Starting phenix.real_space_refine on Sat Dec 9 09:11:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7i_9934/12_2023/6k7i_9934.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7i_9934/12_2023/6k7i_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_9934/12_2023/6k7i_9934.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7i_9934/12_2023/6k7i_9934.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7i_9934/12_2023/6k7i_9934.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7i_9934/12_2023/6k7i_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 6 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: 6.06, per 1000 atoms: 0.57 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: 4.35 Conformation dependent library (CDL) restraints added in 1.9 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: 1.18 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: 3.44 Time building geometry restraints manager: 4.69 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: 6011 22.47 - 44.94: 486 44.94 - 67.40: 46 67.40 - 89.87: 13 89.87 - 112.34: 3 Dihedral angle restraints: 6559 sinusoidal: 2736 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 6556 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: 0.870 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: 4.140 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 30.990 Find NCS groups from input model: 0.270 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.230 ------------------------------------------------------------------------------- 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 : 15.474 112.339 4084 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 : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 141 average time/residue: 0.2602 time to fit residues: 50.8451 Evaluate side-chains 110 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 103 time to evaluate : 1.188 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1021 time to fit residues: 2.9795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 33 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.7980 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10841 Z= 0.192 Angle : 0.683 8.894 14722 Z= 0.352 Chirality : 0.047 0.428 1683 Planarity : 0.005 0.052 1832 Dihedral : 9.751 106.689 1600 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.85 % Favored : 93.00 % Rotamer: Outliers : 1.83 % Allowed : 11.39 % Favored : 86.78 % 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: -2.90 (0.21), residues: 1300 helix: -1.28 (0.19), residues: 573 sheet: -1.41 (0.40), residues: 144 loop : -2.72 (0.23), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 927 HIS 0.003 0.001 HIS A 682 PHE 0.023 0.001 PHE A 368 TYR 0.014 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 135 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 114 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 6 residues processed: 131 average time/residue: 0.2594 time to fit residues: 48.5198 Evaluate side-chains 105 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 1.247 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1018 time to fit residues: 2.8173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 9.9990 chunk 36 optimal weight: 0.2980 chunk 98 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 40 optimal weight: 20.0000 chunk 94 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 397 ASN ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 813 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10841 Z= 0.219 Angle : 0.659 9.285 14722 Z= 0.335 Chirality : 0.047 0.370 1683 Planarity : 0.004 0.056 1832 Dihedral : 9.200 96.107 1600 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.69 % Favored : 92.23 % Rotamer: Outliers : 2.09 % Allowed : 14.26 % Favored : 83.65 % 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: -2.21 (0.22), residues: 1300 helix: -0.56 (0.20), residues: 575 sheet: -1.19 (0.40), residues: 146 loop : -2.49 (0.24), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 927 HIS 0.004 0.001 HIS A 682 PHE 0.019 0.001 PHE A 368 TYR 0.013 0.001 TYR C 297 ARG 0.005 0.000 ARG A 540 *********************** 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 132 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 108 time to evaluate : 1.179 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 7 residues processed: 126 average time/residue: 0.2454 time to fit residues: 43.9738 Evaluate side-chains 98 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 1.167 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0987 time to fit residues: 2.9696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 61 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 56 optimal weight: 40.0000 chunk 79 optimal weight: 0.9980 chunk 118 optimal weight: 0.3980 chunk 125 optimal weight: 0.0980 chunk 62 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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: 0.7979 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10841 Z= 0.220 Angle : 0.639 10.498 14722 Z= 0.324 Chirality : 0.047 0.341 1683 Planarity : 0.004 0.046 1832 Dihedral : 8.623 85.734 1600 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.92 % Favored : 93.00 % Rotamer: Outliers : 2.00 % Allowed : 16.61 % Favored : 81.39 % 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: -1.81 (0.22), residues: 1300 helix: -0.19 (0.21), residues: 579 sheet: -1.17 (0.40), residues: 149 loop : -2.28 (0.24), residues: 572 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 0.017 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 126 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 103 time to evaluate : 1.177 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 10 residues processed: 124 average time/residue: 0.2155 time to fit residues: 39.8318 Evaluate side-chains 106 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 1.273 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1060 time to fit residues: 3.7311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 1 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 64 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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** C 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 10841 Z= 0.416 Angle : 0.725 10.401 14722 Z= 0.367 Chirality : 0.050 0.321 1683 Planarity : 0.005 0.048 1832 Dihedral : 8.622 82.650 1600 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.77 % Favored : 92.15 % Rotamer: Outliers : 1.57 % Allowed : 18.26 % Favored : 80.17 % 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: -1.82 (0.22), residues: 1300 helix: -0.29 (0.21), residues: 578 sheet: -1.24 (0.40), residues: 154 loop : -2.15 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 927 HIS 0.006 0.001 HIS A 682 PHE 0.020 0.002 PHE A 368 TYR 0.022 0.002 TYR C 297 ARG 0.004 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 117 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 113 average time/residue: 0.2589 time to fit residues: 42.4973 Evaluate side-chains 107 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 1.209 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1559 time to fit residues: 4.4537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 73 optimal weight: 3.9990 chunk 31 optimal weight: 0.2980 chunk 125 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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 323 HIS ** 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: 0.8005 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10841 Z= 0.274 Angle : 0.664 10.257 14722 Z= 0.334 Chirality : 0.047 0.325 1683 Planarity : 0.004 0.046 1832 Dihedral : 8.000 77.958 1600 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.23 % Favored : 92.69 % Rotamer: Outliers : 0.78 % Allowed : 19.13 % 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: -1.57 (0.22), residues: 1300 helix: -0.04 (0.21), residues: 571 sheet: -1.06 (0.43), residues: 136 loop : -2.05 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 927 HIS 0.004 0.001 HIS A 682 PHE 0.018 0.001 PHE A 368 TYR 0.017 0.001 TYR C 297 ARG 0.002 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 103 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 1.290 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 102 average time/residue: 0.2504 time to fit residues: 36.4537 Evaluate side-chains 92 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 1.139 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0972 time to fit residues: 2.1810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 0.4980 chunk 14 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 125 optimal weight: 0.2980 chunk 78 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 10841 Z= 0.156 Angle : 0.600 9.921 14722 Z= 0.300 Chirality : 0.044 0.315 1683 Planarity : 0.004 0.043 1832 Dihedral : 7.323 72.834 1600 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 1.13 % Allowed : 19.39 % 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: -1.15 (0.23), residues: 1300 helix: 0.39 (0.22), residues: 582 sheet: -0.98 (0.42), residues: 144 loop : -1.93 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 927 HIS 0.003 0.001 HIS A 323 PHE 0.014 0.001 PHE A 368 TYR 0.011 0.001 TYR C 297 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 112 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 1.137 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 111 average time/residue: 0.2196 time to fit residues: 36.3685 Evaluate side-chains 98 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 1.195 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1067 time to fit residues: 2.6326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 24 optimal weight: 2.9990 chunk 79 optimal weight: 0.0000 chunk 85 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 0.0170 chunk 98 optimal weight: 0.0070 chunk 113 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 overall best weight: 0.2640 ------------------------------------------------------------------------------- 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** C 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2759 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= 0.137 Angle : 0.584 9.755 14722 Z= 0.292 Chirality : 0.043 0.299 1683 Planarity : 0.004 0.047 1832 Dihedral : 7.010 69.850 1600 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.43 % Allowed : 19.74 % Favored : 79.83 % 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: -0.93 (0.23), residues: 1300 helix: 0.70 (0.22), residues: 571 sheet: -1.05 (0.38), residues: 176 loop : -1.88 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 927 HIS 0.005 0.001 HIS A 473 PHE 0.013 0.001 PHE A 368 TYR 0.010 0.001 TYR C 82 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 101 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 1.050 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 101 average time/residue: 0.2351 time to fit residues: 34.8695 Evaluate side-chains 92 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 90 time to evaluate : 1.201 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1024 time to fit residues: 2.0556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 5.9990 chunk 116 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2687 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= 0.194 Angle : 0.610 11.873 14722 Z= 0.306 Chirality : 0.045 0.291 1683 Planarity : 0.004 0.049 1832 Dihedral : 7.042 68.743 1600 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.17 % Allowed : 19.91 % Favored : 79.91 % 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: -0.92 (0.23), residues: 1300 helix: 0.65 (0.22), residues: 577 sheet: -1.05 (0.39), residues: 164 loop : -1.83 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 927 HIS 0.004 0.001 HIS A 323 PHE 0.013 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 97 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 1.178 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 97 average time/residue: 0.2407 time to fit residues: 34.2160 Evaluate side-chains 93 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.173 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 4.9990 chunk 58 optimal weight: 0.0470 chunk 85 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 103 optimal weight: 0.0270 chunk 10 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10841 Z= 0.143 Angle : 0.587 12.110 14722 Z= 0.292 Chirality : 0.043 0.286 1683 Planarity : 0.004 0.049 1832 Dihedral : 6.833 66.257 1600 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.17 % Allowed : 20.09 % Favored : 79.74 % 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: -0.77 (0.24), residues: 1300 helix: 0.79 (0.22), residues: 579 sheet: -0.91 (0.38), residues: 176 loop : -1.81 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 927 HIS 0.002 0.001 HIS A 264 PHE 0.013 0.001 PHE A 368 TYR 0.010 0.001 TYR C 297 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 93 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 1.191 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 93 average time/residue: 0.2364 time to fit residues: 32.1611 Evaluate side-chains 91 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.082 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 106 optimal weight: 0.9980 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.210660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.180626 restraints weight = 10529.501| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 1.46 r_work: 0.3714 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10841 Z= 0.331 Angle : 0.675 12.189 14722 Z= 0.338 Chirality : 0.048 0.288 1683 Planarity : 0.004 0.048 1832 Dihedral : 7.234 67.378 1600 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.35 % Allowed : 20.09 % Favored : 79.57 % 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: -1.05 (0.23), residues: 1300 helix: 0.40 (0.22), residues: 577 sheet: -0.92 (0.39), residues: 163 loop : -1.78 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 927 HIS 0.005 0.001 HIS A 323 PHE 0.016 0.002 PHE C 214 TYR 0.018 0.002 TYR C 297 ARG 0.004 0.000 ARG C 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2176.33 seconds wall clock time: 40 minutes 28.19 seconds (2428.19 seconds total)