Starting phenix.real_space_refine on Wed Mar 4 01:58:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x23_32956/03_2026/7x23_32956.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x23_32956/03_2026/7x23_32956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7x23_32956/03_2026/7x23_32956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x23_32956/03_2026/7x23_32956.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x23_32956/03_2026/7x23_32956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x23_32956/03_2026/7x23_32956.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.003 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 S 50 5.16 5 Na 3 4.78 5 C 6395 2.51 5 N 1650 2.21 5 O 1875 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9976 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7666 Classifications: {'peptide': 985} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 36, 'TRANS': 948} Chain: "B" Number of atoms: 2255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2255 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 257} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' NA': 3, 'ACP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 1.86, per 1000 atoms: 0.19 Number of scatterers: 9976 At special positions: 0 Unit cell: (122.84, 93.79, 160.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 50 16.00 P 3 15.00 Na 3 11.00 O 1875 8.00 N 1650 7.00 C 6395 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: 0.76 Conformation dependent library (CDL) restraints added in 444.1 milliseconds 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 10 sheets defined 48.5% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 61 through 69 removed outlier: 4.087A pdb=" N GLU A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN A 66 " --> pdb=" O THR A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 89 removed outlier: 3.594A pdb=" N ALA A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 110 Processing helix chain 'A' and resid 113 through 135 removed outlier: 3.575A pdb=" N LEU A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 176 removed outlier: 3.671A pdb=" N MET A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) 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 277 through 282 Processing helix chain 'A' and resid 294 through 325 Processing helix chain 'A' and resid 328 through 344 Processing helix chain 'A' and resid 347 through 366 removed outlier: 3.758A pdb=" N LYS A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 381 removed outlier: 3.743A pdb=" N THR A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 441 removed outlier: 3.521A pdb=" N ASN A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 476 Processing helix chain 'A' and resid 478 through 486 Processing helix chain 'A' and resid 522 through 529 Processing helix chain 'A' and resid 543 through 559 Processing helix chain 'A' and resid 610 through 621 Processing helix chain 'A' and resid 632 through 644 Processing helix chain 'A' and resid 652 through 661 Processing helix chain 'A' and resid 679 through 684 Processing helix chain 'A' and resid 686 through 697 Processing helix chain 'A' and resid 706 through 720 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 758 Processing helix chain 'A' and resid 767 through 794 removed outlier: 3.639A pdb=" N VAL A 771 " --> pdb=" O PHE A 767 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR A 793 " --> pdb=" O ALA A 789 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N SER A 794 " --> pdb=" O TYR A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 809 removed outlier: 3.621A pdb=" N GLU A 798 " --> pdb=" O SER A 794 " (cutoff:3.500A) Proline residue: A 801 - end of helix Processing helix chain 'A' and resid 815 through 827 Processing helix chain 'A' and resid 828 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: 4.075A pdb=" N ARG A 846 " --> pdb=" O ILE A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 868 Processing helix chain 'A' and resid 868 through 889 Processing helix chain 'A' and resid 898 through 903 Processing helix chain 'A' and resid 919 through 949 Processing helix chain 'A' and resid 955 through 960 Processing helix chain 'A' and resid 964 through 984 removed outlier: 3.929A 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 1034 Processing helix chain 'B' and resid 29 through 60 removed outlier: 3.787A pdb=" N LYS B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 110 removed outlier: 4.253A pdb=" N TYR B 98 " --> pdb=" O ASP B 94 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA B 100 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N TYR B 101 " --> pdb=" O SER B 97 " (cutoff:3.500A) 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 152 through 156 Processing helix chain 'B' and resid 166 through 170 removed outlier: 3.582A pdb=" N TYR B 169 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS B 170 " --> pdb=" O TYR B 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 166 through 170' Processing helix chain 'B' and resid 218 through 225 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 180 through 185 removed outlier: 3.709A pdb=" N VAL A 183 " --> pdb=" O LYS A 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 206 removed outlier: 4.053A pdb=" N THR A 260 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS A 224 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N GLY A 264 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N GLY A 222 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA A 266 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N SER A 220 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLY A 268 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL A 218 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL A 270 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ARG A 216 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN A 272 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 202 through 206 removed outlier: 4.053A pdb=" N THR A 260 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS A 224 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N GLY A 264 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N GLY A 222 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA A 266 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N SER A 220 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLY A 268 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL A 218 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL A 270 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ARG A 216 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN A 272 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 368 through 370 removed outlier: 5.926A pdb=" N GLY A 743 " --> pdb=" O MET A 760 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LEU A 762 " --> pdb=" O GLY A 743 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA A 745 " --> pdb=" O LEU A 762 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL A 724 " --> pdb=" O ILE A 742 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE A 744 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N VAL A 726 " --> pdb=" O ILE A 744 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N MET A 746 " --> pdb=" O VAL A 726 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N GLY A 728 " --> pdb=" O MET A 746 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE A 385 " --> pdb=" O ILE A 626 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL A 628 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N SER A 387 " --> pdb=" O VAL A 628 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL A 625 " --> pdb=" O ILE A 700 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N PHE A 702 " --> pdb=" O VAL A 625 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N MET A 627 " --> pdb=" O PHE A 702 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA A 675 " --> pdb=" O VAL A 701 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ALA A 703 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL A 677 " --> pdb=" O ALA A 703 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 409 through 411 removed outlier: 6.194A pdb=" N VAL A 400 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE A 604 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N HIS A 402 " --> pdb=" O SER A 602 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N PHE A 595 " --> pdb=" O TYR A 571 " (cutoff:3.500A) removed outlier: 9.124A pdb=" N TYR A 571 " --> pdb=" O PHE A 595 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N PHE A 597 " --> pdb=" O HIS A 569 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N HIS A 569 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY A 599 " --> pdb=" O PHE A 567 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE A 567 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS A 505 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 518 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 503 " --> pdb=" O VAL A 518 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 520 " --> pdb=" O GLN A 501 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N PHE A 500 " --> pdb=" O PHE A 494 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE A 494 " --> pdb=" O PHE A 500 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA A 490 " --> pdb=" O ILE A 504 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 409 through 411 removed outlier: 6.194A pdb=" N VAL A 400 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE A 604 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N HIS A 402 " --> pdb=" O SER A 602 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N CYS A 530 " --> pdb=" O PHE A 595 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE A 597 " --> pdb=" O CYS A 530 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N THR A 532 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N GLY A 599 " --> pdb=" O THR A 532 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N MET A 534 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 12.841A pdb=" N LEU A 601 " --> pdb=" O MET A 534 " (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 79 Processing sheet with id=AA9, first strand: chain 'B' and resid 87 through 90 removed outlier: 3.912A pdb=" N PHE B 90 " --> pdb=" O GLU B 301 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 123 through 124 488 hydrogen bonds defined for protein. 1407 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: 1.75 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3174 1.34 - 1.46: 1499 1.46 - 1.58: 5412 1.58 - 1.69: 6 1.69 - 1.81: 81 Bond restraints: 10172 Sorted by residual: bond pdb=" O2B ACP A1101 " pdb=" PB ACP A1101 " ideal model delta sigma weight residual 1.507 1.610 -0.103 2.00e-02 2.50e+03 2.63e+01 bond pdb=" O3A ACP A1101 " pdb=" PB ACP A1101 " ideal model delta sigma weight residual 1.698 1.609 0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C4 ACP A1101 " pdb=" C5 ACP A1101 " ideal model delta sigma weight residual 1.386 1.471 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" CG PRO A 612 " pdb=" CD PRO A 612 " ideal model delta sigma weight residual 1.503 1.370 0.133 3.40e-02 8.65e+02 1.54e+01 bond pdb=" O3G ACP A1101 " pdb=" PG ACP A1101 " ideal model delta sigma weight residual 1.532 1.610 -0.078 2.00e-02 2.50e+03 1.53e+01 ... (remaining 10167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 13650 2.39 - 4.78: 125 4.78 - 7.17: 17 7.17 - 9.56: 6 9.56 - 11.95: 3 Bond angle restraints: 13801 Sorted by residual: angle pdb=" N PRO A 612 " pdb=" CD PRO A 612 " pdb=" CG PRO A 612 " ideal model delta sigma weight residual 103.20 93.40 9.80 1.50e+00 4.44e-01 4.27e+01 angle pdb=" C3B ACP A1101 " pdb=" PB ACP A1101 " pdb=" O3A ACP A1101 " ideal model delta sigma weight residual 98.05 110.00 -11.95 3.00e+00 1.11e-01 1.59e+01 angle pdb=" N ASN B 206 " pdb=" CA ASN B 206 " pdb=" C ASN B 206 " ideal model delta sigma weight residual 109.81 117.62 -7.81 2.21e+00 2.05e-01 1.25e+01 angle pdb=" O1B ACP A1101 " pdb=" PB ACP A1101 " pdb=" O2B ACP A1101 " ideal model delta sigma weight residual 119.60 109.41 10.19 3.00e+00 1.11e-01 1.15e+01 angle pdb=" C LEU A 867 " pdb=" N HIS A 868 " pdb=" CA HIS A 868 " ideal model delta sigma weight residual 122.56 117.50 5.06 1.50e+00 4.44e-01 1.14e+01 ... (remaining 13796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 5533 16.05 - 32.10: 470 32.10 - 48.15: 121 48.15 - 64.21: 25 64.21 - 80.26: 9 Dihedral angle restraints: 6158 sinusoidal: 2499 harmonic: 3659 Sorted by residual: dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 148.58 -55.58 1 1.00e+01 1.00e-02 4.17e+01 dihedral pdb=" CA TYR B 247 " pdb=" C TYR B 247 " pdb=" N GLY B 248 " pdb=" CA GLY B 248 " ideal model delta harmonic sigma weight residual 180.00 160.37 19.63 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA TYR A 983 " pdb=" C TYR A 983 " pdb=" N GLY A 984 " pdb=" CA GLY A 984 " ideal model delta harmonic sigma weight residual 180.00 162.76 17.24 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 6155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1256 0.049 - 0.098: 258 0.098 - 0.147: 64 0.147 - 0.196: 2 0.196 - 0.246: 2 Chirality restraints: 1582 Sorted by residual: chirality pdb=" C1 NAG B 401 " pdb=" ND2 ASN B 158 " pdb=" C2 NAG B 401 " pdb=" O5 NAG B 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ASN B 206 " pdb=" N ASN B 206 " pdb=" C ASN B 206 " pdb=" CB ASN B 206 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.90e-01 chirality pdb=" CB VAL A 110 " pdb=" CA VAL A 110 " pdb=" CG1 VAL A 110 " pdb=" CG2 VAL A 110 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.70e-01 ... (remaining 1579 not shown) Planarity restraints: 1752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 401 " -0.055 2.00e-02 2.50e+03 4.49e-02 2.52e+01 pdb=" C7 NAG B 401 " 0.016 2.00e-02 2.50e+03 pdb=" C8 NAG B 401 " -0.042 2.00e-02 2.50e+03 pdb=" N2 NAG B 401 " 0.071 2.00e-02 2.50e+03 pdb=" O7 NAG B 401 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 686 " -0.043 5.00e-02 4.00e+02 6.62e-02 7.01e+00 pdb=" N PRO A 687 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 687 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 687 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 632 " -0.034 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO A 633 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 633 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 633 " -0.029 5.00e-02 4.00e+02 ... (remaining 1749 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1650 2.77 - 3.30: 9912 3.30 - 3.83: 16809 3.83 - 4.37: 19518 4.37 - 4.90: 33808 Nonbonded interactions: 81697 Sorted by model distance: nonbonded pdb=" OG1 THR A 793 " pdb="NA NA A1104 " model vdw 2.232 2.470 nonbonded pdb=" OG1 THR A 390 " pdb=" O3G ACP A1101 " model vdw 2.254 3.040 nonbonded pdb=" OE2 GLU A 692 " pdb=" ND2 ASN A 696 " model vdw 2.256 3.120 nonbonded pdb=" OD1 ASP A 782 " pdb=" NH1 ARG A 952 " model vdw 2.261 3.120 nonbonded pdb=" OH TYR A 914 " pdb=" O SER B 62 " model vdw 2.262 3.040 ... (remaining 81692 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: 1.030 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.800 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 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 : 0.004 0.133 10177 Z= 0.174 Angle : 0.589 11.954 13810 Z= 0.296 Chirality : 0.042 0.246 1582 Planarity : 0.004 0.066 1751 Dihedral : 13.252 80.256 3797 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.24), residues: 1258 helix: 2.19 (0.23), residues: 543 sheet: 0.28 (0.41), residues: 158 loop : -0.30 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 295 TYR 0.014 0.001 TYR A 881 PHE 0.019 0.001 PHE A 318 TRP 0.006 0.001 TRP B 32 HIS 0.003 0.001 HIS A 632 Details of bonding type rmsd covalent geometry : bond 0.00376 (10172) covalent geometry : angle 0.58857 (13801) SS BOND : bond 0.00289 ( 3) SS BOND : angle 0.26007 ( 6) hydrogen bonds : bond 0.15597 ( 476) hydrogen bonds : angle 5.81471 ( 1407) Misc. bond : bond 0.00008 ( 1) link_NAG-ASN : bond 0.00311 ( 1) link_NAG-ASN : angle 2.05016 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.1780 (mtt) cc_final: 0.0394 (ptm) REVERT: A 107 LYS cc_start: 0.5045 (tttt) cc_final: 0.4718 (ttmm) REVERT: A 176 MET cc_start: 0.1800 (pmm) cc_final: 0.0525 (ptm) REVERT: A 392 THR cc_start: 0.4597 (m) cc_final: 0.4267 (m) REVERT: A 455 MET cc_start: 0.1474 (ptp) cc_final: 0.1148 (ptm) REVERT: A 613 ASP cc_start: 0.5107 (t70) cc_final: 0.4740 (t70) REVERT: A 746 MET cc_start: 0.5926 (mpp) cc_final: 0.5384 (mmp) REVERT: A 842 ASP cc_start: 0.5850 (t70) cc_final: 0.5535 (t0) REVERT: A 976 ILE cc_start: 0.7888 (mm) cc_final: 0.7466 (mt) REVERT: A 995 MET cc_start: 0.7137 (mtp) cc_final: 0.6895 (mtm) REVERT: A 1017 MET cc_start: 0.6661 (mmp) cc_final: 0.6420 (mmt) REVERT: B 91 ARG cc_start: 0.5144 (ttm-80) cc_final: 0.4833 (ttp-110) REVERT: B 274 ARG cc_start: 0.6115 (mtt180) cc_final: 0.5850 (mtp85) REVERT: B 297 ASP cc_start: 0.7134 (m-30) cc_final: 0.6844 (m-30) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1202 time to fit residues: 32.5890 Evaluate side-chains 118 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 123 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 396 ASN ** A 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 GLN A 958 GLN A1033 ASN B 213 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.219208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.169146 restraints weight = 12272.565| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.02 r_work: 0.3353 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10177 Z= 0.139 Angle : 0.569 7.269 13810 Z= 0.297 Chirality : 0.044 0.201 1582 Planarity : 0.005 0.064 1751 Dihedral : 5.436 47.056 1412 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.01 % Allowed : 7.16 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.23), residues: 1258 helix: 1.88 (0.22), residues: 558 sheet: 0.11 (0.40), residues: 151 loop : -0.23 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 704 TYR 0.016 0.002 TYR A 881 PHE 0.015 0.001 PHE A 318 TRP 0.007 0.001 TRP A 902 HIS 0.005 0.001 HIS A 632 Details of bonding type rmsd covalent geometry : bond 0.00318 (10172) covalent geometry : angle 0.56860 (13801) SS BOND : bond 0.00312 ( 3) SS BOND : angle 0.39570 ( 6) hydrogen bonds : bond 0.04435 ( 476) hydrogen bonds : angle 4.74428 ( 1407) Misc. bond : bond 0.00062 ( 1) link_NAG-ASN : bond 0.00650 ( 1) link_NAG-ASN : angle 2.15163 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.298 Fit side-chains REVERT: A 52 MET cc_start: 0.2058 (mtt) cc_final: 0.0586 (ptm) REVERT: A 107 LYS cc_start: 0.4983 (tttt) cc_final: 0.4673 (ttmm) REVERT: A 176 MET cc_start: 0.2464 (pmm) cc_final: 0.1573 (mtm) REVERT: A 298 ILE cc_start: 0.7004 (mt) cc_final: 0.6625 (pt) REVERT: A 455 MET cc_start: 0.1856 (ptp) cc_final: 0.1193 (ptm) REVERT: A 555 MET cc_start: 0.5072 (tmm) cc_final: 0.4686 (ptt) REVERT: A 613 ASP cc_start: 0.6273 (t70) cc_final: 0.5759 (t70) REVERT: A 718 GLN cc_start: 0.5433 (OUTLIER) cc_final: 0.4856 (mt0) REVERT: A 746 MET cc_start: 0.6869 (mpp) cc_final: 0.5933 (mmp) REVERT: A 842 ASP cc_start: 0.6233 (t70) cc_final: 0.5866 (t0) REVERT: A 906 ASP cc_start: 0.6979 (m-30) cc_final: 0.6608 (m-30) REVERT: A 976 ILE cc_start: 0.7988 (mm) cc_final: 0.7475 (mt) REVERT: A 995 MET cc_start: 0.7822 (mtp) cc_final: 0.7612 (mtm) REVERT: B 39 TYR cc_start: 0.7331 (m-10) cc_final: 0.7020 (m-10) REVERT: B 91 ARG cc_start: 0.6368 (ttm-80) cc_final: 0.6168 (ttp-110) REVERT: B 95 PRO cc_start: 0.6716 (Cg_exo) cc_final: 0.6473 (Cg_endo) REVERT: B 170 LYS cc_start: 0.6253 (OUTLIER) cc_final: 0.5764 (pttm) REVERT: B 179 LYS cc_start: 0.8717 (pttt) cc_final: 0.8456 (pttt) outliers start: 11 outliers final: 7 residues processed: 140 average time/residue: 0.0974 time to fit residues: 18.8751 Evaluate side-chains 120 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 718 GLN Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 267 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 11 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 107 optimal weight: 0.1980 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 168 ASN A 396 ASN ** A 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 GLN B 263 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.220147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.169686 restraints weight = 12219.713| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.02 r_work: 0.3359 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10177 Z= 0.115 Angle : 0.512 7.562 13810 Z= 0.268 Chirality : 0.042 0.181 1582 Planarity : 0.004 0.062 1751 Dihedral : 5.147 46.289 1412 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.10 % Allowed : 9.08 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.23), residues: 1258 helix: 1.84 (0.22), residues: 565 sheet: -0.02 (0.40), residues: 151 loop : -0.23 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 704 TYR 0.016 0.001 TYR A 881 PHE 0.010 0.001 PHE B 38 TRP 0.007 0.001 TRP A 902 HIS 0.006 0.001 HIS A 632 Details of bonding type rmsd covalent geometry : bond 0.00259 (10172) covalent geometry : angle 0.51194 (13801) SS BOND : bond 0.00212 ( 3) SS BOND : angle 0.45801 ( 6) hydrogen bonds : bond 0.03931 ( 476) hydrogen bonds : angle 4.49504 ( 1407) Misc. bond : bond 0.00045 ( 1) link_NAG-ASN : bond 0.00461 ( 1) link_NAG-ASN : angle 1.61883 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.370 Fit side-chains REVERT: A 52 MET cc_start: 0.2237 (mtt) cc_final: 0.0679 (ptm) REVERT: A 107 LYS cc_start: 0.5024 (tttt) cc_final: 0.4648 (ttmm) REVERT: A 176 MET cc_start: 0.2386 (pmm) cc_final: 0.1672 (mtm) REVERT: A 298 ILE cc_start: 0.7019 (mt) cc_final: 0.6639 (pt) REVERT: A 455 MET cc_start: 0.1872 (ptp) cc_final: 0.1151 (ptm) REVERT: A 555 MET cc_start: 0.5144 (tmm) cc_final: 0.4817 (ptt) REVERT: A 680 MET cc_start: 0.6049 (mpp) cc_final: 0.5453 (tmm) REVERT: A 746 MET cc_start: 0.6798 (mpp) cc_final: 0.5885 (mmp) REVERT: A 842 ASP cc_start: 0.6485 (t70) cc_final: 0.6152 (t0) REVERT: A 906 ASP cc_start: 0.7058 (m-30) cc_final: 0.6672 (m-30) REVERT: A 976 ILE cc_start: 0.8005 (mm) cc_final: 0.7470 (mt) REVERT: A 995 MET cc_start: 0.7877 (mtp) cc_final: 0.7673 (mtm) REVERT: B 125 ASP cc_start: 0.6675 (t70) cc_final: 0.6239 (p0) REVERT: B 170 LYS cc_start: 0.6229 (OUTLIER) cc_final: 0.5754 (pttm) REVERT: B 179 LYS cc_start: 0.8761 (pttt) cc_final: 0.8473 (pttt) outliers start: 12 outliers final: 10 residues processed: 132 average time/residue: 0.1058 time to fit residues: 19.2652 Evaluate side-chains 125 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 268 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 5 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 12 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 168 ASN ** A 569 HIS ** 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 = 0.4454 r_free = 0.4454 target = 0.220382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.169954 restraints weight = 12396.635| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 2.06 r_work: 0.3379 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10177 Z= 0.104 Angle : 0.494 7.482 13810 Z= 0.257 Chirality : 0.041 0.184 1582 Planarity : 0.004 0.061 1751 Dihedral : 5.084 46.440 1412 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.47 % Allowed : 10.00 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.23), residues: 1258 helix: 1.89 (0.22), residues: 571 sheet: -0.03 (0.40), residues: 151 loop : -0.22 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 704 TYR 0.016 0.001 TYR A 881 PHE 0.009 0.001 PHE A 935 TRP 0.006 0.001 TRP A 902 HIS 0.006 0.001 HIS A 632 Details of bonding type rmsd covalent geometry : bond 0.00228 (10172) covalent geometry : angle 0.49377 (13801) SS BOND : bond 0.00186 ( 3) SS BOND : angle 0.45441 ( 6) hydrogen bonds : bond 0.03614 ( 476) hydrogen bonds : angle 4.34320 ( 1407) Misc. bond : bond 0.00139 ( 1) link_NAG-ASN : bond 0.00462 ( 1) link_NAG-ASN : angle 1.46225 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.305 Fit side-chains REVERT: A 52 MET cc_start: 0.2320 (mtt) cc_final: 0.0727 (ptm) REVERT: A 107 LYS cc_start: 0.5078 (tttt) cc_final: 0.4691 (ttmm) REVERT: A 176 MET cc_start: 0.2555 (pmm) cc_final: 0.1819 (mtm) REVERT: A 298 ILE cc_start: 0.6957 (mt) cc_final: 0.6574 (pt) REVERT: A 340 ILE cc_start: 0.8159 (mm) cc_final: 0.7951 (mp) REVERT: A 455 MET cc_start: 0.1969 (ptp) cc_final: 0.1231 (ptm) REVERT: A 551 HIS cc_start: 0.4746 (m-70) cc_final: 0.4347 (t-170) REVERT: A 555 MET cc_start: 0.5137 (tmm) cc_final: 0.4830 (ptp) REVERT: A 641 LYS cc_start: 0.7146 (ttmt) cc_final: 0.6498 (ttmm) REVERT: A 680 MET cc_start: 0.5912 (mpp) cc_final: 0.5354 (tmm) REVERT: A 697 TYR cc_start: 0.6274 (m-80) cc_final: 0.5966 (m-80) REVERT: A 746 MET cc_start: 0.6711 (mpp) cc_final: 0.5839 (mmp) REVERT: A 842 ASP cc_start: 0.6535 (t70) cc_final: 0.6205 (t0) REVERT: A 843 ILE cc_start: 0.8395 (tp) cc_final: 0.8151 (tp) REVERT: A 906 ASP cc_start: 0.7022 (m-30) cc_final: 0.6664 (m-30) REVERT: A 976 ILE cc_start: 0.8000 (mm) cc_final: 0.7452 (mt) REVERT: A 995 MET cc_start: 0.7869 (mtp) cc_final: 0.7663 (mtm) REVERT: B 125 ASP cc_start: 0.6665 (t70) cc_final: 0.6213 (p0) REVERT: B 129 MET cc_start: 0.6607 (mmm) cc_final: 0.5883 (tpt) REVERT: B 170 LYS cc_start: 0.6280 (OUTLIER) cc_final: 0.5831 (pttm) REVERT: B 179 LYS cc_start: 0.8783 (pttt) cc_final: 0.8482 (pttt) REVERT: B 241 LEU cc_start: 0.8674 (mp) cc_final: 0.8455 (mm) outliers start: 16 outliers final: 13 residues processed: 140 average time/residue: 0.1080 time to fit residues: 20.6523 Evaluate side-chains 135 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 283 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 46 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 23 optimal weight: 20.0000 chunk 111 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 168 ASN A 396 ASN A 569 HIS ** A 632 HIS ** 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 = 0.4455 r_free = 0.4455 target = 0.220267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.171256 restraints weight = 12341.580| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 2.13 r_work: 0.3355 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10177 Z= 0.120 Angle : 0.516 7.605 13810 Z= 0.268 Chirality : 0.042 0.176 1582 Planarity : 0.004 0.061 1751 Dihedral : 5.242 49.911 1412 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.74 % Allowed : 10.18 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.23), residues: 1258 helix: 1.87 (0.22), residues: 569 sheet: -0.21 (0.39), residues: 157 loop : -0.22 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 704 TYR 0.017 0.001 TYR A 881 PHE 0.011 0.001 PHE B 38 TRP 0.007 0.001 TRP A 902 HIS 0.006 0.001 HIS A 632 Details of bonding type rmsd covalent geometry : bond 0.00275 (10172) covalent geometry : angle 0.51566 (13801) SS BOND : bond 0.00245 ( 3) SS BOND : angle 0.54556 ( 6) hydrogen bonds : bond 0.03807 ( 476) hydrogen bonds : angle 4.31458 ( 1407) Misc. bond : bond 0.00198 ( 1) link_NAG-ASN : bond 0.00331 ( 1) link_NAG-ASN : angle 1.47596 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.392 Fit side-chains REVERT: A 107 LYS cc_start: 0.5173 (tttt) cc_final: 0.4748 (ttmm) REVERT: A 176 MET cc_start: 0.2720 (pmm) cc_final: 0.2035 (mtm) REVERT: A 455 MET cc_start: 0.2045 (ptp) cc_final: 0.1219 (ptm) REVERT: A 551 HIS cc_start: 0.4637 (m-70) cc_final: 0.4300 (t-170) REVERT: A 555 MET cc_start: 0.5193 (tmm) cc_final: 0.4942 (ptp) REVERT: A 697 TYR cc_start: 0.6347 (m-80) cc_final: 0.6117 (m-80) REVERT: A 737 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7241 (mp) REVERT: A 746 MET cc_start: 0.6781 (mpp) cc_final: 0.5937 (mmp) REVERT: A 827 ASP cc_start: 0.6632 (m-30) cc_final: 0.6240 (m-30) REVERT: A 842 ASP cc_start: 0.6802 (t70) cc_final: 0.6520 (t70) REVERT: A 906 ASP cc_start: 0.7111 (m-30) cc_final: 0.6883 (m-30) REVERT: A 995 MET cc_start: 0.7882 (mtp) cc_final: 0.7681 (mtm) REVERT: B 125 ASP cc_start: 0.6595 (t0) cc_final: 0.6239 (p0) REVERT: B 129 MET cc_start: 0.6505 (mmm) cc_final: 0.5767 (tpt) REVERT: B 170 LYS cc_start: 0.6298 (OUTLIER) cc_final: 0.5895 (pttm) REVERT: B 241 LEU cc_start: 0.8701 (mp) cc_final: 0.8461 (mm) REVERT: B 301 GLU cc_start: 0.6429 (OUTLIER) cc_final: 0.5983 (pp20) outliers start: 19 outliers final: 13 residues processed: 134 average time/residue: 0.1036 time to fit residues: 19.0400 Evaluate side-chains 132 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 283 ASN Chi-restraints excluded: chain B residue 301 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 0 optimal weight: 20.0000 chunk 2 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 115 optimal weight: 7.9990 chunk 12 optimal weight: 0.0370 chunk 28 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 168 ASN A 396 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.219831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.166196 restraints weight = 12394.098| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.19 r_work: 0.3341 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10177 Z= 0.116 Angle : 0.507 7.448 13810 Z= 0.262 Chirality : 0.042 0.178 1582 Planarity : 0.004 0.061 1751 Dihedral : 5.286 50.520 1412 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.11 % Allowed : 10.37 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.24), residues: 1258 helix: 1.90 (0.22), residues: 568 sheet: -0.20 (0.39), residues: 157 loop : -0.23 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 704 TYR 0.017 0.001 TYR A 881 PHE 0.010 0.001 PHE A 935 TRP 0.006 0.001 TRP A 902 HIS 0.005 0.001 HIS A 632 Details of bonding type rmsd covalent geometry : bond 0.00265 (10172) covalent geometry : angle 0.50645 (13801) SS BOND : bond 0.00216 ( 3) SS BOND : angle 0.56238 ( 6) hydrogen bonds : bond 0.03703 ( 476) hydrogen bonds : angle 4.26364 ( 1407) Misc. bond : bond 0.00114 ( 1) link_NAG-ASN : bond 0.00353 ( 1) link_NAG-ASN : angle 1.38620 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 107 LYS cc_start: 0.5252 (tttt) cc_final: 0.4842 (ttmm) REVERT: A 176 MET cc_start: 0.2821 (pmm) cc_final: 0.2107 (mtm) REVERT: A 388 ASP cc_start: 0.6174 (m-30) cc_final: 0.5147 (p0) REVERT: A 455 MET cc_start: 0.1996 (ptp) cc_final: 0.1194 (ptm) REVERT: A 551 HIS cc_start: 0.4653 (m-70) cc_final: 0.4314 (t-170) REVERT: A 555 MET cc_start: 0.5178 (tmm) cc_final: 0.4905 (ptp) REVERT: A 697 TYR cc_start: 0.6349 (m-80) cc_final: 0.6097 (m-80) REVERT: A 737 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7247 (mp) REVERT: A 746 MET cc_start: 0.6824 (mpp) cc_final: 0.6000 (mmm) REVERT: A 827 ASP cc_start: 0.6629 (m-30) cc_final: 0.6176 (m-30) REVERT: A 842 ASP cc_start: 0.6832 (t70) cc_final: 0.6548 (t70) REVERT: B 125 ASP cc_start: 0.6502 (t0) cc_final: 0.6215 (p0) REVERT: B 129 MET cc_start: 0.6552 (mmm) cc_final: 0.5773 (tpt) REVERT: B 170 LYS cc_start: 0.6283 (OUTLIER) cc_final: 0.5863 (pttm) REVERT: B 241 LEU cc_start: 0.8665 (mp) cc_final: 0.8440 (mm) REVERT: B 301 GLU cc_start: 0.6432 (OUTLIER) cc_final: 0.5968 (pp20) outliers start: 23 outliers final: 15 residues processed: 138 average time/residue: 0.0913 time to fit residues: 17.7457 Evaluate side-chains 132 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 283 ASN Chi-restraints excluded: chain B residue 301 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 57 optimal weight: 7.9990 chunk 42 optimal weight: 0.2980 chunk 22 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 111 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 396 ASN A 536 ASN ** A 632 HIS ** 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 = 0.4439 r_free = 0.4439 target = 0.218866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.166722 restraints weight = 12277.863| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.03 r_work: 0.3341 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 10177 Z= 0.152 Angle : 0.558 11.880 13810 Z= 0.288 Chirality : 0.043 0.174 1582 Planarity : 0.004 0.062 1751 Dihedral : 5.528 51.981 1412 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.02 % Allowed : 11.28 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.23), residues: 1258 helix: 1.71 (0.22), residues: 568 sheet: -0.32 (0.39), residues: 158 loop : -0.31 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 704 TYR 0.019 0.002 TYR A 881 PHE 0.013 0.001 PHE A 935 TRP 0.007 0.001 TRP A 968 HIS 0.007 0.001 HIS A 632 Details of bonding type rmsd covalent geometry : bond 0.00369 (10172) covalent geometry : angle 0.55717 (13801) SS BOND : bond 0.00269 ( 3) SS BOND : angle 0.65035 ( 6) hydrogen bonds : bond 0.04138 ( 476) hydrogen bonds : angle 4.39265 ( 1407) Misc. bond : bond 0.00120 ( 1) link_NAG-ASN : bond 0.00177 ( 1) link_NAG-ASN : angle 1.51295 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 107 LYS cc_start: 0.5164 (tttt) cc_final: 0.4722 (ttmm) REVERT: A 176 MET cc_start: 0.2916 (pmm) cc_final: 0.2171 (mtm) REVERT: A 388 ASP cc_start: 0.6281 (m-30) cc_final: 0.5364 (p0) REVERT: A 396 ASN cc_start: 0.5504 (OUTLIER) cc_final: 0.4843 (m110) REVERT: A 455 MET cc_start: 0.2098 (ptp) cc_final: 0.1267 (ptm) REVERT: A 551 HIS cc_start: 0.4589 (m-70) cc_final: 0.4343 (t-170) REVERT: A 555 MET cc_start: 0.5149 (tmm) cc_final: 0.4882 (ptp) REVERT: A 697 TYR cc_start: 0.6421 (m-80) cc_final: 0.6217 (m-80) REVERT: A 737 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7290 (mp) REVERT: A 746 MET cc_start: 0.6598 (mpp) cc_final: 0.5831 (mmm) REVERT: A 827 ASP cc_start: 0.6538 (m-30) cc_final: 0.6033 (m-30) REVERT: A 842 ASP cc_start: 0.6798 (t70) cc_final: 0.6506 (t70) REVERT: B 122 ILE cc_start: 0.7000 (OUTLIER) cc_final: 0.6336 (tt) REVERT: B 125 ASP cc_start: 0.6488 (t0) cc_final: 0.6167 (p0) REVERT: B 129 MET cc_start: 0.6538 (mmm) cc_final: 0.5839 (tpt) REVERT: B 170 LYS cc_start: 0.6220 (OUTLIER) cc_final: 0.5796 (pttm) REVERT: B 241 LEU cc_start: 0.8692 (mp) cc_final: 0.8432 (mm) REVERT: B 301 GLU cc_start: 0.6365 (OUTLIER) cc_final: 0.5890 (pp20) outliers start: 22 outliers final: 16 residues processed: 136 average time/residue: 0.0913 time to fit residues: 17.8024 Evaluate side-chains 139 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 283 ASN Chi-restraints excluded: chain B residue 301 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 66 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 396 ASN A 540 GLN ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.218570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.166380 restraints weight = 12187.491| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.03 r_work: 0.3326 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10177 Z= 0.156 Angle : 0.569 11.998 13810 Z= 0.293 Chirality : 0.044 0.174 1582 Planarity : 0.004 0.062 1751 Dihedral : 5.762 55.973 1412 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.20 % Allowed : 11.93 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.23), residues: 1258 helix: 1.60 (0.21), residues: 569 sheet: -0.35 (0.39), residues: 160 loop : -0.30 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 704 TYR 0.018 0.002 TYR A 881 PHE 0.018 0.002 PHE A 335 TRP 0.007 0.001 TRP A 968 HIS 0.008 0.001 HIS A 632 Details of bonding type rmsd covalent geometry : bond 0.00373 (10172) covalent geometry : angle 0.56840 (13801) SS BOND : bond 0.00271 ( 3) SS BOND : angle 0.69866 ( 6) hydrogen bonds : bond 0.04254 ( 476) hydrogen bonds : angle 4.41582 ( 1407) Misc. bond : bond 0.00233 ( 1) link_NAG-ASN : bond 0.00134 ( 1) link_NAG-ASN : angle 1.47612 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 107 LYS cc_start: 0.5235 (tttt) cc_final: 0.4741 (ttmm) REVERT: A 176 MET cc_start: 0.2944 (OUTLIER) cc_final: 0.2055 (mtm) REVERT: A 340 ILE cc_start: 0.8117 (mm) cc_final: 0.7803 (mp) REVERT: A 388 ASP cc_start: 0.6362 (m-30) cc_final: 0.5284 (p0) REVERT: A 396 ASN cc_start: 0.5470 (OUTLIER) cc_final: 0.4610 (m-40) REVERT: A 455 MET cc_start: 0.2047 (ptp) cc_final: 0.1266 (ptm) REVERT: A 551 HIS cc_start: 0.4638 (m-70) cc_final: 0.4348 (t-170) REVERT: A 555 MET cc_start: 0.5115 (tmm) cc_final: 0.4855 (ptp) REVERT: A 697 TYR cc_start: 0.6553 (m-80) cc_final: 0.6131 (m-80) REVERT: A 737 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7322 (mp) REVERT: A 746 MET cc_start: 0.6658 (mpp) cc_final: 0.5893 (mmm) REVERT: A 827 ASP cc_start: 0.6477 (m-30) cc_final: 0.6044 (m-30) REVERT: A 842 ASP cc_start: 0.6849 (t70) cc_final: 0.6548 (t70) REVERT: B 122 ILE cc_start: 0.6988 (OUTLIER) cc_final: 0.6327 (tt) REVERT: B 125 ASP cc_start: 0.6460 (t0) cc_final: 0.6143 (p0) REVERT: B 129 MET cc_start: 0.6584 (mmm) cc_final: 0.5891 (tpt) REVERT: B 170 LYS cc_start: 0.6275 (OUTLIER) cc_final: 0.5854 (pttm) REVERT: B 241 LEU cc_start: 0.8723 (mp) cc_final: 0.8468 (mm) REVERT: B 272 GLU cc_start: 0.6417 (tp30) cc_final: 0.6186 (mm-30) REVERT: B 301 GLU cc_start: 0.6361 (OUTLIER) cc_final: 0.5440 (tt0) outliers start: 24 outliers final: 14 residues processed: 138 average time/residue: 0.0845 time to fit residues: 16.9526 Evaluate side-chains 141 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 283 ASN Chi-restraints excluded: chain B residue 301 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 2 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 23 optimal weight: 8.9990 chunk 75 optimal weight: 0.7980 chunk 63 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 54 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 168 ASN A 396 ASN A 632 HIS B 208 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.219549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.167722 restraints weight = 12263.055| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 2.04 r_work: 0.3351 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10177 Z= 0.118 Angle : 0.528 13.038 13810 Z= 0.271 Chirality : 0.042 0.182 1582 Planarity : 0.005 0.106 1751 Dihedral : 5.584 54.991 1412 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.29 % Allowed : 12.11 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.24), residues: 1258 helix: 1.75 (0.22), residues: 570 sheet: -0.33 (0.39), residues: 158 loop : -0.30 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 704 TYR 0.016 0.001 TYR A 881 PHE 0.012 0.001 PHE A 935 TRP 0.006 0.001 TRP A 902 HIS 0.006 0.001 HIS A 632 Details of bonding type rmsd covalent geometry : bond 0.00272 (10172) covalent geometry : angle 0.52726 (13801) SS BOND : bond 0.00226 ( 3) SS BOND : angle 0.59950 ( 6) hydrogen bonds : bond 0.03846 ( 476) hydrogen bonds : angle 4.30286 ( 1407) Misc. bond : bond 0.00296 ( 1) link_NAG-ASN : bond 0.00214 ( 1) link_NAG-ASN : angle 1.31415 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 107 LYS cc_start: 0.5273 (tttt) cc_final: 0.4764 (ttmm) REVERT: A 176 MET cc_start: 0.2966 (OUTLIER) cc_final: 0.2075 (mtm) REVERT: A 340 ILE cc_start: 0.8100 (mm) cc_final: 0.7786 (mp) REVERT: A 388 ASP cc_start: 0.6424 (m-30) cc_final: 0.5355 (p0) REVERT: A 396 ASN cc_start: 0.5265 (OUTLIER) cc_final: 0.4436 (m-40) REVERT: A 455 MET cc_start: 0.1888 (ptp) cc_final: 0.1100 (ptm) REVERT: A 555 MET cc_start: 0.5124 (tmm) cc_final: 0.4889 (ptp) REVERT: A 697 TYR cc_start: 0.6540 (m-80) cc_final: 0.6157 (m-80) REVERT: A 737 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7293 (mp) REVERT: A 746 MET cc_start: 0.6539 (mpp) cc_final: 0.5833 (mmm) REVERT: A 827 ASP cc_start: 0.6530 (m-30) cc_final: 0.6038 (m-30) REVERT: A 842 ASP cc_start: 0.6867 (t70) cc_final: 0.6576 (t70) REVERT: B 122 ILE cc_start: 0.6965 (OUTLIER) cc_final: 0.6308 (tt) REVERT: B 125 ASP cc_start: 0.6477 (t0) cc_final: 0.6199 (p0) REVERT: B 129 MET cc_start: 0.6591 (mmm) cc_final: 0.5909 (tpt) REVERT: B 170 LYS cc_start: 0.6277 (OUTLIER) cc_final: 0.5864 (pttm) REVERT: B 272 GLU cc_start: 0.6398 (tp30) cc_final: 0.6189 (mm-30) REVERT: B 301 GLU cc_start: 0.6326 (OUTLIER) cc_final: 0.5417 (tt0) outliers start: 25 outliers final: 17 residues processed: 138 average time/residue: 0.0971 time to fit residues: 19.0128 Evaluate side-chains 147 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 283 ASN Chi-restraints excluded: chain B residue 301 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 10 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 396 ASN B 208 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.219818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.168062 restraints weight = 12171.108| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 2.02 r_work: 0.3357 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10177 Z= 0.120 Angle : 0.529 12.756 13810 Z= 0.272 Chirality : 0.042 0.158 1582 Planarity : 0.004 0.079 1751 Dihedral : 5.641 57.452 1412 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.20 % Allowed : 12.20 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.24), residues: 1258 helix: 1.77 (0.22), residues: 570 sheet: -0.31 (0.40), residues: 153 loop : -0.32 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 704 TYR 0.017 0.001 TYR A 881 PHE 0.011 0.001 PHE A 935 TRP 0.007 0.001 TRP A 902 HIS 0.004 0.001 HIS A 569 Details of bonding type rmsd covalent geometry : bond 0.00280 (10172) covalent geometry : angle 0.52893 (13801) SS BOND : bond 0.00228 ( 3) SS BOND : angle 0.57897 ( 6) hydrogen bonds : bond 0.03820 ( 476) hydrogen bonds : angle 4.28553 ( 1407) Misc. bond : bond 0.00320 ( 1) link_NAG-ASN : bond 0.00220 ( 1) link_NAG-ASN : angle 1.34613 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 107 LYS cc_start: 0.5265 (tttt) cc_final: 0.4763 (ttmm) REVERT: A 176 MET cc_start: 0.2911 (OUTLIER) cc_final: 0.2066 (mtm) REVERT: A 340 ILE cc_start: 0.8107 (mm) cc_final: 0.7792 (mp) REVERT: A 388 ASP cc_start: 0.6395 (m-30) cc_final: 0.5305 (p0) REVERT: A 455 MET cc_start: 0.1532 (ptp) cc_final: 0.0712 (ptm) REVERT: A 555 MET cc_start: 0.5018 (tmm) cc_final: 0.4810 (ptp) REVERT: A 697 TYR cc_start: 0.6525 (m-80) cc_final: 0.6175 (m-80) REVERT: A 737 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7356 (mp) REVERT: A 746 MET cc_start: 0.6503 (mpp) cc_final: 0.5819 (mmm) REVERT: A 827 ASP cc_start: 0.6526 (m-30) cc_final: 0.6017 (m-30) REVERT: A 842 ASP cc_start: 0.6893 (t70) cc_final: 0.6605 (t70) REVERT: B 39 TYR cc_start: 0.7284 (m-10) cc_final: 0.7083 (m-10) REVERT: B 122 ILE cc_start: 0.6921 (OUTLIER) cc_final: 0.6276 (tt) REVERT: B 125 ASP cc_start: 0.6446 (t0) cc_final: 0.6186 (p0) REVERT: B 129 MET cc_start: 0.6599 (mmm) cc_final: 0.5914 (tpt) REVERT: B 170 LYS cc_start: 0.6280 (OUTLIER) cc_final: 0.5877 (pttm) REVERT: B 272 GLU cc_start: 0.6412 (tp30) cc_final: 0.6212 (mm-30) REVERT: B 301 GLU cc_start: 0.6331 (OUTLIER) cc_final: 0.5424 (tt0) outliers start: 24 outliers final: 18 residues processed: 137 average time/residue: 0.0981 time to fit residues: 19.0114 Evaluate side-chains 144 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 283 ASN Chi-restraints excluded: chain B residue 301 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 74 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 55 optimal weight: 0.0270 chunk 52 optimal weight: 8.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN B 242 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.220188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.168793 restraints weight = 12235.131| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 2.03 r_work: 0.3364 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10177 Z= 0.111 Angle : 0.519 12.579 13810 Z= 0.267 Chirality : 0.042 0.188 1582 Planarity : 0.004 0.062 1751 Dihedral : 5.539 56.286 1412 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.83 % Allowed : 12.57 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.24), residues: 1258 helix: 1.83 (0.22), residues: 571 sheet: -0.38 (0.40), residues: 153 loop : -0.33 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 704 TYR 0.016 0.001 TYR A 881 PHE 0.010 0.001 PHE A 935 TRP 0.007 0.001 TRP A 902 HIS 0.004 0.001 HIS A 569 Details of bonding type rmsd covalent geometry : bond 0.00251 (10172) covalent geometry : angle 0.51889 (13801) SS BOND : bond 0.00206 ( 3) SS BOND : angle 0.54211 ( 6) hydrogen bonds : bond 0.03686 ( 476) hydrogen bonds : angle 4.24337 ( 1407) Misc. bond : bond 0.00350 ( 1) link_NAG-ASN : bond 0.00252 ( 1) link_NAG-ASN : angle 1.31595 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2614.14 seconds wall clock time: 45 minutes 25.88 seconds (2725.88 seconds total)