 49 67.40 - 89.87: 15 89.87 - 112.34: 3 Dihedral angle restraints: 6578 sinusoidal: 2755 harmonic: 3823 Sorted by residual: dihedral pdb=" CA ARG A 510 " pdb=" C ARG A 510 " pdb=" N THR A 511 " pdb=" CA THR A 511 " ideal model delta harmonic sigma weight residual 180.00 144.75 35.25 0 5.00e+00 4.00e-02 4.97e+01 dihedral pdb=" CA HIS A 682 " pdb=" C HIS A 682 " pdb=" N SER A 683 " pdb=" CA SER A 683 " ideal model delta harmonic sigma weight residual 180.00 147.44 32.56 0 5.00e+00 4.00e-02 4.24e+01 dihedral pdb=" CA PHE A 534 " pdb=" C PHE A 534 " pdb=" N THR A 535 " pdb=" CA THR A 535 " ideal model delta harmonic sigma weight residual -180.00 -150.71 -29.29 0 5.00e+00 4.00e-02 3.43e+01 ... (remaining 6575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1415 0.100 - 0.199: 244 0.199 - 0.298: 19 0.298 - 0.398: 3 0.398 - 0.497: 2 Chirality restraints: 1683 Sorted by residual: chirality pdb=" CB ILE A 159 " pdb=" CA ILE A 159 " pdb=" CG1 ILE A 159 " pdb=" CG2 ILE A 159 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.50 2.00e-01 2.50e+01 6.19e+00 chirality pdb=" CB THR A 511 " pdb=" CA THR A 511 " pdb=" OG1 THR A 511 " pdb=" CG2 THR A 511 " both_signs ideal model delta sigma weight residual False 2.55 2.14 0.41 2.00e-01 2.50e+01 4.29e+00 chirality pdb=" C1 NAG C 401 " pdb=" ND2 ASN C 294 " pdb=" C2 NAG C 401 " pdb=" O5 NAG C 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.88e+00 ... (remaining 1680 not shown) Planarity restraints: 1835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.356 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG B 1 " -0.089 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.136 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.543 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " 0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 402 " -0.254 2.00e-02 2.50e+03 2.11e-01 5.58e+02 pdb=" C7 NAG C 402 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG C 402 " -0.175 2.00e-02 2.50e+03 pdb=" N2 NAG C 402 " 0.351 2.00e-02 2.50e+03 pdb=" O7 NAG C 402 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " 0.167 2.00e-02 2.50e+03 1.38e-01 2.40e+02 pdb=" C7 NAG C 401 " -0.046 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " 0.123 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " -0.225 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " -0.019 2.00e-02 2.50e+03 ... (remaining 1832 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2461 2.78 - 3.31: 9477 3.31 - 3.84: 17662 3.84 - 4.37: 21051 4.37 - 4.90: 36325 Nonbonded interactions: 86976 Sorted by model distance: nonbonded pdb=" O ASP A 409 " pdb=" OG1 THR A 413 " model vdw 2.253 2.440 nonbonded pdb=" OG1 THR A 670 " pdb=" N GLY A 671 " model vdw 2.309 2.520 nonbonded pdb=" O TYR A 881 " pdb=" OG1 THR A 886 " model vdw 2.310 2.440 nonbonded pdb=" O TYR A 573 " pdb=" OG1 THR A 577 " model vdw 2.314 2.440 nonbonded pdb=" O SER A 394 " pdb=" ND2 ASN A 397 " model vdw 2.316 2.520 ... (remaining 86971 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.130 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 30.780 Find NCS groups from input model: 0.290 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 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 : 0.015 0.128 10841 Z= 0.955 Angle : 1.315 14.519 14722 Z= 0.692 Chirality : 0.076 0.497 1683 Planarity : 0.013 0.306 1832 Dihedral : 15.636 112.339 4103 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.92 % Favored : 90.69 % Rotamer: Outliers : 0.78 % Allowed : 8.43 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.41 (0.18), residues: 1300 helix: -2.90 (0.15), residues: 587 sheet: -1.92 (0.38), residues: 149 loop : -3.13 (0.22), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP A 860 HIS 0.009 0.002 HIS A 124 PHE 0.039 0.004 PHE C 304 TYR 0.035 0.004 TYR A 59 ARG 0.016 0.001 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 133 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.6687 (mmtt) cc_final: 0.4681 (mttm) REVERT: A 392 ARG cc_start: 0.7757 (mtt-85) cc_final: 0.7326 (mtt-85) REVERT: A 663 ASP cc_start: 0.7688 (t70) cc_final: 0.7299 (t0) REVERT: A 693 MET cc_start: 0.1202 (mmt) cc_final: -0.0638 (tpp) REVERT: A 727 LEU cc_start: 0.6848 (mp) cc_final: 0.6625 (mt) REVERT: A 732 LYS cc_start: 0.7982 (mttm) cc_final: 0.7328 (tptp) REVERT: A 1013 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8018 (pp) REVERT: C 151 LEU cc_start: 0.8640 (mt) cc_final: 0.8423 (mt) REVERT: C 184 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8052 (mt-10) REVERT: C 337 PHE cc_start: 0.8131 (t80) cc_final: 0.7924 (t80) outliers start: 9 outliers final: 7 residues processed: 141 average time/residue: 0.2614 time to fit residues: 51.0959 Evaluate side-chains 114 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 106 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 922 ASN Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain C residue 195 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 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 60 ASN A 78 ASN A 124 HIS A 134 GLN A 279 ASN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 HIS A 434 ASN A 679 ASN ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 813 ASN A 838 ASN C 36 GLN C 131 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10841 Z= 0.200 Angle : 0.692 8.941 14722 Z= 0.356 Chirality : 0.047 0.434 1683 Planarity : 0.005 0.053 1832 Dihedral : 10.880 106.865 1632 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.85 % Favored : 93.00 % Rotamer: Outliers : 2.35 % Allowed : 10.96 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.93 (0.21), residues: 1300 helix: -1.29 (0.19), residues: 572 sheet: -1.46 (0.40), residues: 146 loop : -2.73 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 927 HIS 0.004 0.001 HIS A 682 PHE 0.023 0.001 PHE A 368 TYR 0.015 0.001 TYR A 59 ARG 0.005 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 122 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.6478 (mmtt) cc_final: 0.4516 (mttt) REVERT: A 390 MET cc_start: 0.7026 (ttt) cc_final: 0.6596 (ttm) REVERT: A 663 ASP cc_start: 0.7792 (t0) cc_final: 0.7351 (t0) REVERT: A 693 MET cc_start: 0.1358 (mmt) cc_final: -0.0472 (tpp) REVERT: A 732 LYS cc_start: 0.7927 (mttm) cc_final: 0.7374 (tptp) REVERT: A 747 LEU cc_start: 0.6252 (OUTLIER) cc_final: 0.6032 (mm) REVERT: A 831 ILE cc_start: 0.8399 (pt) cc_final: 0.7992 (mt) REVERT: A 874 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7732 (tp30) REVERT: A 1013 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7472 (pp) REVERT: C 102 CYS cc_start: 0.6515 (p) cc_final: 0.6224 (p) REVERT: C 184 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7832 (mt-10) REVERT: C 337 PHE cc_start: 0.7956 (t80) cc_final: 0.7724 (t80) outliers start: 27 outliers final: 10 residues processed: 144 average time/residue: 0.2383 time to fit residues: 47.9933 Evaluate side-chains 118 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 434 ASN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 922 ASN Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 165 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 98 optimal weight: 0.1980 chunk 80 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 127 optimal weight: 0.0670 chunk 105 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 40 optimal weight: 20.0000 chunk 94 optimal weight: 0.0470 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 ASN ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 813 ASN C 92 ASN C 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10841 Z= 0.171 Angle : 0.639 9.435 14722 Z= 0.324 Chirality : 0.046 0.382 1683 Planarity : 0.004 0.059 1832 Dihedral : 10.196 96.980 1629 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.46 % Favored : 92.46 % Rotamer: Outliers : 2.43 % Allowed : 13.48 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: -2.23 (0.22), residues: 1300 helix: -0.54 (0.20), residues: 574 sheet: -1.23 (0.40), residues: 148 loop : -2.53 (0.23), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 927 HIS 0.004 0.001 HIS A 682 PHE 0.018 0.001 PHE A 368 TYR 0.011 0.001 TYR A 382 ARG 0.003 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 110 time to evaluate : 1.220 Fit side-chains revert: symmetry clash REVERT: A 207 LYS cc_start: 0.6382 (mmtt) cc_final: 0.4543 (mttt) REVERT: A 260 THR cc_start: 0.2883 (OUTLIER) cc_final: 0.2562 (p) REVERT: A 263 VAL cc_start: 0.6268 (OUTLIER) cc_final: 0.5939 (m) REVERT: A 663 ASP cc_start: 0.7830 (t0) cc_final: 0.7404 (t0) REVERT: A 693 MET cc_start: 0.0974 (mmt) cc_final: -0.0788 (tpp) REVERT: A 732 LYS cc_start: 0.7877 (mttm) cc_final: 0.7371 (tptp) REVERT: A 747 LEU cc_start: 0.6393 (OUTLIER) cc_final: 0.6146 (mm) REVERT: A 826 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7968 (ttmm) REVERT: A 831 ILE cc_start: 0.8239 (pt) cc_final: 0.8020 (mt) REVERT: A 874 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7653 (tp30) REVERT: A 1013 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7413 (pp) REVERT: C 102 CYS cc_start: 0.6523 (p) cc_final: 0.6272 (p) REVERT: C 152 ASN cc_start: 0.7898 (t0) cc_final: 0.7571 (t0) REVERT: C 184 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7791 (mt-10) REVERT: C 337 PHE cc_start: 0.7954 (t80) cc_final: 0.7721 (t80) outliers start: 28 outliers final: 10 residues processed: 133 average time/residue: 0.2446 time to fit residues: 46.0222 Evaluate side-chains 116 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 195 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 56 optimal weight: 40.0000 chunk 79 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10841 Z= 0.240 Angle : 0.653 10.457 14722 Z= 0.331 Chirality : 0.047 0.341 1683 Planarity : 0.004 0.046 1832 Dihedral : 9.724 93.674 1626 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.23 % Favored : 92.69 % Rotamer: Outliers : 2.87 % Allowed : 15.48 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1300 helix: -0.24 (0.21), residues: 579 sheet: -1.11 (0.41), residues: 144 loop : -2.26 (0.24), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 927 HIS 0.004 0.001 HIS A 682 PHE 0.018 0.001 PHE A 368 TYR 0.014 0.001 TYR C 297 ARG 0.003 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 104 time to evaluate : 1.106 Fit side-chains revert: symmetry clash REVERT: A 207 LYS cc_start: 0.6374 (mmtt) cc_final: 0.4468 (mttt) REVERT: A 644 ILE cc_start: 0.2291 (OUTLIER) cc_final: 0.2002 (pt) REVERT: A 663 ASP cc_start: 0.7927 (t0) cc_final: 0.7527 (t0) REVERT: A 693 MET cc_start: 0.0813 (mmt) cc_final: -0.0912 (tpp) REVERT: A 732 LYS cc_start: 0.7890 (mttm) cc_final: 0.7376 (tptp) REVERT: A 747 LEU cc_start: 0.6387 (OUTLIER) cc_final: 0.6118 (mm) REVERT: A 831 ILE cc_start: 0.8454 (pt) cc_final: 0.8088 (mt) REVERT: A 874 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7713 (tp30) REVERT: A 1013 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7498 (pp) REVERT: C 102 CYS cc_start: 0.6541 (p) cc_final: 0.6308 (p) REVERT: C 184 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7812 (mt-10) REVERT: C 337 PHE cc_start: 0.7978 (t80) cc_final: 0.7698 (t80) outliers start: 33 outliers final: 16 residues processed: 131 average time/residue: 0.2362 time to fit residues: 44.4636 Evaluate side-chains 116 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 922 ASN Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 195 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 51 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 10841 Z= 0.411 Angle : 0.732 10.471 14722 Z= 0.370 Chirality : 0.051 0.313 1683 Planarity : 0.005 0.048 1832 Dihedral : 9.626 89.551 1626 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.85 % Favored : 92.00 % Rotamer: Outliers : 3.30 % Allowed : 16.61 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: -1.92 (0.22), residues: 1300 helix: -0.39 (0.21), residues: 585 sheet: -1.31 (0.40), residues: 154 loop : -2.18 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 927 HIS 0.006 0.001 HIS A 682 PHE 0.020 0.002 PHE A 368 TYR 0.020 0.002 TYR C 122 ARG 0.005 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 103 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.6441 (mmtt) cc_final: 0.4607 (mttt) REVERT: A 260 THR cc_start: 0.3257 (OUTLIER) cc_final: 0.2939 (p) REVERT: A 644 ILE cc_start: 0.2480 (OUTLIER) cc_final: 0.2196 (pt) REVERT: A 663 ASP cc_start: 0.7861 (t0) cc_final: 0.7440 (t0) REVERT: A 693 MET cc_start: 0.0963 (mmt) cc_final: -0.0763 (tpp) REVERT: A 732 LYS cc_start: 0.7804 (mttm) cc_final: 0.7299 (tptp) REVERT: A 747 LEU cc_start: 0.6402 (OUTLIER) cc_final: 0.6128 (mm) REVERT: A 874 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7824 (tp30) REVERT: A 1013 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7560 (pp) REVERT: C 102 CYS cc_start: 0.6412 (p) cc_final: 0.6201 (p) REVERT: C 184 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7863 (mt-10) REVERT: C 337 PHE cc_start: 0.8047 (t80) cc_final: 0.7739 (t80) outliers start: 38 outliers final: 21 residues processed: 134 average time/residue: 0.2420 time to fit residues: 46.2416 Evaluate side-chains 124 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 98 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 922 ASN Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 195 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 40.0000 chunk 113 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10841 Z= 0.302 Angle : 0.678 10.148 14722 Z= 0.341 Chirality : 0.048 0.309 1683 Planarity : 0.004 0.044 1832 Dihedral : 9.109 89.358 1626 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.31 % Favored : 92.62 % Rotamer: Outliers : 2.52 % Allowed : 18.00 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.22), residues: 1300 helix: -0.22 (0.21), residues: 581 sheet: -1.15 (0.41), residues: 148 loop : -2.16 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 927 HIS 0.005 0.001 HIS A 682 PHE 0.018 0.002 PHE A 368 TYR 0.015 0.002 TYR C 297 ARG 0.003 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 102 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.6437 (mmtt) cc_final: 0.4617 (mttt) REVERT: A 260 THR cc_start: 0.3087 (OUTLIER) cc_final: 0.2774 (p) REVERT: A 644 ILE cc_start: 0.2510 (OUTLIER) cc_final: 0.2240 (pt) REVERT: A 663 ASP cc_start: 0.7789 (t0) cc_final: 0.7367 (t0) REVERT: A 693 MET cc_start: 0.1020 (mmt) cc_final: -0.0709 (tpp) REVERT: A 732 LYS cc_start: 0.7830 (mttm) cc_final: 0.7268 (tptp) REVERT: A 747 LEU cc_start: 0.6311 (OUTLIER) cc_final: 0.6045 (mm) REVERT: A 874 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7823 (tp30) REVERT: A 1013 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7492 (pp) REVERT: C 102 CYS cc_start: 0.6415 (p) cc_final: 0.6200 (p) REVERT: C 184 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7832 (mt-10) REVERT: C 337 PHE cc_start: 0.8022 (t80) cc_final: 0.7717 (t80) outliers start: 29 outliers final: 22 residues processed: 125 average time/residue: 0.2390 time to fit residues: 42.5553 Evaluate side-chains 121 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 94 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 922 ASN Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 223 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 0.6980 chunk 14 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 57 optimal weight: 0.0970 chunk 77 optimal weight: 0.6980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10841 Z= 0.158 Angle : 0.600 9.182 14722 Z= 0.301 Chirality : 0.044 0.298 1683 Planarity : 0.004 0.042 1832 Dihedral : 8.438 85.914 1626 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.17 % Allowed : 18.87 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: -1.33 (0.23), residues: 1300 helix: 0.24 (0.22), residues: 580 sheet: -1.03 (0.42), residues: 144 loop : -2.03 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 927 HIS 0.004 0.001 HIS A 832 PHE 0.015 0.001 PHE A 368 TYR 0.010 0.001 TYR C 121 ARG 0.008 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 102 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.6404 (mmtt) cc_final: 0.4534 (mttt) REVERT: A 261 GLN cc_start: 0.6661 (OUTLIER) cc_final: 0.6422 (tm-30) REVERT: A 644 ILE cc_start: 0.2454 (OUTLIER) cc_final: 0.2240 (pt) REVERT: A 663 ASP cc_start: 0.7763 (t0) cc_final: 0.7354 (t0) REVERT: A 693 MET cc_start: 0.1047 (mmt) cc_final: -0.0733 (tpp) REVERT: A 732 LYS cc_start: 0.7697 (mttm) cc_final: 0.7212 (tptp) REVERT: A 747 LEU cc_start: 0.6291 (OUTLIER) cc_final: 0.6048 (mm) REVERT: A 874 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7603 (tp30) REVERT: A 1013 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7442 (pp) REVERT: C 102 CYS cc_start: 0.6540 (p) cc_final: 0.6311 (p) REVERT: C 184 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7698 (mt-10) REVERT: C 337 PHE cc_start: 0.8010 (t80) cc_final: 0.7729 (t80) outliers start: 25 outliers final: 14 residues processed: 125 average time/residue: 0.2118 time to fit residues: 38.4520 Evaluate side-chains 116 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 97 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 922 ASN Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 165 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 9.9990 chunk 74 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 11 optimal weight: 0.0970 chunk 98 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10841 Z= 0.205 Angle : 0.622 11.401 14722 Z= 0.312 Chirality : 0.045 0.316 1683 Planarity : 0.004 0.042 1832 Dihedral : 8.318 82.734 1626 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.35 % Allowed : 18.70 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.23), residues: 1300 helix: 0.41 (0.22), residues: 568 sheet: -0.94 (0.42), residues: 144 loop : -2.00 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 927 HIS 0.004 0.001 HIS A 323 PHE 0.015 0.001 PHE A 368 TYR 0.011 0.001 TYR C 297 ARG 0.005 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 98 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.6426 (mmtt) cc_final: 0.4556 (mttt) REVERT: A 663 ASP cc_start: 0.7747 (t0) cc_final: 0.7339 (t0) REVERT: A 693 MET cc_start: 0.1071 (mmt) cc_final: -0.0670 (tpp) REVERT: A 732 LYS cc_start: 0.7626 (mttm) cc_final: 0.7199 (tptp) REVERT: A 747 LEU cc_start: 0.6269 (OUTLIER) cc_final: 0.6030 (mm) REVERT: A 1013 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7469 (pp) REVERT: C 102 CYS cc_start: 0.6553 (p) cc_final: 0.6329 (p) REVERT: C 184 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7732 (mt-10) REVERT: C 337 PHE cc_start: 0.8033 (t80) cc_final: 0.7761 (t80) outliers start: 27 outliers final: 18 residues processed: 122 average time/residue: 0.2261 time to fit residues: 40.1799 Evaluate side-chains 116 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 922 ASN Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 195 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 70 optimal weight: 0.1980 chunk 50 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 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 261 GLN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10841 Z= 0.226 Angle : 0.631 12.090 14722 Z= 0.316 Chirality : 0.045 0.308 1683 Planarity : 0.004 0.043 1832 Dihedral : 8.177 76.364 1626 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.17 % Allowed : 18.78 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.23), residues: 1300 helix: 0.36 (0.22), residues: 574 sheet: -0.99 (0.41), residues: 150 loop : -1.98 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 927 HIS 0.004 0.001 HIS A 323 PHE 0.015 0.001 PHE A 368 TYR 0.013 0.001 TYR C 297 ARG 0.005 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 98 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.6426 (mmtt) cc_final: 0.4567 (mttt) REVERT: A 663 ASP cc_start: 0.7741 (t0) cc_final: 0.7496 (t0) REVERT: A 693 MET cc_start: 0.0977 (mmt) cc_final: -0.0767 (tpp) REVERT: A 732 LYS cc_start: 0.7613 (mttm) cc_final: 0.7155 (tptp) REVERT: A 747 LEU cc_start: 0.6244 (OUTLIER) cc_final: 0.6001 (mm) REVERT: A 1013 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7512 (pp) REVERT: C 102 CYS cc_start: 0.6530 (p) cc_final: 0.6302 (p) REVERT: C 184 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7801 (mt-10) REVERT: C 337 PHE cc_start: 0.8051 (t80) cc_final: 0.7743 (t80) outliers start: 25 outliers final: 21 residues processed: 120 average time/residue: 0.2364 time to fit residues: 41.3007 Evaluate side-chains 118 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 95 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 922 ASN Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 195 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 0.0070 chunk 58 optimal weight: 0.0970 chunk 85 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 chunk 103 optimal weight: 0.0010 chunk 10 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 81 optimal weight: 0.1980 chunk 109 optimal weight: 0.8980 overall best weight: 0.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10841 Z= 0.140 Angle : 0.593 12.442 14722 Z= 0.297 Chirality : 0.044 0.306 1683 Planarity : 0.004 0.048 1832 Dihedral : 7.833 69.377 1626 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.39 % Allowed : 19.57 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: -0.95 (0.23), residues: 1300 helix: 0.66 (0.22), residues: 570 sheet: -0.95 (0.39), residues: 171 loop : -1.90 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 927 HIS 0.005 0.001 HIS A 264 PHE 0.013 0.001 PHE A 368 TYR 0.010 0.001 TYR C 121 ARG 0.005 0.000 ARG C 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.6312 (mmtt) cc_final: 0.4475 (mttt) REVERT: A 326 LYS cc_start: 0.8314 (mttt) cc_final: 0.7697 (mtmt) REVERT: A 663 ASP cc_start: 0.7691 (t0) cc_final: 0.7462 (t0) REVERT: A 693 MET cc_start: 0.0946 (mmt) cc_final: -0.0778 (tpp) REVERT: A 732 LYS cc_start: 0.7563 (mttm) cc_final: 0.7100 (tptp) REVERT: A 1013 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7489 (pp) REVERT: C 102 CYS cc_start: 0.6559 (p) cc_final: 0.6322 (p) REVERT: C 184 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7708 (mt-10) REVERT: C 337 PHE cc_start: 0.7963 (t80) cc_final: 0.7674 (t80) outliers start: 16 outliers final: 12 residues processed: 115 average time/residue: 0.2392 time to fit residues: 39.5276 Evaluate side-chains 111 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 922 ASN Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain C residue 53 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 103 optimal weight: 0.0030 chunk 43 optimal weight: 0.0870 chunk 106 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 chunk 19 optimal weight: 0.0000 chunk 90 optimal weight: 1.9990 chunk 5 optimal weight: 0.0980 overall best weight: 0.2372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.221904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.194559 restraints weight = 10500.493| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 1.20 r_work: 0.3890 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10841 Z= 0.136 Angle : 0.577 12.701 14722 Z= 0.288 Chirality : 0.043 0.314 1683 Planarity : 0.004 0.047 1832 Dihedral : 7.155 65.044 1625 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.22 % Allowed : 19.83 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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 (0.24), residues: 1300 helix: 0.78 (0.22), residues: 579 sheet: -0.91 (0.38), residues: 175 loop : -1.86 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 860 HIS 0.002 0.001 HIS A 264 PHE 0.013 0.001 PHE A 368 TYR 0.009 0.001 TYR C 121 ARG 0.005 0.000 ARG C 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2182.69 seconds wall clock time: 40 minutes 13.05 seconds (2413.05 seconds total)