Starting phenix.real_space_refine (version: dev) on Mon Dec 12 13:36:06 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7n_9942/12_2022/6k7n_9942_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7n_9942/12_2022/6k7n_9942.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7n_9942/12_2022/6k7n_9942.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7n_9942/12_2022/6k7n_9942.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7n_9942/12_2022/6k7n_9942_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7n_9942/12_2022/6k7n_9942_updated.pdb" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.005 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 220": "OE1" <-> "OE2" 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 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 383": "OE1" <-> "OE2" Residue "A PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 409": "OD1" <-> "OD2" Residue "A TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 464": "OE1" <-> "OE2" Residue "A ASP 482": "OD1" <-> "OD2" Residue "A GLU 523": "OE1" <-> "OE2" Residue "A ASP 565": "OD1" <-> "OD2" Residue "A TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 645": "OE1" <-> "OE2" Residue "A ASP 646": "OD1" <-> "OD2" Residue "A ASP 650": "OD1" <-> "OD2" Residue "A ASP 672": "OD1" <-> "OD2" Residue "A PHE 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 771": "OE1" <-> "OE2" 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 ARG 875": "NH1" <-> "NH2" Residue "A PHE 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 903": "OE1" <-> "OE2" Residue "A TYR 908": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 920": "OD1" <-> "OD2" 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 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 111": "OE1" <-> "OE2" Residue "C PHE 119": "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 TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 215": "NH1" <-> "NH2" Residue "C GLU 225": "OE1" <-> "OE2" Residue "C PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 246": "OD1" <-> "OD2" Residue "C ASP 248": "OD1" <-> "OD2" Residue "C PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 277": "OE1" <-> "OE2" Residue "C TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 10544 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7821 Classifications: {'peptide': 983} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 952} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2615 Classifications: {'peptide': 325} Link IDs: {'PCIS': 3, 'PTRANS': 22, '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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {' MG': 1, 'ALF': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.40, per 1000 atoms: 0.61 Number of scatterers: 10544 At special positions: 0 Unit cell: (68.89, 109.56, 165.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 56 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1903 8.00 N 1745 7.00 C 6834 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=2.02 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.03 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: 4.44 Conformation dependent library (CDL) restraints added in 1.6 seconds 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2462 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 9 sheets defined 42.8% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 64 through 74 Processing helix chain 'A' and resid 76 through 89 removed outlier: 4.025A pdb=" N GLN A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 130 Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 271 through 273 No H-bonds generated for 'chain 'A' and resid 271 through 273' Processing helix chain 'A' and resid 276 through 279 No H-bonds generated for 'chain 'A' and resid 276 through 279' Processing helix chain 'A' and resid 289 through 323 Processing helix chain 'A' and resid 340 through 354 removed outlier: 5.317A pdb=" N ASN A 353 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 376 Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 399 through 401 No H-bonds generated for 'chain 'A' and resid 399 through 401' Processing helix chain 'A' and resid 447 through 455 Processing helix chain 'A' and resid 463 through 465 No H-bonds generated for 'chain 'A' and resid 463 through 465' Processing helix chain 'A' and resid 468 through 471 No H-bonds generated for 'chain 'A' and resid 468 through 471' Processing helix chain 'A' and resid 491 through 502 Processing helix chain 'A' and resid 560 through 563 No H-bonds generated for 'chain 'A' and resid 560 through 563' Processing helix chain 'A' and resid 571 through 587 removed outlier: 5.569A pdb=" N ILE A 576 " --> pdb=" O LYS A 572 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYS A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 616 removed outlier: 4.154A pdb=" N GLU A 606 " --> pdb=" O SER A 602 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N TRP A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA A 609 " --> pdb=" O GLN A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 631 Processing helix chain 'A' and resid 652 through 661 Processing helix chain 'A' and resid 674 through 684 removed outlier: 4.588A pdb=" N ASN A 679 " --> pdb=" O GLU A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 738 Processing helix chain 'A' and resid 740 through 752 removed outlier: 3.535A pdb=" N ARG A 743 " --> pdb=" O PHE A 740 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLN A 744 " --> pdb=" O GLY A 741 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR A 745 " --> pdb=" O VAL A 742 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASP A 748 " --> pdb=" O TYR A 745 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU A 751 " --> pdb=" O ASP A 748 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 752 " --> pdb=" O LEU A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 776 Processing helix chain 'A' and resid 791 through 796 Processing helix chain 'A' and resid 810 through 814 Processing helix chain 'A' and resid 822 through 830 removed outlier: 3.509A pdb=" N LYS A 826 " --> pdb=" O LYS A 823 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 829 " --> pdb=" O LYS A 826 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET A 830 " --> pdb=" O ASN A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 855 Processing helix chain 'A' and resid 857 through 865 removed outlier: 3.657A pdb=" N PHE A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL A 864 " --> pdb=" O TRP A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 880 Processing helix chain 'A' and resid 887 through 895 removed outlier: 3.993A pdb=" N LEU A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 907 Processing helix chain 'A' and resid 909 through 918 removed outlier: 3.525A pdb=" N LYS A 913 " --> pdb=" O GLU A 910 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR A 914 " --> pdb=" O LEU A 911 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER A 915 " --> pdb=" O TYR A 912 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A 918 " --> pdb=" O SER A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Proline residue: A 944 - end of helix Processing helix chain 'A' and resid 962 through 984 Processing helix chain 'A' and resid 990 through 1013 removed outlier: 3.652A pdb=" N SER A1012 " --> pdb=" O GLY A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1023 No H-bonds generated for 'chain 'A' and resid 1021 through 1023' Processing helix chain 'A' and resid 1026 through 1032 Processing helix chain 'A' and resid 1034 through 1061 Proline residue: A1044 - end of helix removed outlier: 5.155A pdb=" N LEU A1050 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASP A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 35 No H-bonds generated for 'chain 'C' and resid 32 through 35' Processing helix chain 'C' and resid 51 through 73 Proline residue: C 63 - end of helix Processing helix chain 'C' and resid 132 through 135 No H-bonds generated for 'chain 'C' and resid 132 through 135' Processing helix chain 'C' and resid 140 through 144 Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 173 through 176 No H-bonds generated for 'chain 'C' and resid 173 through 176' Processing helix chain 'C' and resid 207 through 211 Processing helix chain 'C' and resid 223 through 226 No H-bonds generated for 'chain 'C' and resid 223 through 226' Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' Processing helix chain 'C' and resid 251 through 253 No H-bonds generated for 'chain 'C' and resid 251 through 253' Processing helix chain 'C' and resid 255 through 261 Processing helix chain 'C' and resid 324 through 349 Processing sheet with id= A, first strand: chain 'A' and resid 156 through 159 removed outlier: 3.985A pdb=" N VAL A 263 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER A 173 " --> pdb=" O HIS A 264 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ILE A 266 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LEU A 171 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 180 through 183 Processing sheet with id= C, first strand: chain 'A' and resid 219 through 221 Processing sheet with id= D, first strand: chain 'A' and resid 727 through 730 removed outlier: 6.736A pdb=" N ILE A 666 " --> pdb=" O VAL A 756 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N CYS A 758 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE A 668 " --> pdb=" O CYS A 758 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL A 780 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE A 406 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A 782 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N SER A 408 " --> pdb=" O LEU A 782 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE A 784 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N TYR A 817 " --> pdb=" O GLY A 802 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 514 through 517 Processing sheet with id= F, first strand: chain 'A' and resid 545 through 547 Processing sheet with id= G, first strand: chain 'A' and resid 419 through 425 removed outlier: 6.581A pdb=" N ALA A 643 " --> pdb=" O LYS A 422 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N CYS A 424 " --> pdb=" O ALA A 641 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ALA A 641 " --> pdb=" O CYS A 424 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 77 through 81 removed outlier: 5.944A pdb=" N TYR C 122 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LEU C 272 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU C 124 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ARG C 270 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 102 through 110 removed outlier: 4.343A pdb=" N CYS C 102 " --> pdb=" O TYR C 297 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 295 " --> pdb=" O CYS C 104 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR C 182 " --> pdb=" O THR C 296 " (cutoff:3.500A) 397 hydrogen bonds defined for protein. 1131 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: 3.22 Time building geometry restraints manager: 4.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1846 1.32 - 1.44: 2834 1.44 - 1.57: 6020 1.57 - 1.69: 1 1.69 - 1.82: 89 Bond restraints: 10790 Sorted by residual: bond pdb=" F1 ALF A1301 " pdb="AL ALF A1301 " ideal model delta sigma weight residual 1.684 1.791 -0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" F3 ALF A1301 " pdb="AL ALF A1301 " ideal model delta sigma weight residual 1.685 1.792 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" F4 ALF A1301 " pdb="AL ALF A1301 " ideal model delta sigma weight residual 1.686 1.793 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" F2 ALF A1301 " pdb="AL ALF A1301 " ideal model delta sigma weight residual 1.685 1.790 -0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" C ILE C 62 " pdb=" N PRO C 63 " ideal model delta sigma weight residual 1.335 1.380 -0.045 1.36e-02 5.41e+03 1.09e+01 ... (remaining 10785 not shown) Histogram of bond angle deviations from ideal: 88.85 - 107.03: 369 107.03 - 125.20: 14044 125.20 - 143.38: 234 143.38 - 161.55: 0 161.55 - 179.73: 2 Bond angle restraints: 14649 Sorted by residual: angle pdb=" F1 ALF A1301 " pdb="AL ALF A1301 " pdb=" F2 ALF A1301 " ideal model delta sigma weight residual 108.68 179.73 -71.05 3.00e+00 1.11e-01 5.61e+02 angle pdb=" F3 ALF A1301 " pdb="AL ALF A1301 " pdb=" F4 ALF A1301 " ideal model delta sigma weight residual 109.63 177.39 -67.76 3.00e+00 1.11e-01 5.10e+02 angle pdb=" F2 ALF A1301 " pdb="AL ALF A1301 " pdb=" F4 ALF A1301 " ideal model delta sigma weight residual 110.21 88.85 21.36 3.00e+00 1.11e-01 5.07e+01 angle pdb=" F1 ALF A1301 " pdb="AL ALF A1301 " pdb=" F3 ALF A1301 " ideal model delta sigma weight residual 109.69 89.52 20.17 3.00e+00 1.11e-01 4.52e+01 angle pdb=" F2 ALF A1301 " pdb="AL ALF A1301 " pdb=" F3 ALF A1301 " ideal model delta sigma weight residual 109.59 90.70 18.89 3.00e+00 1.11e-01 3.96e+01 ... (remaining 14644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.68: 5765 19.68 - 39.36: 546 39.36 - 59.04: 77 59.04 - 78.72: 11 78.72 - 98.40: 8 Dihedral angle restraints: 6407 sinusoidal: 2590 harmonic: 3817 Sorted by residual: dihedral pdb=" CA ARG A 479 " pdb=" C ARG A 479 " pdb=" N GLU A 480 " pdb=" CA GLU A 480 " ideal model delta harmonic sigma weight residual 180.00 146.31 33.69 0 5.00e+00 4.00e-02 4.54e+01 dihedral pdb=" CA THR A 535 " pdb=" C THR A 535 " pdb=" N SER A 536 " pdb=" CA SER A 536 " ideal model delta harmonic sigma weight residual -180.00 -146.87 -33.13 0 5.00e+00 4.00e-02 4.39e+01 dihedral pdb=" CA THR C 100 " pdb=" C THR C 100 " pdb=" N PRO C 101 " pdb=" CA PRO C 101 " ideal model delta harmonic sigma weight residual 0.00 32.24 -32.24 0 5.00e+00 4.00e-02 4.16e+01 ... (remaining 6404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1383 0.094 - 0.187: 272 0.187 - 0.281: 21 0.281 - 0.375: 1 0.375 - 0.468: 1 Chirality restraints: 1678 Sorted by residual: chirality pdb=" CB ILE A 694 " pdb=" CA ILE A 694 " pdb=" CG1 ILE A 694 " pdb=" CG2 ILE A 694 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.48e+00 chirality pdb=" CG LEU A 854 " pdb=" CB LEU A 854 " pdb=" CD1 LEU A 854 " pdb=" CD2 LEU A 854 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CB ILE A 784 " pdb=" CA ILE A 784 " pdb=" CG1 ILE A 784 " pdb=" CG2 ILE A 784 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 1675 not shown) Planarity restraints: 1831 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 402 " -0.265 2.00e-02 2.50e+03 2.26e-01 6.40e+02 pdb=" C7 NAG C 402 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG C 402 " -0.168 2.00e-02 2.50e+03 pdb=" N2 NAG C 402 " 0.391 2.00e-02 2.50e+03 pdb=" O7 NAG C 402 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " 0.220 2.00e-02 2.50e+03 1.83e-01 4.17e+02 pdb=" C7 NAG C 401 " -0.058 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " 0.157 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " -0.300 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " -0.058 2.00e-02 2.50e+03 5.08e-02 3.22e+01 pdb=" C7 NAG B 1 " 0.009 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.012 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " 0.084 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.047 2.00e-02 2.50e+03 ... (remaining 1828 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 111 2.62 - 3.19: 8697 3.19 - 3.76: 17180 3.76 - 4.33: 24372 4.33 - 4.90: 38957 Nonbonded interactions: 89317 Sorted by model distance: nonbonded pdb=" F3 ALF A1301 " pdb="MG MG A1303 " model vdw 2.046 2.120 nonbonded pdb=" OD2 ASP A 409 " pdb="MG MG A1303 " model vdw 2.233 2.170 nonbonded pdb=" OH TYR C 134 " pdb=" OG SER C 177 " model vdw 2.243 2.440 nonbonded pdb=" OG SER A 767 " pdb=" OG SER A 792 " model vdw 2.293 2.440 nonbonded pdb=" O TYR A 881 " pdb=" OG1 THR A 886 " model vdw 2.297 2.440 ... (remaining 89312 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 Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Al 1 5.89 5 Mg 1 5.21 5 S 56 5.16 5 C 6834 2.51 5 N 1745 2.21 5 O 1903 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.710 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: 4.920 Check model and map are aligned: 0.180 Convert atoms to be neutral: 0.100 Process input model: 31.380 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:11.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 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 : 0.013 0.107 10790 Z= 0.825 Angle : 1.532 71.046 14649 Z= 0.742 Chirality : 0.072 0.468 1678 Planarity : 0.011 0.226 1828 Dihedral : 15.455 98.400 3936 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.01 % Favored : 91.91 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.19), residues: 1298 helix: -2.16 (0.16), residues: 560 sheet: -1.53 (0.39), residues: 144 loop : -3.03 (0.21), residues: 594 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 118 time to evaluate : 1.262 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 123 average time/residue: 1.2458 time to fit residues: 165.6242 Evaluate side-chains 89 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 1.241 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 1 average time/residue: 1.2706 time to fit residues: 3.1531 ------------------------------------------------------------------------------- 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: 1.9990 chunk 98 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 30.0000 chunk 61 optimal weight: 0.8980 chunk 75 optimal weight: 0.3980 chunk 118 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 227 HIS A 234 ASN A 433 GLN A 454 ASN A 605 GLN A 612 GLN A 682 HIS A 765 GLN A 967 ASN C 92 ASN C 176 ASN C 222 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 10790 Z= 0.207 Angle : 0.693 11.242 14649 Z= 0.359 Chirality : 0.045 0.188 1678 Planarity : 0.006 0.067 1828 Dihedral : 8.339 101.375 1458 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.09 % Favored : 93.76 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -2.52 (0.21), residues: 1298 helix: -0.83 (0.20), residues: 574 sheet: -1.42 (0.40), residues: 146 loop : -2.61 (0.23), residues: 578 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 99 time to evaluate : 1.262 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 9 residues processed: 114 average time/residue: 1.1082 time to fit residues: 138.1623 Evaluate side-chains 92 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 1.255 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 4 residues processed: 5 average time/residue: 0.3441 time to fit residues: 3.9179 ------------------------------------------------------------------------------- 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: 10.0000 chunk 36 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 127 optimal weight: 0.0770 chunk 105 optimal weight: 0.3980 chunk 117 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.0944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS A 381 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 10790 Z= 0.207 Angle : 0.625 8.380 14649 Z= 0.324 Chirality : 0.043 0.163 1678 Planarity : 0.005 0.056 1828 Dihedral : 7.778 101.298 1458 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.93 % Favored : 93.99 % Rotamer Outliers : 3.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: 1298 helix: -0.13 (0.21), residues: 571 sheet: -1.06 (0.38), residues: 180 loop : -2.31 (0.25), residues: 547 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 90 time to evaluate : 1.283 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 13 residues processed: 115 average time/residue: 1.0044 time to fit residues: 127.5305 Evaluate side-chains 94 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 1.243 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 6 average time/residue: 0.3217 time to fit residues: 4.2090 ------------------------------------------------------------------------------- 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: 0.9980 chunk 61 optimal weight: 0.9980 chunk 13 optimal weight: 9.9990 chunk 56 optimal weight: 30.0000 chunk 79 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 125 optimal weight: 0.5980 chunk 62 optimal weight: 6.9990 chunk 112 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 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 776 GLN A 810 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 10790 Z= 0.181 Angle : 0.597 9.128 14649 Z= 0.306 Chirality : 0.043 0.162 1678 Planarity : 0.004 0.056 1828 Dihedral : 7.559 101.836 1458 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -1.29 (0.23), residues: 1298 helix: 0.22 (0.22), residues: 571 sheet: -0.78 (0.41), residues: 166 loop : -2.03 (0.25), residues: 561 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 85 time to evaluate : 1.235 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 102 average time/residue: 0.9436 time to fit residues: 107.1451 Evaluate side-chains 93 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 1.252 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 3 average time/residue: 0.1294 time to fit residues: 2.4014 ------------------------------------------------------------------------------- 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: 2.9990 chunk 71 optimal weight: 4.9990 chunk 1 optimal weight: 20.0000 chunk 93 optimal weight: 0.5980 chunk 51 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 64 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 31 optimal weight: 0.0060 overall best weight: 1.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A 674 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 10790 Z= 0.222 Angle : 0.609 8.509 14649 Z= 0.312 Chirality : 0.044 0.163 1678 Planarity : 0.004 0.056 1828 Dihedral : 7.471 101.461 1458 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer Outliers : 3.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -1.12 (0.23), residues: 1298 helix: 0.36 (0.22), residues: 566 sheet: -0.72 (0.40), residues: 177 loop : -1.91 (0.26), residues: 555 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 87 time to evaluate : 1.318 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 18 residues processed: 112 average time/residue: 0.9056 time to fit residues: 113.0704 Evaluate side-chains 100 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 1.183 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 10 residues processed: 8 average time/residue: 0.4060 time to fit residues: 5.6471 ------------------------------------------------------------------------------- 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: 30.0000 chunk 113 optimal weight: 0.5980 chunk 24 optimal weight: 8.9990 chunk 73 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 125 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 10790 Z= 0.169 Angle : 0.574 8.620 14649 Z= 0.293 Chirality : 0.043 0.164 1678 Planarity : 0.004 0.056 1828 Dihedral : 7.289 101.686 1458 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer Outliers : 3.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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 (0.24), residues: 1298 helix: 0.46 (0.22), residues: 576 sheet: -0.55 (0.41), residues: 177 loop : -1.80 (0.26), residues: 545 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 88 time to evaluate : 1.284 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 15 residues processed: 114 average time/residue: 0.9024 time to fit residues: 115.1271 Evaluate side-chains 100 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 1.349 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 2 average time/residue: 0.2200 time to fit residues: 2.5474 ------------------------------------------------------------------------------- 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: 3.9990 chunk 14 optimal weight: 20.0000 chunk 71 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 57 optimal weight: 6.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 10790 Z= 0.165 Angle : 0.575 8.745 14649 Z= 0.291 Chirality : 0.042 0.157 1678 Planarity : 0.004 0.056 1828 Dihedral : 7.180 101.767 1458 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -0.74 (0.24), residues: 1298 helix: 0.58 (0.22), residues: 576 sheet: -0.34 (0.42), residues: 175 loop : -1.70 (0.27), residues: 547 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 88 time to evaluate : 1.218 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 17 residues processed: 108 average time/residue: 0.9988 time to fit residues: 119.4874 Evaluate side-chains 102 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 1.355 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 13 residues processed: 4 average time/residue: 0.6480 time to fit residues: 4.8280 ------------------------------------------------------------------------------- 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: 50.0000 chunk 74 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 chunk 120 optimal weight: 3.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN ** A 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.055 10790 Z= 0.416 Angle : 0.693 8.391 14649 Z= 0.353 Chirality : 0.048 0.181 1678 Planarity : 0.005 0.055 1828 Dihedral : 7.523 100.657 1458 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.93 % Favored : 92.99 % Rotamer Outliers : 2.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -1.17 (0.23), residues: 1298 helix: 0.13 (0.21), residues: 572 sheet: -0.38 (0.43), residues: 169 loop : -1.86 (0.26), residues: 557 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 88 time to evaluate : 1.354 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 20 residues processed: 110 average time/residue: 0.9485 time to fit residues: 115.9382 Evaluate side-chains 103 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 83 time to evaluate : 1.263 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 15 residues processed: 5 average time/residue: 0.5622 time to fit residues: 5.0377 ------------------------------------------------------------------------------- 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: 0.6980 chunk 116 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 50 optimal weight: 50.0000 chunk 91 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 810 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 10790 Z= 0.166 Angle : 0.583 8.629 14649 Z= 0.296 Chirality : 0.042 0.163 1678 Planarity : 0.004 0.054 1828 Dihedral : 7.232 101.741 1458 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -0.82 (0.24), residues: 1298 helix: 0.48 (0.22), residues: 579 sheet: -0.34 (0.42), residues: 175 loop : -1.73 (0.27), residues: 544 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 17 residues processed: 102 average time/residue: 0.9460 time to fit residues: 107.4097 Evaluate side-chains 97 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 1.227 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 15 residues processed: 2 average time/residue: 0.1506 time to fit residues: 2.3760 ------------------------------------------------------------------------------- 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: 3.9990 chunk 58 optimal weight: 30.0000 chunk 85 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 79 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 10790 Z= 0.299 Angle : 0.641 8.467 14649 Z= 0.325 Chirality : 0.045 0.161 1678 Planarity : 0.005 0.054 1828 Dihedral : 7.350 101.276 1458 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: 1298 helix: 0.37 (0.22), residues: 572 sheet: -0.37 (0.42), residues: 175 loop : -1.73 (0.26), residues: 551 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 79 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 17 residues processed: 96 average time/residue: 0.9805 time to fit residues: 105.0747 Evaluate side-chains 94 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 1.265 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 15 residues processed: 2 average time/residue: 1.1466 time to fit residues: 4.2747 ------------------------------------------------------------------------------- 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: 0.2980 chunk 95 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.210160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.157249 restraints weight = 10154.180| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.52 r_work: 0.3128 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 10790 Z= 0.171 Angle : 0.582 9.018 14649 Z= 0.294 Chirality : 0.042 0.166 1678 Planarity : 0.004 0.053 1828 Dihedral : 7.136 101.894 1458 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -0.74 (0.24), residues: 1298 helix: 0.57 (0.22), residues: 578 sheet: -0.32 (0.42), residues: 175 loop : -1.70 (0.27), residues: 545 =============================================================================== Job complete usr+sys time: 3103.70 seconds wall clock time: 56 minutes 30.90 seconds (3390.90 seconds total)