Starting phenix.real_space_refine on Mon Jul 28 04:24:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x23_32956/07_2025/7x23_32956.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x23_32956/07_2025/7x23_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7x23_32956/07_2025/7x23_32956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x23_32956/07_2025/7x23_32956.map" model { file = "/net/cci-nas-00/data/ceres_data/7x23_32956/07_2025/7x23_32956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x23_32956/07_2025/7x23_32956.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.53, per 1000 atoms: 0.65 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: 2.85 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.38 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: 3.60 Time building geometry restraints manager: 3.15 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: 1.250 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: 0.000 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.430 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.390 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (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 TRP 0.006 0.001 TRP B 32 HIS 0.003 0.001 HIS A 632 PHE 0.019 0.001 PHE A 318 TYR 0.014 0.001 TYR A 881 ARG 0.003 0.000 ARG B 295 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 1) link_NAG-ASN : angle 2.05016 ( 3) hydrogen bonds : bond 0.15597 ( 476) hydrogen bonds : angle 5.81471 ( 1407) SS BOND : bond 0.00289 ( 3) SS BOND : angle 0.26007 ( 6) covalent geometry : bond 0.00376 (10172) covalent geometry : angle 0.58857 (13801) Misc. bond : bond 0.00008 ( 1) *********************** 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 : 1.195 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: 0.4596 (m) cc_final: 0.4267 (m) REVERT: A 455 MET cc_start: 0.1475 (ptp) cc_final: 0.1148 (ptm) REVERT: A 613 ASP cc_start: 0.5106 (t70) cc_final: 0.4740 (t70) REVERT: A 746 MET cc_start: 0.5926 (mpp) cc_final: 0.5385 (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: 0.2967 time to fit residues: 80.7590 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 : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 97 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 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 ** A 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 GLN A 958 GLN B 213 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.219676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.169045 restraints weight = 12259.454| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.02 r_work: 0.3353 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1745 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= 0.131 Angle : 0.553 7.599 13810 Z= 0.289 Chirality : 0.043 0.198 1582 Planarity : 0.004 0.062 1751 Dihedral : 5.400 47.654 1412 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.01 % Allowed : 6.61 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.23), residues: 1258 helix: 1.94 (0.22), residues: 558 sheet: 0.17 (0.40), residues: 151 loop : -0.22 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 902 HIS 0.005 0.001 HIS A 632 PHE 0.013 0.001 PHE A 318 TYR 0.015 0.002 TYR A 881 ARG 0.004 0.000 ARG B 295 Details of bonding type rmsd link_NAG-ASN : bond 0.00726 ( 1) link_NAG-ASN : angle 2.11076 ( 3) hydrogen bonds : bond 0.04321 ( 476) hydrogen bonds : angle 4.72740 ( 1407) SS BOND : bond 0.00273 ( 3) SS BOND : angle 0.33866 ( 6) covalent geometry : bond 0.00297 (10172) covalent geometry : angle 0.55179 (13801) Misc. bond : bond 0.00029 ( 1) *********************** 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 144 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 1.136 Fit side-chains REVERT: A 52 MET cc_start: 0.2037 (mtt) cc_final: 0.0584 (ptm) REVERT: A 107 LYS cc_start: 0.5054 (tttt) cc_final: 0.4760 (ttmm) REVERT: A 176 MET cc_start: 0.2389 (pmm) cc_final: 0.1506 (mtm) REVERT: A 298 ILE cc_start: 0.6989 (mt) cc_final: 0.6595 (pt) REVERT: A 392 THR cc_start: 0.5277 (m) cc_final: 0.5074 (m) REVERT: A 455 MET cc_start: 0.1842 (ptp) cc_final: 0.1185 (ptm) REVERT: A 555 MET cc_start: 0.5046 (tmm) cc_final: 0.4668 (ptt) REVERT: A 613 ASP cc_start: 0.6259 (t70) cc_final: 0.5739 (t70) REVERT: A 718 GLN cc_start: 0.5429 (OUTLIER) cc_final: 0.4814 (mt0) REVERT: A 746 MET cc_start: 0.6869 (mpp) cc_final: 0.5914 (mmp) REVERT: A 838 LYS cc_start: 0.7326 (mmtp) cc_final: 0.7117 (mmtm) REVERT: A 842 ASP cc_start: 0.6248 (t70) cc_final: 0.5882 (t0) REVERT: A 906 ASP cc_start: 0.6990 (m-30) cc_final: 0.6628 (m-30) REVERT: A 976 ILE cc_start: 0.8005 (mm) cc_final: 0.7510 (mt) REVERT: A 995 MET cc_start: 0.7830 (mtp) cc_final: 0.7622 (mtm) REVERT: B 39 TYR cc_start: 0.7316 (m-10) cc_final: 0.6987 (m-80) REVERT: B 91 ARG cc_start: 0.6349 (ttm-80) cc_final: 0.6145 (ttp-110) REVERT: B 95 PRO cc_start: 0.6709 (Cg_exo) cc_final: 0.6469 (Cg_endo) REVERT: B 170 LYS cc_start: 0.6238 (OUTLIER) cc_final: 0.5733 (pttm) REVERT: B 179 LYS cc_start: 0.8703 (pttt) cc_final: 0.8448 (pttt) outliers start: 11 outliers final: 7 residues processed: 139 average time/residue: 0.2465 time to fit residues: 47.9234 Evaluate side-chains 123 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 22 optimal weight: 1.9990 chunk 87 optimal weight: 0.4980 chunk 32 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.218532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.166279 restraints weight = 12334.369| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.05 r_work: 0.3337 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2158 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= 0.144 Angle : 0.551 7.544 13810 Z= 0.287 Chirality : 0.043 0.181 1582 Planarity : 0.004 0.062 1751 Dihedral : 5.267 46.027 1412 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.10 % Allowed : 9.36 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.23), residues: 1258 helix: 1.73 (0.22), residues: 565 sheet: -0.07 (0.40), residues: 151 loop : -0.25 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 902 HIS 0.008 0.001 HIS A 632 PHE 0.013 0.002 PHE B 38 TYR 0.017 0.002 TYR A 881 ARG 0.004 0.000 ARG A 704 Details of bonding type rmsd link_NAG-ASN : bond 0.00356 ( 1) link_NAG-ASN : angle 1.70091 ( 3) hydrogen bonds : bond 0.04310 ( 476) hydrogen bonds : angle 4.57525 ( 1407) SS BOND : bond 0.00275 ( 3) SS BOND : angle 0.54676 ( 6) covalent geometry : bond 0.00337 (10172) covalent geometry : angle 0.55035 (13801) Misc. bond : bond 0.00414 ( 1) *********************** 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 137 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 1.212 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.2299 (mtt) cc_final: 0.0732 (ptm) REVERT: A 107 LYS cc_start: 0.5106 (tttt) cc_final: 0.4742 (ttmm) REVERT: A 176 MET cc_start: 0.2385 (pmm) cc_final: 0.1662 (mtm) REVERT: A 298 ILE cc_start: 0.6975 (mt) cc_final: 0.6601 (pt) REVERT: A 392 THR cc_start: 0.5319 (m) cc_final: 0.5110 (m) REVERT: A 455 MET cc_start: 0.1851 (ptp) cc_final: 0.1125 (ptm) REVERT: A 551 HIS cc_start: 0.4733 (m-70) cc_final: 0.4342 (t-170) REVERT: A 555 MET cc_start: 0.5110 (tmm) cc_final: 0.4788 (ptt) REVERT: A 680 MET cc_start: 0.5942 (mpp) cc_final: 0.5348 (tmm) REVERT: A 697 TYR cc_start: 0.6377 (m-80) cc_final: 0.6022 (m-80) REVERT: A 746 MET cc_start: 0.6929 (mpp) cc_final: 0.6013 (mmp) REVERT: A 842 ASP cc_start: 0.6594 (t70) cc_final: 0.6328 (t70) REVERT: A 872 MET cc_start: 0.7902 (mtp) cc_final: 0.7665 (mtp) REVERT: A 906 ASP cc_start: 0.7149 (m-30) cc_final: 0.6843 (m-30) REVERT: A 995 MET cc_start: 0.7888 (mtp) cc_final: 0.7686 (mtm) REVERT: B 91 ARG cc_start: 0.6311 (ttm-80) cc_final: 0.6094 (ttp-110) REVERT: B 125 ASP cc_start: 0.6703 (t70) cc_final: 0.6267 (p0) REVERT: B 129 MET cc_start: 0.6674 (mmm) cc_final: 0.5919 (tpt) REVERT: B 170 LYS cc_start: 0.6229 (OUTLIER) cc_final: 0.5780 (pttm) REVERT: B 179 LYS cc_start: 0.8776 (pttt) cc_final: 0.8476 (pttt) outliers start: 12 outliers final: 11 residues processed: 129 average time/residue: 0.2523 time to fit residues: 45.0653 Evaluate side-chains 127 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 45 optimal weight: 0.0770 chunk 29 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.7338 ------------------------------------------------------------------------------- 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** B 263 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.220314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.168901 restraints weight = 12260.163| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.01 r_work: 0.3366 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2302 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= 0.111 Angle : 0.506 7.505 13810 Z= 0.264 Chirality : 0.042 0.185 1582 Planarity : 0.004 0.061 1751 Dihedral : 5.217 46.041 1412 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.65 % Allowed : 10.09 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.23), residues: 1258 helix: 1.82 (0.22), residues: 570 sheet: -0.10 (0.40), residues: 151 loop : -0.24 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 902 HIS 0.004 0.001 HIS A 632 PHE 0.010 0.001 PHE A 935 TYR 0.016 0.001 TYR A 881 ARG 0.012 0.000 ARG A 704 Details of bonding type rmsd link_NAG-ASN : bond 0.00424 ( 1) link_NAG-ASN : angle 1.50313 ( 3) hydrogen bonds : bond 0.03799 ( 476) hydrogen bonds : angle 4.40369 ( 1407) SS BOND : bond 0.00206 ( 3) SS BOND : angle 0.55712 ( 6) covalent geometry : bond 0.00248 (10172) covalent geometry : angle 0.50511 (13801) Misc. bond : bond 0.00131 ( 1) *********************** 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 145 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.2351 (mtt) cc_final: 0.0778 (ptm) REVERT: A 107 LYS cc_start: 0.5106 (tttt) cc_final: 0.4706 (ttmm) REVERT: A 135 ASN cc_start: 0.5940 (m-40) cc_final: 0.5702 (m110) REVERT: A 176 MET cc_start: 0.2493 (pmm) cc_final: 0.1873 (mtm) REVERT: A 392 THR cc_start: 0.5300 (m) cc_final: 0.5061 (m) REVERT: A 455 MET cc_start: 0.1963 (ptp) cc_final: 0.1225 (ptm) REVERT: A 551 HIS cc_start: 0.4747 (m-70) cc_final: 0.4316 (t-170) REVERT: A 555 MET cc_start: 0.5161 (tmm) cc_final: 0.4834 (ptp) REVERT: A 641 LYS cc_start: 0.7082 (ttmt) cc_final: 0.6843 (ttmt) REVERT: A 680 MET cc_start: 0.5906 (mpp) cc_final: 0.5335 (tmm) REVERT: A 697 TYR cc_start: 0.6314 (m-80) cc_final: 0.6005 (m-80) REVERT: A 746 MET cc_start: 0.6870 (mpp) cc_final: 0.5993 (mmp) REVERT: A 842 ASP cc_start: 0.6604 (t70) cc_final: 0.6343 (t70) REVERT: A 872 MET cc_start: 0.7817 (mtp) cc_final: 0.7551 (mtp) REVERT: B 125 ASP cc_start: 0.6553 (t0) cc_final: 0.6172 (p0) REVERT: B 170 LYS cc_start: 0.6271 (OUTLIER) cc_final: 0.5825 (pttm) REVERT: B 179 LYS cc_start: 0.8779 (pttt) cc_final: 0.8471 (pttt) REVERT: B 241 LEU cc_start: 0.8662 (mp) cc_final: 0.8433 (mm) REVERT: B 301 GLU cc_start: 0.6435 (OUTLIER) cc_final: 0.6010 (pp20) outliers start: 18 outliers final: 15 residues processed: 135 average time/residue: 0.2613 time to fit residues: 47.9485 Evaluate side-chains 134 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 823 ASP Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain B residue 59 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 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 Chi-restraints excluded: chain B residue 301 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 118 optimal weight: 3.9990 chunk 14 optimal weight: 0.1980 chunk 42 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 632 HIS 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 = 0.218747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.167722 restraints weight = 12211.878| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.08 r_work: 0.3331 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 10177 Z= 0.141 Angle : 0.546 7.425 13810 Z= 0.284 Chirality : 0.043 0.184 1582 Planarity : 0.004 0.064 1751 Dihedral : 5.431 50.094 1412 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.11 % Allowed : 10.18 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.23), residues: 1258 helix: 1.69 (0.22), residues: 569 sheet: -0.25 (0.40), residues: 157 loop : -0.26 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 902 HIS 0.007 0.001 HIS A 632 PHE 0.012 0.001 PHE A 935 TYR 0.017 0.002 TYR A 881 ARG 0.007 0.000 ARG A 704 Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 1) link_NAG-ASN : angle 1.59756 ( 3) hydrogen bonds : bond 0.04123 ( 476) hydrogen bonds : angle 4.45581 ( 1407) SS BOND : bond 0.00261 ( 3) SS BOND : angle 0.63052 ( 6) covalent geometry : bond 0.00334 (10172) covalent geometry : angle 0.54518 (13801) Misc. bond : bond 0.00149 ( 1) *********************** 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 144 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 1.026 Fit side-chains REVERT: A 107 LYS cc_start: 0.5201 (tttt) cc_final: 0.4766 (ttmm) REVERT: A 176 MET cc_start: 0.2883 (pmm) cc_final: 0.2129 (mtm) REVERT: A 455 MET cc_start: 0.1936 (ptp) cc_final: 0.1121 (ptm) REVERT: A 551 HIS cc_start: 0.4718 (m-70) cc_final: 0.4369 (t-170) REVERT: A 555 MET cc_start: 0.5181 (tmm) cc_final: 0.4881 (ptp) REVERT: A 697 TYR cc_start: 0.6446 (m-80) cc_final: 0.6176 (m-80) REVERT: A 737 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7256 (mp) REVERT: A 746 MET cc_start: 0.6945 (mpp) cc_final: 0.6331 (mmm) REVERT: A 842 ASP cc_start: 0.6798 (t70) cc_final: 0.6516 (t70) REVERT: A 906 ASP cc_start: 0.7070 (m-30) cc_final: 0.6667 (m-30) REVERT: B 39 TYR cc_start: 0.7269 (m-10) cc_final: 0.6883 (m-10) REVERT: B 122 ILE cc_start: 0.7009 (OUTLIER) cc_final: 0.6360 (tt) REVERT: B 125 ASP cc_start: 0.6539 (t0) cc_final: 0.6171 (p0) REVERT: B 129 MET cc_start: 0.6600 (mmm) cc_final: 0.5850 (tpt) REVERT: B 170 LYS cc_start: 0.6244 (OUTLIER) cc_final: 0.5816 (pttm) REVERT: B 241 LEU cc_start: 0.8667 (mp) cc_final: 0.8411 (mm) REVERT: B 301 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.5849 (tm-30) outliers start: 23 outliers final: 16 residues processed: 132 average time/residue: 0.2245 time to fit residues: 41.7732 Evaluate side-chains 134 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 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 823 ASP 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 59 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 215 THR 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 116 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.219430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.167024 restraints weight = 12221.862| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.04 r_work: 0.3346 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 10177 Z= 0.134 Angle : 0.536 7.994 13810 Z= 0.279 Chirality : 0.043 0.176 1582 Planarity : 0.004 0.061 1751 Dihedral : 5.500 51.103 1412 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.20 % Allowed : 11.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.23), residues: 1258 helix: 1.71 (0.22), residues: 569 sheet: -0.33 (0.39), residues: 158 loop : -0.32 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 968 HIS 0.003 0.001 HIS A 868 PHE 0.012 0.001 PHE A 935 TYR 0.017 0.001 TYR A 881 ARG 0.010 0.000 ARG A 704 Details of bonding type rmsd link_NAG-ASN : bond 0.00268 ( 1) link_NAG-ASN : angle 1.42903 ( 3) hydrogen bonds : bond 0.04018 ( 476) hydrogen bonds : angle 4.41341 ( 1407) SS BOND : bond 0.00228 ( 3) SS BOND : angle 0.61122 ( 6) covalent geometry : bond 0.00320 (10172) covalent geometry : angle 0.53558 (13801) Misc. bond : bond 0.00235 ( 1) *********************** 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 147 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 1.172 Fit side-chains revert: symmetry clash REVERT: A 107 LYS cc_start: 0.5223 (tttt) cc_final: 0.4744 (ttmm) REVERT: A 176 MET cc_start: 0.2866 (pmm) cc_final: 0.2110 (mtm) REVERT: A 388 ASP cc_start: 0.6045 (m-30) cc_final: 0.5333 (p0) REVERT: A 455 MET cc_start: 0.1950 (ptp) cc_final: 0.1145 (ptm) REVERT: A 551 HIS cc_start: 0.4668 (m-70) cc_final: 0.4336 (t-170) REVERT: A 555 MET cc_start: 0.5101 (tmm) cc_final: 0.4838 (ptp) REVERT: A 680 MET cc_start: 0.6138 (mpp) cc_final: 0.5442 (tmm) REVERT: A 697 TYR cc_start: 0.6403 (m-80) cc_final: 0.6162 (m-80) REVERT: A 737 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7265 (mp) REVERT: A 746 MET cc_start: 0.6921 (mpp) cc_final: 0.6255 (mmm) REVERT: A 827 ASP cc_start: 0.6462 (m-30) cc_final: 0.5974 (m-30) REVERT: A 842 ASP cc_start: 0.6780 (t70) cc_final: 0.6489 (t70) REVERT: A 906 ASP cc_start: 0.7073 (m-30) cc_final: 0.6732 (m-30) REVERT: B 39 TYR cc_start: 0.7163 (m-10) cc_final: 0.6789 (m-10) REVERT: B 122 ILE cc_start: 0.6993 (OUTLIER) cc_final: 0.6344 (tt) REVERT: B 125 ASP cc_start: 0.6510 (t0) cc_final: 0.6181 (p0) REVERT: B 129 MET cc_start: 0.6614 (mmm) cc_final: 0.5851 (tpt) REVERT: B 170 LYS cc_start: 0.6276 (OUTLIER) cc_final: 0.5852 (pttm) REVERT: B 241 LEU cc_start: 0.8667 (mp) cc_final: 0.8421 (mm) REVERT: B 301 GLU cc_start: 0.6341 (OUTLIER) cc_final: 0.5578 (tm-30) outliers start: 24 outliers final: 17 residues processed: 133 average time/residue: 0.2481 time to fit residues: 46.4922 Evaluate side-chains 138 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 1.184 ------------------------------------------------------------------------------- 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 939 MET Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 60 THR 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 267 LEU 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 24 optimal weight: 0.1980 chunk 76 optimal weight: 0.4980 chunk 103 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 13 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 5 optimal weight: 0.0020 chunk 32 optimal weight: 1.9990 overall best weight: 0.3988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.220627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.163741 restraints weight = 12384.833| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 1.99 r_work: 0.3386 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 10177 Z= 0.100 Angle : 0.491 7.336 13810 Z= 0.256 Chirality : 0.041 0.174 1582 Planarity : 0.004 0.060 1751 Dihedral : 5.260 51.465 1412 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.74 % Allowed : 11.74 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.24), residues: 1258 helix: 1.91 (0.22), residues: 569 sheet: -0.34 (0.39), residues: 161 loop : -0.26 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 968 HIS 0.003 0.000 HIS A 868 PHE 0.009 0.001 PHE A 935 TYR 0.016 0.001 TYR A 881 ARG 0.011 0.000 ARG A 704 Details of bonding type rmsd link_NAG-ASN : bond 0.00365 ( 1) link_NAG-ASN : angle 1.25794 ( 3) hydrogen bonds : bond 0.03439 ( 476) hydrogen bonds : angle 4.24490 ( 1407) SS BOND : bond 0.00187 ( 3) SS BOND : angle 0.47917 ( 6) covalent geometry : bond 0.00221 (10172) covalent geometry : angle 0.49030 (13801) Misc. bond : bond 0.00135 ( 1) *********************** 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 144 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 1.800 Fit side-chains revert: symmetry clash REVERT: A 107 LYS cc_start: 0.5156 (tttt) cc_final: 0.4701 (ttmm) REVERT: A 176 MET cc_start: 0.2967 (pmm) cc_final: 0.2181 (mtm) REVERT: A 455 MET cc_start: 0.1883 (ptp) cc_final: 0.1271 (mtp) REVERT: A 551 HIS cc_start: 0.4602 (m-70) cc_final: 0.4355 (t-170) REVERT: A 555 MET cc_start: 0.5105 (tmm) cc_final: 0.4842 (ptp) REVERT: A 680 MET cc_start: 0.6086 (mpp) cc_final: 0.5426 (tmm) REVERT: A 697 TYR cc_start: 0.6424 (m-80) cc_final: 0.6218 (m-80) REVERT: A 737 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7234 (mp) REVERT: A 746 MET cc_start: 0.6759 (mpp) cc_final: 0.6204 (mmm) REVERT: A 842 ASP cc_start: 0.6756 (t70) cc_final: 0.6477 (t70) REVERT: A 906 ASP cc_start: 0.6948 (m-30) cc_final: 0.6610 (m-30) REVERT: A 963 ARG cc_start: 0.6588 (mmm-85) cc_final: 0.6290 (mmm-85) REVERT: A 976 ILE cc_start: 0.8007 (mm) cc_final: 0.7315 (mt) REVERT: B 39 TYR cc_start: 0.7042 (m-10) cc_final: 0.6670 (m-10) REVERT: B 125 ASP cc_start: 0.6481 (t0) cc_final: 0.6238 (p0) REVERT: B 129 MET cc_start: 0.6557 (mmm) cc_final: 0.5884 (tpt) REVERT: B 170 LYS cc_start: 0.6299 (OUTLIER) cc_final: 0.5868 (pttm) REVERT: B 241 LEU cc_start: 0.8651 (mp) cc_final: 0.8404 (mm) REVERT: B 301 GLU cc_start: 0.6246 (OUTLIER) cc_final: 0.5852 (pp20) outliers start: 19 outliers final: 14 residues processed: 136 average time/residue: 0.4400 time to fit residues: 84.3276 Evaluate side-chains 136 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 1.369 ------------------------------------------------------------------------------- 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 396 ASN Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 762 LEU 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 59 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 122 ILE 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 268 THR 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 54 optimal weight: 9.9990 chunk 101 optimal weight: 0.0980 chunk 66 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 32 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 79 optimal weight: 0.1980 chunk 14 optimal weight: 0.5980 overall best weight: 0.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 536 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 = 0.4458 r_free = 0.4458 target = 0.220660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.165593 restraints weight = 12253.230| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 2.00 r_work: 0.3379 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 10177 Z= 0.103 Angle : 0.489 7.359 13810 Z= 0.256 Chirality : 0.041 0.176 1582 Planarity : 0.004 0.060 1751 Dihedral : 5.280 53.929 1412 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.65 % Allowed : 12.29 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.24), residues: 1258 helix: 1.96 (0.22), residues: 569 sheet: -0.39 (0.39), residues: 161 loop : -0.24 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 902 HIS 0.002 0.000 HIS A 868 PHE 0.010 0.001 PHE A 105 TYR 0.016 0.001 TYR A 881 ARG 0.007 0.000 ARG A 704 Details of bonding type rmsd link_NAG-ASN : bond 0.00368 ( 1) link_NAG-ASN : angle 1.27896 ( 3) hydrogen bonds : bond 0.03375 ( 476) hydrogen bonds : angle 4.20466 ( 1407) SS BOND : bond 0.00179 ( 3) SS BOND : angle 0.41950 ( 6) covalent geometry : bond 0.00239 (10172) covalent geometry : angle 0.48893 (13801) Misc. bond : bond 0.00121 ( 1) *********************** 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 143 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 1.099 Fit side-chains revert: symmetry clash REVERT: A 107 LYS cc_start: 0.5189 (tttt) cc_final: 0.4776 (ttmm) REVERT: A 176 MET cc_start: 0.2877 (OUTLIER) cc_final: 0.2077 (mtm) REVERT: A 388 ASP cc_start: 0.6198 (m-30) cc_final: 0.5159 (p0) REVERT: A 455 MET cc_start: 0.1879 (ptp) cc_final: 0.1283 (mtp) REVERT: A 551 HIS cc_start: 0.4545 (m-70) cc_final: 0.4306 (t-170) REVERT: A 555 MET cc_start: 0.5130 (tmm) cc_final: 0.4860 (ptp) REVERT: A 680 MET cc_start: 0.6093 (mpp) cc_final: 0.5433 (tmm) REVERT: A 737 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7277 (mp) REVERT: A 746 MET cc_start: 0.6759 (mpp) cc_final: 0.6005 (mmm) REVERT: A 842 ASP cc_start: 0.6794 (t70) cc_final: 0.6519 (t70) REVERT: A 906 ASP cc_start: 0.7017 (m-30) cc_final: 0.6689 (m-30) REVERT: A 976 ILE cc_start: 0.8033 (mm) cc_final: 0.7341 (mt) REVERT: B 39 TYR cc_start: 0.7003 (m-10) cc_final: 0.6656 (m-10) REVERT: B 125 ASP cc_start: 0.6406 (t0) cc_final: 0.6163 (p0) REVERT: B 129 MET cc_start: 0.6629 (mmm) cc_final: 0.5913 (tpt) REVERT: B 170 LYS cc_start: 0.6293 (OUTLIER) cc_final: 0.5859 (pttm) REVERT: B 241 LEU cc_start: 0.8653 (mp) cc_final: 0.8417 (mm) REVERT: B 301 GLU cc_start: 0.6244 (OUTLIER) cc_final: 0.5838 (pp20) outliers start: 18 outliers final: 14 residues processed: 133 average time/residue: 0.2332 time to fit residues: 44.0453 Evaluate side-chains 136 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 315 ASP Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 737 LEU 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 59 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 82 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 101 optimal weight: 0.5980 chunk 120 optimal weight: 0.0470 chunk 20 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 93 optimal weight: 0.0000 chunk 35 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.5286 ------------------------------------------------------------------------------- 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** B 208 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.221150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.168721 restraints weight = 12249.598| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 2.05 r_work: 0.3396 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 10177 Z= 0.102 Angle : 0.491 7.422 13810 Z= 0.256 Chirality : 0.041 0.179 1582 Planarity : 0.004 0.074 1751 Dihedral : 5.184 52.970 1412 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.93 % Allowed : 12.57 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.24), residues: 1258 helix: 1.96 (0.22), residues: 572 sheet: -0.51 (0.39), residues: 157 loop : -0.21 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 902 HIS 0.003 0.000 HIS A 868 PHE 0.009 0.001 PHE A 105 TYR 0.016 0.001 TYR A 881 ARG 0.020 0.000 ARG A 704 Details of bonding type rmsd link_NAG-ASN : bond 0.00359 ( 1) link_NAG-ASN : angle 1.31512 ( 3) hydrogen bonds : bond 0.03354 ( 476) hydrogen bonds : angle 4.14855 ( 1407) SS BOND : bond 0.00182 ( 3) SS BOND : angle 0.40168 ( 6) covalent geometry : bond 0.00232 (10172) covalent geometry : angle 0.49037 (13801) Misc. bond : bond 0.00230 ( 1) *********************** 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 147 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.5244 (tttt) cc_final: 0.4817 (ttmm) REVERT: A 176 MET cc_start: 0.2922 (OUTLIER) cc_final: 0.2119 (mtm) REVERT: A 388 ASP cc_start: 0.6226 (m-30) cc_final: 0.5224 (p0) REVERT: A 455 MET cc_start: 0.1820 (ptp) cc_final: 0.1276 (mtp) REVERT: A 551 HIS cc_start: 0.4543 (m-70) cc_final: 0.4303 (t-170) REVERT: A 555 MET cc_start: 0.5075 (tmm) cc_final: 0.4853 (ptp) REVERT: A 680 MET cc_start: 0.6076 (mpp) cc_final: 0.5454 (tmm) REVERT: A 737 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7316 (mp) REVERT: A 746 MET cc_start: 0.6673 (mpp) cc_final: 0.5941 (mmm) REVERT: A 827 ASP cc_start: 0.6265 (m-30) cc_final: 0.5971 (m-30) REVERT: A 842 ASP cc_start: 0.6836 (t70) cc_final: 0.6469 (t0) REVERT: A 906 ASP cc_start: 0.7069 (m-30) cc_final: 0.6652 (m-30) REVERT: A 963 ARG cc_start: 0.6607 (mmm-85) cc_final: 0.6328 (mmm-85) REVERT: B 39 TYR cc_start: 0.6976 (m-10) cc_final: 0.6648 (m-10) REVERT: B 129 MET cc_start: 0.6629 (mmm) cc_final: 0.5923 (tpt) REVERT: B 170 LYS cc_start: 0.6304 (OUTLIER) cc_final: 0.5875 (pttm) REVERT: B 224 LYS cc_start: 0.7360 (mtpt) cc_final: 0.7150 (ptmt) REVERT: B 301 GLU cc_start: 0.6231 (OUTLIER) cc_final: 0.5831 (pp20) outliers start: 21 outliers final: 14 residues processed: 136 average time/residue: 0.2327 time to fit residues: 44.7127 Evaluate side-chains 140 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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 315 ASP Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 762 LEU 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 59 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 72 VAL 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 301 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 48 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 23 optimal weight: 0.0370 chunk 119 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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** B 208 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.220745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.167170 restraints weight = 12324.054| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.11 r_work: 0.3383 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 10177 Z= 0.104 Angle : 0.500 8.299 13810 Z= 0.258 Chirality : 0.041 0.163 1582 Planarity : 0.004 0.060 1751 Dihedral : 5.182 53.710 1412 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.83 % Allowed : 12.66 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.24), residues: 1258 helix: 1.96 (0.22), residues: 572 sheet: -0.47 (0.39), residues: 161 loop : -0.18 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 902 HIS 0.003 0.001 HIS A 868 PHE 0.009 0.001 PHE A 105 TYR 0.016 0.001 TYR A 881 ARG 0.011 0.000 ARG A 704 Details of bonding type rmsd link_NAG-ASN : bond 0.00350 ( 1) link_NAG-ASN : angle 1.34472 ( 3) hydrogen bonds : bond 0.03384 ( 476) hydrogen bonds : angle 4.14313 ( 1407) SS BOND : bond 0.00206 ( 3) SS BOND : angle 0.41098 ( 6) covalent geometry : bond 0.00242 (10172) covalent geometry : angle 0.49957 (13801) Misc. bond : bond 0.00187 ( 1) ********************** 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 143 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 1.126 Fit side-chains revert: symmetry clash REVERT: A 107 LYS cc_start: 0.5293 (tttt) cc_final: 0.4881 (ttmm) REVERT: A 176 MET cc_start: 0.2956 (OUTLIER) cc_final: 0.2079 (mtm) REVERT: A 388 ASP cc_start: 0.6241 (m-30) cc_final: 0.5260 (p0) REVERT: A 455 MET cc_start: 0.1845 (ptp) cc_final: 0.1297 (mtp) REVERT: A 551 HIS cc_start: 0.4512 (m-70) cc_final: 0.4283 (t-170) REVERT: A 555 MET cc_start: 0.5096 (tmm) cc_final: 0.4883 (ptp) REVERT: A 680 MET cc_start: 0.6093 (mpp) cc_final: 0.5474 (tmm) REVERT: A 737 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7360 (mp) REVERT: A 746 MET cc_start: 0.6606 (mpp) cc_final: 0.5907 (mmm) REVERT: A 827 ASP cc_start: 0.6366 (m-30) cc_final: 0.6061 (m-30) REVERT: A 842 ASP cc_start: 0.6835 (t70) cc_final: 0.6461 (t0) REVERT: A 906 ASP cc_start: 0.7089 (m-30) cc_final: 0.6678 (m-30) REVERT: A 963 ARG cc_start: 0.6705 (mmm-85) cc_final: 0.6420 (mmm-85) REVERT: B 39 TYR cc_start: 0.6992 (m-10) cc_final: 0.6649 (m-10) REVERT: B 129 MET cc_start: 0.6492 (mmm) cc_final: 0.5784 (tpt) REVERT: B 170 LYS cc_start: 0.6273 (OUTLIER) cc_final: 0.5854 (pttm) outliers start: 20 outliers final: 15 residues processed: 135 average time/residue: 0.2307 time to fit residues: 44.0878 Evaluate side-chains 137 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 1.143 ------------------------------------------------------------------------------- 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 315 ASP 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 816 THR Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 72 VAL 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 18 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN ** A 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN B 242 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.220436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.167796 restraints weight = 12184.437| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.12 r_work: 0.3375 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10177 Z= 0.109 Angle : 0.504 8.255 13810 Z= 0.260 Chirality : 0.041 0.164 1582 Planarity : 0.004 0.060 1751 Dihedral : 5.278 54.814 1412 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.11 % Allowed : 12.39 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.24), residues: 1258 helix: 1.95 (0.22), residues: 572 sheet: -0.44 (0.39), residues: 158 loop : -0.19 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 902 HIS 0.002 0.000 HIS A 868 PHE 0.010 0.001 PHE A 821 TYR 0.016 0.001 TYR A 881 ARG 0.012 0.000 ARG A 704 Details of bonding type rmsd link_NAG-ASN : bond 0.00323 ( 1) link_NAG-ASN : angle 1.36828 ( 3) hydrogen bonds : bond 0.03447 ( 476) hydrogen bonds : angle 4.16743 ( 1407) SS BOND : bond 0.00223 ( 3) SS BOND : angle 0.43506 ( 6) covalent geometry : bond 0.00255 (10172) covalent geometry : angle 0.50350 (13801) Misc. bond : bond 0.00262 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6244.27 seconds wall clock time: 110 minutes 2.48 seconds (6602.48 seconds total)