Starting phenix.real_space_refine on Tue May 13 22:40:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ijl_35488/05_2025/8ijl_35488.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ijl_35488/05_2025/8ijl_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/cci-nas-00/data/ceres_data/8ijl_35488/05_2025/8ijl_35488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ijl_35488/05_2025/8ijl_35488.map" model { file = "/net/cci-nas-00/data/ceres_data/8ijl_35488/05_2025/8ijl_35488.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ijl_35488/05_2025/8ijl_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-5687/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: 7.62, per 1000 atoms: 0.74 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: 2.75 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: 1.17 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: 3.62 Time building geometry restraints manager: 3.17 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: 6.620 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.400 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.320 ------------------------------------------------------------------------------- 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 : 0.008 0.607 10577 Z= 0.657 Angle : 1.260 70.417 14347 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00267 ( 1) link_NAG-ASN : angle 1.21361 ( 3) hydrogen bonds : bond 0.16979 ( 482) hydrogen bonds : angle 6.61846 ( 1401) SS BOND : bond 0.00087 ( 3) SS BOND : angle 0.84447 ( 6) covalent geometry : bond 0.00586 (10572) covalent geometry : angle 1.26014 (14338) Misc. bond : bond 0.60703 ( 1) *********************** 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 : 1.062 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: 1.1945 time to fit residues: 178.5983 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 : 1.030 ------------------------------------------------------------------------------- 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: 0.8980 overall best weight: 0.7438 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.149438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.114158 restraints weight = 10619.748| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.46 r_work: 0.3175 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.0700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10577 Z= 0.140 Angle : 0.866 30.751 14347 Z= 0.359 Chirality : 0.046 0.257 1643 Planarity : 0.004 0.051 1752 Dihedral : 18.692 174.355 2238 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.72 % Allowed : 18.99 % 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: 0.67 (0.24), residues: 1242 helix: 1.27 (0.23), residues: 562 sheet: 0.30 (0.43), residues: 121 loop : -0.29 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 968 HIS 0.005 0.001 HIS A 245 PHE 0.013 0.001 PHE A1021 TYR 0.020 0.002 TYR A 805 ARG 0.005 0.000 ARG A 442 Details of bonding type rmsd link_NAG-ASN : bond 0.00530 ( 1) link_NAG-ASN : angle 1.22580 ( 3) hydrogen bonds : bond 0.04408 ( 482) hydrogen bonds : angle 4.89061 ( 1401) SS BOND : bond 0.00121 ( 3) SS BOND : angle 0.90580 ( 6) covalent geometry : bond 0.00320 (10572) covalent geometry : angle 0.86569 (14338) Misc. bond : bond 0.00062 ( 1) *********************** 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 147 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 107 time to evaluate : 1.012 Fit side-chains REVERT: A 206 LYS cc_start: 0.8083 (mtmm) cc_final: 0.6801 (mptp) REVERT: A 263 GLU cc_start: 0.8100 (pt0) cc_final: 0.7565 (pt0) REVERT: A 520 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8162 (pttt) REVERT: A 853 LYS cc_start: 0.8018 (mttt) cc_final: 0.7612 (mtmt) REVERT: B 177 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8650 (mm) outliers start: 40 outliers final: 21 residues processed: 142 average time/residue: 1.2343 time to fit residues: 188.3556 Evaluate side-chains 118 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR 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 520 LYS 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 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 177 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 22 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 66 optimal weight: 0.1980 chunk 8 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 4 optimal weight: 0.1980 chunk 102 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.148962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.113677 restraints weight = 10743.667| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.46 r_work: 0.3168 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10577 Z= 0.139 Angle : 0.819 30.961 14347 Z= 0.342 Chirality : 0.045 0.259 1643 Planarity : 0.004 0.055 1752 Dihedral : 15.598 168.729 2211 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.35 % Allowed : 19.74 % Favored : 76.91 % 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: 1.34 (0.23), residues: 564 sheet: 0.25 (0.43), residues: 121 loop : -0.32 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 968 HIS 0.005 0.001 HIS A 245 PHE 0.013 0.001 PHE A1021 TYR 0.021 0.001 TYR A 805 ARG 0.005 0.000 ARG A 442 Details of bonding type rmsd link_NAG-ASN : bond 0.00204 ( 1) link_NAG-ASN : angle 1.12048 ( 3) hydrogen bonds : bond 0.04276 ( 482) hydrogen bonds : angle 4.67208 ( 1401) SS BOND : bond 0.00111 ( 3) SS BOND : angle 0.88241 ( 6) covalent geometry : bond 0.00324 (10572) covalent geometry : angle 0.81921 (14338) Misc. bond : bond 0.00020 ( 1) *********************** 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 135 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 99 time to evaluate : 1.159 Fit side-chains REVERT: A 206 LYS cc_start: 0.8074 (mtmm) cc_final: 0.6807 (mptp) REVERT: A 209 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7876 (t0) REVERT: A 216 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.6173 (tmm160) REVERT: A 263 GLU cc_start: 0.8097 (pt0) cc_final: 0.7569 (pt0) outliers start: 36 outliers final: 21 residues processed: 127 average time/residue: 1.2371 time to fit residues: 169.3995 Evaluate side-chains 114 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER 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 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 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 Chi-restraints excluded: chain B residue 219 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 92 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 121 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 91 optimal weight: 0.0060 chunk 76 optimal weight: 1.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.149784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.114408 restraints weight = 10612.465| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.46 r_work: 0.3177 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10577 Z= 0.126 Angle : 0.801 30.957 14347 Z= 0.333 Chirality : 0.045 0.356 1643 Planarity : 0.004 0.053 1752 Dihedral : 14.213 164.703 2205 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.07 % Allowed : 19.93 % Favored : 77.00 % 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: 0.78 (0.23), residues: 1242 helix: 1.45 (0.22), residues: 564 sheet: 0.21 (0.43), residues: 121 loop : -0.31 (0.25), residues: 557 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00111 ( 1) link_NAG-ASN : angle 1.17482 ( 3) hydrogen bonds : bond 0.03917 ( 482) hydrogen bonds : angle 4.47532 ( 1401) SS BOND : bond 0.00094 ( 3) SS BOND : angle 0.78026 ( 6) covalent geometry : bond 0.00293 (10572) covalent geometry : angle 0.80093 (14338) Misc. bond : bond 0.00034 ( 1) *********************** 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 137 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 1.189 Fit side-chains REVERT: A 206 LYS cc_start: 0.8062 (mtmm) cc_final: 0.6780 (mptp) REVERT: A 216 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.6066 (tmm160) REVERT: A 263 GLU cc_start: 0.8073 (pt0) cc_final: 0.7593 (pt0) REVERT: A 480 MET cc_start: 0.7488 (mmm) cc_final: 0.7110 (mpm) outliers start: 33 outliers final: 22 residues processed: 131 average time/residue: 1.2328 time to fit residues: 174.3587 Evaluate side-chains 122 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 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 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 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 219 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 91 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 120 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 15 optimal weight: 0.0870 chunk 13 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.150497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.114946 restraints weight = 10572.407| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.47 r_work: 0.3184 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10577 Z= 0.116 Angle : 0.782 30.718 14347 Z= 0.324 Chirality : 0.044 0.352 1643 Planarity : 0.004 0.052 1752 Dihedral : 13.317 162.594 2204 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.79 % Allowed : 19.93 % 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: 0.87 (0.24), residues: 1242 helix: 1.55 (0.23), residues: 565 sheet: 0.16 (0.43), residues: 121 loop : -0.27 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 968 HIS 0.004 0.001 HIS A 245 PHE 0.012 0.001 PHE B 264 TYR 0.019 0.001 TYR A 805 ARG 0.005 0.000 ARG A 442 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 1) link_NAG-ASN : angle 1.19460 ( 3) hydrogen bonds : bond 0.03726 ( 482) hydrogen bonds : angle 4.38649 ( 1401) SS BOND : bond 0.00077 ( 3) SS BOND : angle 0.73567 ( 6) covalent geometry : bond 0.00266 (10572) covalent geometry : angle 0.78162 (14338) Misc. bond : bond 0.00037 ( 1) *********************** 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 136 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 1.151 Fit side-chains REVERT: A 87 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.6390 (ttm170) REVERT: A 165 LYS cc_start: 0.7870 (mptp) cc_final: 0.6931 (mmtt) REVERT: A 206 LYS cc_start: 0.8060 (mtmm) cc_final: 0.6783 (mptp) REVERT: A 216 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.6034 (tmm160) REVERT: A 263 GLU cc_start: 0.8069 (pt0) cc_final: 0.7609 (pt0) REVERT: A 480 MET cc_start: 0.7563 (mmm) cc_final: 0.7067 (mpm) outliers start: 30 outliers final: 17 residues processed: 131 average time/residue: 1.2253 time to fit residues: 173.3306 Evaluate side-chains 123 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ARG 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 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 86 THR Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 131 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 13 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 118 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 B 82 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.149797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.115186 restraints weight = 10640.551| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.47 r_work: 0.3188 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10577 Z= 0.164 Angle : 0.814 31.644 14347 Z= 0.345 Chirality : 0.046 0.322 1643 Planarity : 0.004 0.054 1752 Dihedral : 13.492 163.998 2200 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.17 % Allowed : 19.55 % 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: 0.74 (0.23), residues: 1242 helix: 1.42 (0.22), residues: 564 sheet: 0.16 (0.43), residues: 121 loop : -0.33 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 968 HIS 0.007 0.001 HIS A 245 PHE 0.017 0.002 PHE A 128 TYR 0.025 0.002 TYR A 805 ARG 0.006 0.000 ARG A 442 Details of bonding type rmsd link_NAG-ASN : bond 0.00007 ( 1) link_NAG-ASN : angle 1.17786 ( 3) hydrogen bonds : bond 0.04361 ( 482) hydrogen bonds : angle 4.53887 ( 1401) SS BOND : bond 0.00179 ( 3) SS BOND : angle 1.03672 ( 6) covalent geometry : bond 0.00394 (10572) covalent geometry : angle 0.81393 (14338) Misc. bond : bond 0.00030 ( 1) *********************** 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 143 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 1.072 Fit side-chains REVERT: A 154 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8026 (mp) REVERT: A 206 LYS cc_start: 0.8029 (mtmm) cc_final: 0.6636 (mptp) REVERT: A 211 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.7784 (mm) REVERT: A 216 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.6099 (tmm160) REVERT: A 263 GLU cc_start: 0.8083 (pt0) cc_final: 0.7569 (pt0) REVERT: A 480 MET cc_start: 0.7573 (mmm) cc_final: 0.7035 (mpm) REVERT: A 551 HIS cc_start: 0.7038 (t70) cc_final: 0.6817 (t70) REVERT: B 91 ARG cc_start: 0.7900 (ttm110) cc_final: 0.7542 (ttm-80) REVERT: B 249 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8600 (ptpt) outliers start: 34 outliers final: 23 residues processed: 136 average time/residue: 1.2155 time to fit residues: 178.9682 Evaluate side-chains 131 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 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 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 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 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 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 63 optimal weight: 0.0010 chunk 65 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.149823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.113624 restraints weight = 10769.117| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.54 r_work: 0.3197 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10577 Z= 0.126 Angle : 0.782 30.856 14347 Z= 0.329 Chirality : 0.044 0.260 1643 Planarity : 0.004 0.056 1752 Dihedral : 13.301 161.650 2200 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.89 % Allowed : 20.02 % Favored : 77.09 % 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: 0.84 (0.24), residues: 1242 helix: 1.54 (0.22), residues: 564 sheet: 0.09 (0.43), residues: 121 loop : -0.30 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 968 HIS 0.005 0.001 HIS A 551 PHE 0.021 0.002 PHE A 128 TYR 0.020 0.001 TYR A 805 ARG 0.005 0.000 ARG A 442 Details of bonding type rmsd link_NAG-ASN : bond 0.00208 ( 1) link_NAG-ASN : angle 1.20395 ( 3) hydrogen bonds : bond 0.03872 ( 482) hydrogen bonds : angle 4.42561 ( 1401) SS BOND : bond 0.00096 ( 3) SS BOND : angle 0.80354 ( 6) covalent geometry : bond 0.00295 (10572) covalent geometry : angle 0.78152 (14338) Misc. bond : bond 0.00038 ( 1) *********************** 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 138 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 1.209 Fit side-chains REVERT: A 206 LYS cc_start: 0.8039 (mtmm) cc_final: 0.6693 (mptp) REVERT: A 211 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.7830 (mm) REVERT: A 216 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.6126 (tmm160) REVERT: A 263 GLU cc_start: 0.8034 (pt0) cc_final: 0.7527 (pt0) REVERT: A 480 MET cc_start: 0.7635 (mmm) cc_final: 0.7088 (mpm) REVERT: A 485 ARG cc_start: 0.6780 (mtm-85) cc_final: 0.6560 (mtt-85) REVERT: B 91 ARG cc_start: 0.7902 (ttm110) cc_final: 0.7529 (ttm-80) REVERT: B 249 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8566 (ptpt) outliers start: 31 outliers final: 22 residues processed: 130 average time/residue: 1.2630 time to fit residues: 177.4635 Evaluate side-chains 127 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 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 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 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 219 ASP 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 13 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 4 optimal weight: 0.0980 chunk 42 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.150155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.114516 restraints weight = 10641.146| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.48 r_work: 0.3180 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10577 Z= 0.119 Angle : 0.774 30.627 14347 Z= 0.325 Chirality : 0.044 0.179 1643 Planarity : 0.004 0.057 1752 Dihedral : 13.064 159.390 2200 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.79 % Allowed : 20.11 % Favored : 77.09 % 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: 1.59 (0.23), residues: 564 sheet: 0.09 (0.43), residues: 121 loop : -0.29 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 968 HIS 0.004 0.001 HIS A 551 PHE 0.023 0.001 PHE A 128 TYR 0.019 0.001 TYR A 805 ARG 0.007 0.000 ARG A 442 Details of bonding type rmsd link_NAG-ASN : bond 0.00185 ( 1) link_NAG-ASN : angle 1.23852 ( 3) hydrogen bonds : bond 0.03735 ( 482) hydrogen bonds : angle 4.36216 ( 1401) SS BOND : bond 0.00095 ( 3) SS BOND : angle 0.77768 ( 6) covalent geometry : bond 0.00278 (10572) covalent geometry : angle 0.77387 (14338) Misc. bond : bond 0.00030 ( 1) *********************** 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 143 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 1.128 Fit side-chains REVERT: A 206 LYS cc_start: 0.8084 (mtmm) cc_final: 0.6816 (mptp) REVERT: A 216 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.6069 (tmm160) REVERT: A 246 GLU cc_start: 0.7712 (mp0) cc_final: 0.7454 (pm20) REVERT: A 263 GLU cc_start: 0.8059 (pt0) cc_final: 0.7609 (pt0) REVERT: A 480 MET cc_start: 0.7744 (mmm) cc_final: 0.7266 (mpm) REVERT: A 485 ARG cc_start: 0.6906 (mtm-85) cc_final: 0.6690 (mtt-85) REVERT: B 91 ARG cc_start: 0.7933 (ttm110) cc_final: 0.7558 (ttm-80) REVERT: B 249 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8559 (ptpt) outliers start: 30 outliers final: 21 residues processed: 136 average time/residue: 1.1727 time to fit residues: 173.3488 Evaluate side-chains 125 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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 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 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 125 ASP Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 219 ASP 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 41 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 110 optimal weight: 0.0030 chunk 76 optimal weight: 0.1980 chunk 80 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 101 optimal weight: 0.0870 chunk 75 optimal weight: 0.0870 chunk 56 optimal weight: 0.4980 chunk 73 optimal weight: 0.9980 chunk 97 optimal weight: 0.1980 overall best weight: 0.1146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 407 ASN ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 689 GLN B 82 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.155232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.120197 restraints weight = 10666.975| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.47 r_work: 0.3254 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10577 Z= 0.086 Angle : 0.742 29.870 14347 Z= 0.306 Chirality : 0.042 0.165 1643 Planarity : 0.004 0.057 1752 Dihedral : 12.296 153.197 2200 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.86 % Allowed : 21.14 % Favored : 77.00 % 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: 1.22 (0.24), residues: 1242 helix: 2.05 (0.23), residues: 546 sheet: 0.04 (0.42), residues: 122 loop : -0.19 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 430 HIS 0.004 0.001 HIS A 551 PHE 0.025 0.001 PHE A 128 TYR 0.009 0.001 TYR A 328 ARG 0.006 0.000 ARG A 442 Details of bonding type rmsd link_NAG-ASN : bond 0.00508 ( 1) link_NAG-ASN : angle 1.47136 ( 3) hydrogen bonds : bond 0.02889 ( 482) hydrogen bonds : angle 4.07853 ( 1401) SS BOND : bond 0.00050 ( 3) SS BOND : angle 0.61910 ( 6) covalent geometry : bond 0.00185 (10572) covalent geometry : angle 0.74213 (14338) Misc. bond : bond 0.00057 ( 1) *********************** 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 134 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 1.175 Fit side-chains REVERT: A 165 LYS cc_start: 0.7836 (mptp) cc_final: 0.6921 (mmtt) REVERT: A 206 LYS cc_start: 0.8042 (mtmm) cc_final: 0.6831 (mptp) REVERT: A 216 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.6026 (tmm160) REVERT: A 246 GLU cc_start: 0.7530 (mp0) cc_final: 0.7284 (pm20) REVERT: A 263 GLU cc_start: 0.8011 (pt0) cc_final: 0.7580 (pt0) REVERT: A 480 MET cc_start: 0.7759 (mmm) cc_final: 0.7288 (mpm) REVERT: A 485 ARG cc_start: 0.6998 (mtm-85) cc_final: 0.6781 (mtt-85) REVERT: A 496 SER cc_start: 0.7445 (m) cc_final: 0.6872 (p) REVERT: A 671 GLU cc_start: 0.7708 (tp30) cc_final: 0.7278 (tp30) REVERT: A 688 GLU cc_start: 0.7972 (mp0) cc_final: 0.7643 (mp0) REVERT: B 91 ARG cc_start: 0.7895 (ttm110) cc_final: 0.7529 (ttm-80) REVERT: B 249 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8515 (ptpt) outliers start: 20 outliers final: 14 residues processed: 131 average time/residue: 1.3084 time to fit residues: 184.3936 Evaluate side-chains 124 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 99 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 452 VAL 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 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 131 SER Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 249 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 67 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 75 optimal weight: 0.0980 chunk 112 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.150768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.114844 restraints weight = 10683.637| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.49 r_work: 0.3182 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10577 Z= 0.132 Angle : 0.782 30.774 14347 Z= 0.329 Chirality : 0.044 0.173 1643 Planarity : 0.004 0.056 1752 Dihedral : 12.264 155.018 2195 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.58 % Allowed : 21.32 % Favored : 77.09 % 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: 1.06 (0.24), residues: 1242 helix: 1.77 (0.23), residues: 558 sheet: 0.21 (0.43), residues: 121 loop : -0.22 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 430 HIS 0.005 0.001 HIS A 551 PHE 0.028 0.002 PHE A 128 TYR 0.021 0.001 TYR A 805 ARG 0.006 0.000 ARG A 442 Details of bonding type rmsd link_NAG-ASN : bond 0.00115 ( 1) link_NAG-ASN : angle 1.13959 ( 3) hydrogen bonds : bond 0.03787 ( 482) hydrogen bonds : angle 4.27810 ( 1401) SS BOND : bond 0.00131 ( 3) SS BOND : angle 0.81679 ( 6) covalent geometry : bond 0.00311 (10572) covalent geometry : angle 0.78234 (14338) Misc. bond : bond 0.00009 ( 1) ********************** 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 124 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 1.236 Fit side-chains REVERT: A 165 LYS cc_start: 0.7818 (mptp) cc_final: 0.6880 (mmtt) REVERT: A 206 LYS cc_start: 0.8071 (mtmm) cc_final: 0.6820 (mptp) REVERT: A 216 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.6024 (tmm160) REVERT: A 246 GLU cc_start: 0.7684 (mp0) cc_final: 0.7422 (pm20) REVERT: A 263 GLU cc_start: 0.8069 (pt0) cc_final: 0.7611 (pt0) REVERT: A 480 MET cc_start: 0.7779 (mmm) cc_final: 0.7415 (mpm) REVERT: A 551 HIS cc_start: 0.6969 (t70) cc_final: 0.6735 (t70) REVERT: A 671 GLU cc_start: 0.7764 (tp30) cc_final: 0.7323 (tp30) REVERT: B 91 ARG cc_start: 0.7914 (ttm110) cc_final: 0.7531 (ttm-80) outliers start: 17 outliers final: 13 residues processed: 120 average time/residue: 1.2737 time to fit residues: 165.2641 Evaluate side-chains 117 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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 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 460 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 759 ASP Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 131 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 30 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 92 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3714 r_free = 0.3714 target = 0.149486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113643 restraints weight = 10601.233| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.46 r_work: 0.3165 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10577 Z= 0.147 Angle : 0.787 31.099 14347 Z= 0.334 Chirality : 0.045 0.179 1643 Planarity : 0.004 0.056 1752 Dihedral : 12.388 154.349 2195 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.30 % Allowed : 22.16 % Favored : 76.54 % 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: 1.57 (0.22), residues: 564 sheet: 0.27 (0.44), residues: 115 loop : -0.25 (0.25), residues: 563 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 0.029 0.002 PHE A 128 TYR 0.023 0.002 TYR A 805 ARG 0.006 0.000 ARG A 442 Details of bonding type rmsd link_NAG-ASN : bond 0.00185 ( 1) link_NAG-ASN : angle 1.08881 ( 3) hydrogen bonds : bond 0.04058 ( 482) hydrogen bonds : angle 4.37561 ( 1401) SS BOND : bond 0.00140 ( 3) SS BOND : angle 0.93138 ( 6) covalent geometry : bond 0.00351 (10572) covalent geometry : angle 0.78710 (14338) Misc. bond : bond 0.00024 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7967.02 seconds wall clock time: 137 minutes 56.72 seconds (8276.72 seconds total)