Starting phenix.real_space_refine on Sat Nov 16 12:22:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijl_35488/11_2024/8ijl_35488.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijl_35488/11_2024/8ijl_35488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijl_35488/11_2024/8ijl_35488.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijl_35488/11_2024/8ijl_35488.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijl_35488/11_2024/8ijl_35488.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijl_35488/11_2024/8ijl_35488.cif" } resolution = 2.62 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= 0.034 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: 9 Type Number sf(0) Gaussians Al 1 5.89 5 P 7 5.49 5 Mg 1 5.21 5 S 47 5.16 5 Na 2 4.78 5 C 6731 2.51 5 N 1643 2.21 5 O 1924 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 10360 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7638 Classifications: {'peptide': 982} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 35, 'TRANS': 946} Chain: "B" Number of atoms: 2165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2165 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 247} Chain breaks: 1 Chain: "A" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 429 Unusual residues: {' MG': 1, ' NA': 2, 'ADP': 1, 'ALF': 1, 'CLR': 1, 'PCW': 5, 'Q7G': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 120 Unusual residues: {'CLR': 1, 'NAG': 1, 'Q7G': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 41 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Time building chain proxies: 8.20, per 1000 atoms: 0.79 Number of scatterers: 10360 At special positions: 0 Unit cell: (75.53, 89.64, 175.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) S 47 16.00 P 7 15.00 Al 1 13.00 Mg 1 11.99 Na 2 11.00 F 4 9.00 O 1924 8.00 N 1643 7.00 C 6731 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 277 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=1, symmetry=0 Links applied NAG-ASN " NAG B 401 " - " ASN B 158 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.32 Conformation dependent library (CDL) restraints added in 1.4 seconds 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2322 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 10 sheets defined 48.9% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 60 through 68 Processing helix chain 'A' and resid 77 through 89 removed outlier: 3.680A pdb=" N THR A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 107 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 113 through 134 Processing helix chain 'A' and resid 140 through 163 Processing helix chain 'A' and resid 168 through 172 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 273 through 276 Processing helix chain 'A' and resid 277 through 289 Processing helix chain 'A' and resid 294 through 324 removed outlier: 3.663A pdb=" N ALA A 322 " --> pdb=" O PHE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 344 Processing helix chain 'A' and resid 347 through 365 removed outlier: 3.626A pdb=" N LYS A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.871A pdb=" N THR A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 374 through 379' Processing helix chain 'A' and resid 429 through 440 Processing helix chain 'A' and resid 453 through 457 Processing helix chain 'A' and resid 462 through 477 Processing helix chain 'A' and resid 479 through 486 Processing helix chain 'A' and resid 522 through 529 Processing helix chain 'A' and resid 543 through 559 removed outlier: 3.558A pdb=" N SER A 549 " --> pdb=" O SER A 545 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS A 551 " --> pdb=" O ALA A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 621 Processing helix chain 'A' and resid 632 through 643 Processing helix chain 'A' and resid 652 through 661 removed outlier: 3.564A pdb=" N ALA A 657 " --> pdb=" O VAL A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 684 removed outlier: 3.650A pdb=" N ASP A 684 " --> pdb=" O MET A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 697 Processing helix chain 'A' and resid 706 through 719 Processing helix chain 'A' and resid 730 through 732 No H-bonds generated for 'chain 'A' and resid 730 through 732' Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 751 through 757 Processing helix chain 'A' and resid 767 through 809 removed outlier: 4.269A pdb=" N VAL A 771 " --> pdb=" O PHE A 767 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A 785 " --> pdb=" O PHE A 781 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS A 786 " --> pdb=" O ASP A 782 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS A 794 " --> pdb=" O TYR A 790 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASN A 795 " --> pdb=" O THR A 791 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE A 796 " --> pdb=" O LEU A 792 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA A 797 " --> pdb=" O THR A 793 " (cutoff:3.500A) Proline residue: A 801 - end of helix Processing helix chain 'A' and resid 815 through 825 removed outlier: 3.625A pdb=" N LEU A 820 " --> pdb=" O THR A 816 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 821 " --> pdb=" O ILE A 817 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 822 " --> pdb=" O THR A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 834 Processing helix chain 'A' and resid 835 through 837 No H-bonds generated for 'chain 'A' and resid 835 through 837' Processing helix chain 'A' and resid 842 through 846 removed outlier: 3.836A pdb=" N ARG A 846 " --> pdb=" O ILE A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 867 Processing helix chain 'A' and resid 868 through 887 removed outlier: 3.724A pdb=" N MET A 872 " --> pdb=" O HIS A 868 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 880 " --> pdb=" O GLY A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 896 removed outlier: 3.529A pdb=" N LEU A 895 " --> pdb=" O PRO A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 903 Processing helix chain 'A' and resid 919 through 949 removed outlier: 3.571A pdb=" N ALA A 944 " --> pdb=" O ILE A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 960 Processing helix chain 'A' and resid 964 through 984 removed outlier: 4.087A pdb=" N TRP A 968 " --> pdb=" O ASN A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1002 Processing helix chain 'A' and resid 1004 through 1025 Processing helix chain 'A' and resid 1028 through 1035 Processing helix chain 'B' and resid 30 through 60 removed outlier: 3.796A pdb=" N LYS B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 110 Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 114 through 118 removed outlier: 3.709A pdb=" N LYS B 118 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 156 Processing helix chain 'B' and resid 220 through 225 removed outlier: 3.977A pdb=" N LYS B 224 " --> pdb=" O GLU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 242 through 244 No H-bonds generated for 'chain 'B' and resid 242 through 244' Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 193 removed outlier: 4.561A pdb=" N LEU A 182 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL A 202 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N CYS A 261 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL A 225 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLU A 263 " --> pdb=" O CYS A 223 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N CYS A 223 " --> pdb=" O GLU A 263 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE A 269 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N LEU A 217 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ILE A 271 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE A 215 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N CYS A 223 " --> pdb=" O ARG A 239 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 209 through 210 removed outlier: 6.570A pdb=" N CYS A 261 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL A 225 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLU A 263 " --> pdb=" O CYS A 223 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N CYS A 223 " --> pdb=" O GLU A 263 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE A 269 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N LEU A 217 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ILE A 271 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE A 215 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 368 through 370 removed outlier: 6.324A pdb=" N GLY A 743 " --> pdb=" O MET A 760 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU A 762 " --> pdb=" O GLY A 743 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ALA A 745 " --> pdb=" O LEU A 762 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL A 724 " --> pdb=" O ILE A 742 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ILE A 744 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL A 726 " --> pdb=" O ILE A 744 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N MET A 746 " --> pdb=" O VAL A 726 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N GLY A 728 " --> pdb=" O MET A 746 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL A 625 " --> pdb=" O ILE A 700 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N PHE A 702 " --> pdb=" O VAL A 625 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N MET A 627 " --> pdb=" O PHE A 702 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 408 through 411 removed outlier: 5.236A pdb=" N VAL A 400 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE A 604 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N PHE A 595 " --> pdb=" O TYR A 571 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N TYR A 571 " --> pdb=" O PHE A 595 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N PHE A 597 " --> pdb=" O HIS A 569 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N HIS A 569 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY A 599 " --> pdb=" O PHE A 567 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE A 515 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N GLU A 506 " --> pdb=" O LYS A 488 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LYS A 488 " --> pdb=" O GLU A 506 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 408 through 411 removed outlier: 5.236A pdb=" N VAL A 400 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE A 604 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N CYS A 530 " --> pdb=" O PHE A 595 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N PHE A 597 " --> pdb=" O CYS A 530 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR A 532 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N GLY A 599 " --> pdb=" O THR A 532 " (cutoff:3.500A) removed outlier: 9.426A pdb=" N MET A 534 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 12.537A pdb=" N LEU A 601 " --> pdb=" O MET A 534 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 444 through 445 removed outlier: 3.647A pdb=" N GLU A 444 " --> pdb=" O VAL A 460 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 910 through 911 Processing sheet with id=AA8, first strand: chain 'B' and resid 77 through 80 Processing sheet with id=AA9, first strand: chain 'B' and resid 87 through 90 Processing sheet with id=AB1, first strand: chain 'B' and resid 123 through 124 494 hydrogen bonds defined for protein. 1401 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: 3.65 Time building geometry restraints manager: 3.38 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: 1644 1.32 - 1.44: 2663 1.44 - 1.57: 6174 1.57 - 1.69: 13 1.69 - 1.82: 78 Bond restraints: 10572 Sorted by residual: bond pdb=" C11 PCW A1105 " pdb=" O3 PCW A1105 " ideal model delta sigma weight residual 1.326 1.453 -0.127 2.00e-02 2.50e+03 4.05e+01 bond pdb=" C11 PCW A1104 " pdb=" O3 PCW A1104 " ideal model delta sigma weight residual 1.326 1.453 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" C11 PCW A1108 " pdb=" O3 PCW A1108 " ideal model delta sigma weight residual 1.326 1.453 -0.127 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C11 PCW A1107 " pdb=" O3 PCW A1107 " ideal model delta sigma weight residual 1.326 1.451 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" C31 PCW A1104 " pdb=" O2 PCW A1104 " ideal model delta sigma weight residual 1.333 1.455 -0.122 2.00e-02 2.50e+03 3.74e+01 ... (remaining 10567 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.08: 14328 14.08 - 28.17: 8 28.17 - 42.25: 0 42.25 - 56.33: 0 56.33 - 70.42: 2 Bond angle restraints: 14338 Sorted by residual: angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F2 ALF A1101 " ideal model delta sigma weight residual 108.68 179.10 -70.42 3.00e+00 1.11e-01 5.51e+02 angle pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 109.63 179.93 -70.30 3.00e+00 1.11e-01 5.49e+02 angle pdb=" C5 PCW A1107 " pdb=" N PCW A1107 " pdb=" C8 PCW A1107 " ideal model delta sigma weight residual 111.64 86.42 25.22 3.00e+00 1.11e-01 7.06e+01 angle pdb=" C6 PCW A1107 " pdb=" N PCW A1107 " pdb=" C8 PCW A1107 " ideal model delta sigma weight residual 109.11 85.86 23.25 3.00e+00 1.11e-01 6.01e+01 angle pdb=" C7 PCW A1107 " pdb=" N PCW A1107 " pdb=" C8 PCW A1107 " ideal model delta sigma weight residual 108.24 86.95 21.29 3.00e+00 1.11e-01 5.04e+01 ... (remaining 14333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.37: 6411 33.37 - 66.74: 377 66.74 - 100.11: 39 100.11 - 133.48: 40 133.48 - 166.85: 3 Dihedral angle restraints: 6870 sinusoidal: 3257 harmonic: 3613 Sorted by residual: dihedral pdb=" C2' ADP A1103 " pdb=" C1' ADP A1103 " pdb=" N9 ADP A1103 " pdb=" C4 ADP A1103 " ideal model delta sinusoidal sigma weight residual 91.55 -49.80 141.34 1 2.00e+01 2.50e-03 4.27e+01 dihedral pdb=" O1B ADP A1103 " pdb=" O3A ADP A1103 " pdb=" PB ADP A1103 " pdb=" PA ADP A1103 " ideal model delta sinusoidal sigma weight residual 300.00 168.98 131.02 1 2.00e+01 2.50e-03 3.98e+01 dihedral pdb=" N PCW A1106 " pdb=" C4 PCW A1106 " pdb=" C5 PCW A1106 " pdb=" O4P PCW A1106 " ideal model delta sinusoidal sigma weight residual -66.66 100.19 -166.85 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 6867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1422 0.061 - 0.122: 193 0.122 - 0.183: 22 0.183 - 0.244: 4 0.244 - 0.305: 2 Chirality restraints: 1643 Sorted by residual: chirality pdb=" C51 Q7G A1113 " pdb=" C41 Q7G A1113 " pdb=" C61 Q7G A1113 " pdb=" O51 Q7G A1113 " both_signs ideal model delta sigma weight residual False -2.21 -2.52 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" C2 PCW A1108 " pdb=" C1 PCW A1108 " pdb=" C3 PCW A1108 " pdb=" O2 PCW A1108 " both_signs ideal model delta sigma weight residual False -2.32 -2.58 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C13 CLR A1109 " pdb=" C12 CLR A1109 " pdb=" C14 CLR A1109 " pdb=" C17 CLR A1109 " both_signs ideal model delta sigma weight residual False -2.93 -2.69 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 1640 not shown) Planarity restraints: 1753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 Q7G B 404 " 0.009 2.00e-02 2.50e+03 1.73e-01 3.73e+02 pdb=" C13 Q7G B 404 " 0.116 2.00e-02 2.50e+03 pdb=" C14 Q7G B 404 " 0.252 2.00e-02 2.50e+03 pdb=" C15 Q7G B 404 " -0.206 2.00e-02 2.50e+03 pdb=" C16 Q7G B 404 " -0.171 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 401 " -0.176 2.00e-02 2.50e+03 1.45e-01 2.65e+02 pdb=" C7 NAG B 401 " 0.047 2.00e-02 2.50e+03 pdb=" C8 NAG B 401 " -0.129 2.00e-02 2.50e+03 pdb=" N2 NAG B 401 " 0.236 2.00e-02 2.50e+03 pdb=" O7 NAG B 401 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 PCW A1106 " 0.131 2.00e-02 2.50e+03 1.35e-01 1.83e+02 pdb=" C19 PCW A1106 " -0.117 2.00e-02 2.50e+03 pdb=" C20 PCW A1106 " -0.153 2.00e-02 2.50e+03 pdb=" C21 PCW A1106 " 0.139 2.00e-02 2.50e+03 ... (remaining 1750 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 47 2.45 - 3.06: 6433 3.06 - 3.67: 15308 3.67 - 4.29: 24672 4.29 - 4.90: 41008 Nonbonded interactions: 87468 Sorted by model distance: nonbonded pdb=" F3 ALF A1101 " pdb="MG MG A1102 " model vdw 1.836 2.120 nonbonded pdb=" OD1 ASP A 729 " pdb="MG MG A1102 " model vdw 1.975 2.170 nonbonded pdb=" O THR A 390 " pdb="MG MG A1102 " model vdw 2.088 2.170 nonbonded pdb=" F2 ALF A1101 " pdb=" O HOH A1201 " model vdw 2.162 2.990 nonbonded pdb=" O ILE A 169 " pdb=" OG SER A 172 " model vdw 2.174 3.040 ... (remaining 87463 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 4.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.840 Find NCS groups from input model: 0.120 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: 0.010 Load rotamer database and sin/cos tables:13.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 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 : 0.006 0.127 10572 Z= 0.360 Angle : 1.260 70.417 14338 Z= 0.471 Chirality : 0.046 0.305 1643 Planarity : 0.008 0.173 1752 Dihedral : 22.224 166.853 4539 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.82 % Allowed : 20.39 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.58 (0.24), residues: 1242 helix: 1.20 (0.23), residues: 543 sheet: 0.20 (0.44), residues: 125 loop : -0.28 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 968 HIS 0.004 0.001 HIS A 245 PHE 0.024 0.001 PHE A 128 TYR 0.014 0.001 TYR A 328 ARG 0.007 0.000 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 98 time to evaluate : 1.151 Fit side-chains REVERT: A 688 GLU cc_start: 0.7739 (mp0) cc_final: 0.7355 (mp0) outliers start: 41 outliers final: 36 residues processed: 138 average time/residue: 1.2887 time to fit residues: 193.3416 Evaluate side-chains 131 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 95 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 734 SER Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 179 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 0.0270 chunk 50 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 0.4980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN A 887 GLN B 84 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.0767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10572 Z= 0.194 Angle : 0.863 31.551 14338 Z= 0.356 Chirality : 0.045 0.270 1643 Planarity : 0.004 0.051 1752 Dihedral : 18.065 171.817 2238 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.45 % Allowed : 18.99 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.24), residues: 1242 helix: 1.28 (0.23), residues: 562 sheet: 0.22 (0.43), residues: 122 loop : -0.27 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 968 HIS 0.004 0.001 HIS A 245 PHE 0.013 0.001 PHE A 550 TYR 0.019 0.001 TYR A 805 ARG 0.004 0.000 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 1.137 Fit side-chains REVERT: A 206 LYS cc_start: 0.8031 (mtmm) cc_final: 0.6667 (mptp) REVERT: A 263 GLU cc_start: 0.7871 (pt0) cc_final: 0.7322 (pt0) REVERT: A 480 MET cc_start: 0.7294 (mmm) cc_final: 0.6963 (mpm) REVERT: A 853 LYS cc_start: 0.7849 (mttt) cc_final: 0.7538 (mtpt) outliers start: 37 outliers final: 20 residues processed: 140 average time/residue: 1.2981 time to fit residues: 195.9143 Evaluate side-chains 116 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN B 84 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10572 Z= 0.264 Angle : 0.841 31.644 14338 Z= 0.356 Chirality : 0.047 0.269 1643 Planarity : 0.005 0.051 1752 Dihedral : 15.437 172.357 2207 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.26 % Allowed : 19.46 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.59 (0.23), residues: 1242 helix: 1.25 (0.22), residues: 563 sheet: 0.12 (0.43), residues: 124 loop : -0.37 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 968 HIS 0.006 0.001 HIS A 245 PHE 0.017 0.002 PHE A1021 TYR 0.025 0.002 TYR A 805 ARG 0.004 0.000 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 104 time to evaluate : 1.084 Fit side-chains REVERT: A 154 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7975 (mp) REVERT: A 206 LYS cc_start: 0.8020 (mtmm) cc_final: 0.6633 (mptp) REVERT: A 216 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.5929 (tmm160) REVERT: A 263 GLU cc_start: 0.7886 (pt0) cc_final: 0.7356 (pt0) REVERT: A 480 MET cc_start: 0.7485 (mmm) cc_final: 0.7141 (mpm) REVERT: A 555 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7720 (mpp) outliers start: 35 outliers final: 21 residues processed: 131 average time/residue: 1.3071 time to fit residues: 184.5286 Evaluate side-chains 119 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 141 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 75 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 119 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 ASN B 82 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10572 Z= 0.198 Angle : 0.799 31.027 14338 Z= 0.333 Chirality : 0.045 0.377 1643 Planarity : 0.004 0.051 1752 Dihedral : 13.921 168.906 2205 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.26 % Allowed : 19.55 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.23), residues: 1242 helix: 1.40 (0.22), residues: 565 sheet: 0.02 (0.43), residues: 124 loop : -0.31 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 968 HIS 0.004 0.001 HIS A 245 PHE 0.012 0.001 PHE A1021 TYR 0.019 0.001 TYR A 805 ARG 0.006 0.000 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 1.196 Fit side-chains REVERT: A 154 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7942 (mp) REVERT: A 204 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7120 (mt-10) REVERT: A 206 LYS cc_start: 0.8039 (mtmm) cc_final: 0.6684 (mptp) REVERT: A 216 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.5835 (tmm160) REVERT: A 263 GLU cc_start: 0.7849 (pt0) cc_final: 0.7358 (pt0) REVERT: A 301 GLU cc_start: 0.7918 (tt0) cc_final: 0.7648 (mt-10) REVERT: A 457 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7647 (mtm-85) REVERT: A 480 MET cc_start: 0.7509 (mmm) cc_final: 0.7115 (mpm) REVERT: A 555 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7656 (mpp) REVERT: B 177 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8549 (mm) outliers start: 35 outliers final: 22 residues processed: 137 average time/residue: 1.2979 time to fit residues: 191.6256 Evaluate side-chains 128 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 219 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 ASN A 689 GLN B 82 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10572 Z= 0.223 Angle : 0.802 31.208 14338 Z= 0.338 Chirality : 0.045 0.351 1643 Planarity : 0.004 0.051 1752 Dihedral : 13.685 167.908 2204 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.45 % Allowed : 19.09 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.70 (0.23), residues: 1242 helix: 1.42 (0.22), residues: 563 sheet: 0.01 (0.43), residues: 124 loop : -0.35 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 968 HIS 0.006 0.001 HIS A 245 PHE 0.015 0.002 PHE A1021 TYR 0.023 0.002 TYR A 805 ARG 0.004 0.000 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 107 time to evaluate : 1.155 Fit side-chains REVERT: A 87 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.6213 (ttm170) REVERT: A 154 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7983 (mp) REVERT: A 204 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7120 (mt-10) REVERT: A 206 LYS cc_start: 0.8060 (mtmm) cc_final: 0.6668 (mptp) REVERT: A 216 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.5873 (tmm160) REVERT: A 263 GLU cc_start: 0.7890 (pt0) cc_final: 0.7411 (pt0) REVERT: A 457 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7677 (mtm-85) REVERT: A 480 MET cc_start: 0.7594 (mmm) cc_final: 0.7064 (mpm) REVERT: B 177 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8541 (mm) outliers start: 37 outliers final: 23 residues processed: 136 average time/residue: 1.2913 time to fit residues: 189.7458 Evaluate side-chains 129 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 177 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.8980 chunk 107 optimal weight: 0.3980 chunk 23 optimal weight: 0.0370 chunk 70 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 ASN A 551 HIS B 82 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10572 Z= 0.209 Angle : 0.790 30.909 14338 Z= 0.333 Chirality : 0.045 0.291 1643 Planarity : 0.004 0.054 1752 Dihedral : 13.545 166.870 2204 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.17 % Allowed : 19.46 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.76 (0.23), residues: 1242 helix: 1.48 (0.22), residues: 563 sheet: -0.02 (0.43), residues: 124 loop : -0.33 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 968 HIS 0.004 0.001 HIS A 245 PHE 0.013 0.001 PHE A1021 TYR 0.021 0.001 TYR A 805 ARG 0.007 0.000 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 1.142 Fit side-chains REVERT: A 154 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7956 (mp) REVERT: A 204 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7131 (mt-10) REVERT: A 206 LYS cc_start: 0.8072 (mtmm) cc_final: 0.6676 (mptp) REVERT: A 211 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.7815 (mm) REVERT: A 216 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.5871 (tmm160) REVERT: A 246 GLU cc_start: 0.7567 (mp0) cc_final: 0.7297 (pm20) REVERT: A 263 GLU cc_start: 0.7848 (pt0) cc_final: 0.7369 (pt0) REVERT: A 457 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7647 (mtm-85) REVERT: A 480 MET cc_start: 0.7605 (mmm) cc_final: 0.7204 (mpm) REVERT: B 177 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8550 (mm) REVERT: B 249 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8562 (ptpt) outliers start: 34 outliers final: 23 residues processed: 135 average time/residue: 1.2217 time to fit residues: 178.3393 Evaluate side-chains 134 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 249 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 68 optimal weight: 0.3980 chunk 87 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 119 optimal weight: 0.0670 chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 ASN ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10572 Z= 0.177 Angle : 0.774 30.646 14338 Z= 0.325 Chirality : 0.044 0.234 1643 Planarity : 0.004 0.055 1752 Dihedral : 13.316 165.384 2204 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.17 % Allowed : 19.37 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.86 (0.24), residues: 1242 helix: 1.55 (0.23), residues: 564 sheet: 0.11 (0.43), residues: 121 loop : -0.28 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 968 HIS 0.010 0.001 HIS A 551 PHE 0.021 0.001 PHE A 128 TYR 0.019 0.001 TYR A 805 ARG 0.006 0.000 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 1.082 Fit side-chains REVERT: A 204 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7123 (mt-10) REVERT: A 206 LYS cc_start: 0.8044 (mtmm) cc_final: 0.6675 (mptp) REVERT: A 216 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.5848 (tmm160) REVERT: A 263 GLU cc_start: 0.7865 (pt0) cc_final: 0.7397 (pt0) REVERT: A 457 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7665 (mtm-85) REVERT: A 480 MET cc_start: 0.7598 (mmm) cc_final: 0.7024 (mpm) REVERT: A 563 ARG cc_start: 0.8184 (ptm160) cc_final: 0.7905 (ptp-170) REVERT: B 177 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8528 (mm) REVERT: B 249 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8539 (ptpt) outliers start: 34 outliers final: 19 residues processed: 136 average time/residue: 1.3161 time to fit residues: 192.8433 Evaluate side-chains 129 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 249 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 75 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 93 optimal weight: 0.0020 chunk 108 optimal weight: 0.6980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 ASN ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10572 Z= 0.163 Angle : 0.766 30.460 14338 Z= 0.320 Chirality : 0.043 0.176 1643 Planarity : 0.004 0.057 1752 Dihedral : 13.012 163.844 2200 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.79 % Allowed : 19.74 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 1242 helix: 1.60 (0.23), residues: 565 sheet: 0.12 (0.42), residues: 121 loop : -0.23 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 968 HIS 0.010 0.001 HIS A 551 PHE 0.025 0.001 PHE A 128 TYR 0.017 0.001 TYR A 805 ARG 0.005 0.000 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 1.220 Fit side-chains REVERT: A 165 LYS cc_start: 0.7786 (mptp) cc_final: 0.6805 (mmtt) REVERT: A 204 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7103 (mt-10) REVERT: A 206 LYS cc_start: 0.8066 (mtmm) cc_final: 0.6709 (mptp) REVERT: A 211 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.7803 (mm) REVERT: A 216 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.5825 (tmm160) REVERT: A 246 GLU cc_start: 0.7489 (mp0) cc_final: 0.7216 (pm20) REVERT: A 263 GLU cc_start: 0.7861 (pt0) cc_final: 0.7389 (pt0) REVERT: A 457 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7667 (mtm-85) REVERT: A 480 MET cc_start: 0.7629 (mmm) cc_final: 0.7042 (mpm) REVERT: A 563 ARG cc_start: 0.8146 (ptm160) cc_final: 0.7941 (ptp-170) REVERT: B 177 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8516 (mm) REVERT: B 249 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8544 (ptpt) outliers start: 30 outliers final: 19 residues processed: 137 average time/residue: 1.3200 time to fit residues: 195.7531 Evaluate side-chains 130 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 249 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.0470 chunk 104 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 407 ASN ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10572 Z= 0.204 Angle : 0.783 30.816 14338 Z= 0.330 Chirality : 0.044 0.179 1643 Planarity : 0.004 0.056 1752 Dihedral : 13.065 163.668 2199 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.89 % Allowed : 19.65 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.88 (0.24), residues: 1242 helix: 1.55 (0.22), residues: 564 sheet: 0.26 (0.44), residues: 115 loop : -0.28 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 968 HIS 0.011 0.002 HIS A 551 PHE 0.025 0.002 PHE A 128 TYR 0.021 0.001 TYR A 805 ARG 0.006 0.000 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 1.150 Fit side-chains REVERT: A 165 LYS cc_start: 0.7797 (mptp) cc_final: 0.6811 (mmtt) REVERT: A 204 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7129 (mt-10) REVERT: A 206 LYS cc_start: 0.8074 (mtmm) cc_final: 0.6712 (mptp) REVERT: A 216 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.5821 (tmm160) REVERT: A 263 GLU cc_start: 0.7861 (pt0) cc_final: 0.7391 (pt0) REVERT: A 457 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7668 (mtm-85) REVERT: A 480 MET cc_start: 0.7634 (mmm) cc_final: 0.7068 (mpm) REVERT: A 563 ARG cc_start: 0.8133 (ptm160) cc_final: 0.7903 (ptp-170) REVERT: A 688 GLU cc_start: 0.7835 (mp0) cc_final: 0.7449 (mp0) REVERT: B 177 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8540 (mm) outliers start: 31 outliers final: 21 residues processed: 134 average time/residue: 1.2371 time to fit residues: 179.3087 Evaluate side-chains 132 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 177 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 ASN ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10572 Z= 0.216 Angle : 0.791 30.901 14338 Z= 0.335 Chirality : 0.044 0.182 1643 Planarity : 0.004 0.056 1752 Dihedral : 13.039 162.531 2199 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.51 % Allowed : 20.11 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.85 (0.23), residues: 1242 helix: 1.52 (0.22), residues: 564 sheet: 0.26 (0.44), residues: 115 loop : -0.29 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 968 HIS 0.011 0.002 HIS A 551 PHE 0.026 0.002 PHE A 128 TYR 0.022 0.001 TYR A 805 ARG 0.007 0.000 ARG A 442 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 1.138 Fit side-chains REVERT: A 204 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7141 (mt-10) REVERT: A 206 LYS cc_start: 0.8088 (mtmm) cc_final: 0.6698 (mptp) REVERT: A 216 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.5890 (tmm160) REVERT: A 246 GLU cc_start: 0.7540 (mp0) cc_final: 0.7256 (pm20) REVERT: A 263 GLU cc_start: 0.7871 (pt0) cc_final: 0.7398 (pt0) REVERT: A 457 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7659 (mtm-85) REVERT: A 480 MET cc_start: 0.7606 (mmm) cc_final: 0.7033 (mpm) REVERT: A 563 ARG cc_start: 0.8128 (ptm160) cc_final: 0.7887 (ptp-170) REVERT: A 688 GLU cc_start: 0.7854 (mp0) cc_final: 0.7466 (mp0) REVERT: B 177 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8546 (mm) outliers start: 27 outliers final: 20 residues processed: 134 average time/residue: 1.2661 time to fit residues: 183.3399 Evaluate side-chains 131 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 177 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 101 optimal weight: 0.0030 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 ASN ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.150191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.114754 restraints weight = 10596.391| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.46 r_work: 0.3181 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10572 Z= 0.183 Angle : 0.771 30.851 14338 Z= 0.325 Chirality : 0.043 0.178 1643 Planarity : 0.004 0.056 1752 Dihedral : 12.599 160.662 2197 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.70 % Allowed : 19.93 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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 (0.24), residues: 1242 helix: 1.58 (0.22), residues: 564 sheet: 0.25 (0.43), residues: 115 loop : -0.24 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 968 HIS 0.010 0.001 HIS A 551 PHE 0.027 0.002 PHE A 128 TYR 0.018 0.001 TYR A 805 ARG 0.007 0.000 ARG A 442 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4028.19 seconds wall clock time: 73 minutes 22.72 seconds (4402.72 seconds total)