Starting phenix.real_space_refine on Mon May 19 13:15:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wa5_37391/05_2025/8wa5_37391.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wa5_37391/05_2025/8wa5_37391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wa5_37391/05_2025/8wa5_37391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wa5_37391/05_2025/8wa5_37391.map" model { file = "/net/cci-nas-00/data/ceres_data/8wa5_37391/05_2025/8wa5_37391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wa5_37391/05_2025/8wa5_37391.cif" } resolution = 2.51 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= -0.002 sd= 0.089 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9918 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians K 3 8.98 5 Al 1 5.89 5 P 1 5.49 5 Mg 1 5.21 5 S 66 5.16 5 C 6368 2.51 5 N 1648 2.21 5 O 1837 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9929 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7662 Classifications: {'peptide': 987} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 47, 'TRANS': 939} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2100 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 240} Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 37 Unusual residues: {' K': 3, ' MG': 1, 'ALF': 1, 'CLR': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 124 Unusual residues: {'NAG': 5, 'PCW': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 6.22, per 1000 atoms: 0.63 Number of scatterers: 9929 At special positions: 0 Unit cell: (82.17, 87.98, 174.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) K 3 19.00 S 66 16.00 P 1 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1837 8.00 N 1648 7.00 C 6368 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 178 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 262 " 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 302 " - " ASN B 99 " " NAG B 303 " - " ASN B 161 " " NAG B 304 " - " ASN B 221 " " NAG B 305 " - " ASN B 193 " " NAG B 306 " - " ASN B 146 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 1.3 seconds 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2338 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 9 sheets defined 52.2% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 51 through 55 Processing helix chain 'A' and resid 56 through 65 Processing helix chain 'A' and resid 73 through 85 Processing helix chain 'A' and resid 96 through 105 Processing helix chain 'A' and resid 107 through 130 removed outlier: 3.531A pdb=" N GLU A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 160 removed outlier: 4.230A pdb=" N LEU A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 removed outlier: 3.917A pdb=" N SER A 169 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 270 through 273 Processing helix chain 'A' and resid 274 through 285 Processing helix chain 'A' and resid 291 through 324 removed outlier: 4.251A pdb=" N TYR A 324 " --> pdb=" O MET A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 341 Processing helix chain 'A' and resid 344 through 362 Processing helix chain 'A' and resid 371 through 376 removed outlier: 3.903A pdb=" N THR A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 371 through 376' Processing helix chain 'A' and resid 424 through 437 Processing helix chain 'A' and resid 450 through 454 Processing helix chain 'A' and resid 459 through 473 Processing helix chain 'A' and resid 475 through 482 Processing helix chain 'A' and resid 519 through 526 Processing helix chain 'A' and resid 540 through 556 Processing helix chain 'A' and resid 581 through 585 removed outlier: 3.759A pdb=" N MET A 585 " --> pdb=" O VAL A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 618 Processing helix chain 'A' and resid 629 through 640 Processing helix chain 'A' and resid 649 through 658 Processing helix chain 'A' and resid 660 through 664 Processing helix chain 'A' and resid 665 through 669 Processing helix chain 'A' and resid 676 through 682 Processing helix chain 'A' and resid 683 through 694 Processing helix chain 'A' and resid 703 through 717 removed outlier: 3.626A pdb=" N LEU A 717 " --> pdb=" O SER A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 737 Processing helix chain 'A' and resid 748 through 755 Processing helix chain 'A' and resid 765 through 791 removed outlier: 4.117A pdb=" N LYS A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 806 Proline residue: A 798 - end of helix Processing helix chain 'A' and resid 812 through 822 Processing helix chain 'A' and resid 824 through 830 Processing helix chain 'A' and resid 831 through 834 Processing helix chain 'A' and resid 839 through 843 Processing helix chain 'A' and resid 855 through 885 removed outlier: 3.921A pdb=" N ILE A 866 " --> pdb=" O SER A 862 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A 869 " --> pdb=" O GLN A 865 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU A 885 " --> pdb=" O ALA A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 893 Processing helix chain 'A' and resid 895 through 900 Processing helix chain 'A' and resid 916 through 946 Processing helix chain 'A' and resid 952 through 957 Processing helix chain 'A' and resid 961 through 981 Processing helix chain 'A' and resid 983 through 988 Processing helix chain 'A' and resid 994 through 1000 Processing helix chain 'A' and resid 1001 through 1022 Processing helix chain 'A' and resid 1025 through 1031 Processing helix chain 'B' and resid 33 through 66 Processing helix chain 'B' and resid 103 through 119 removed outlier: 4.685A pdb=" N GLY B 108 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LEU B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 126 removed outlier: 6.020A pdb=" N ALA B 123 " --> pdb=" O TYR B 120 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU B 126 " --> pdb=" O ALA B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 164 removed outlier: 6.665A pdb=" N ASN B 161 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY B 164 " --> pdb=" O ASN B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 223 removed outlier: 4.132A pdb=" N THR B 223 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 229 Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 189 removed outlier: 4.853A pdb=" N THR A 179 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU A 199 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N CYS A 258 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LYS A 221 " --> pdb=" O CYS A 258 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N GLU A 260 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY A 219 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N THR A 262 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ALA A 217 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLN A 264 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASP A 211 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N CYS A 220 " --> pdb=" O ARG A 236 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 189 removed outlier: 4.853A pdb=" N THR A 179 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU A 199 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N CYS A 258 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LYS A 221 " --> pdb=" O CYS A 258 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N GLU A 260 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY A 219 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N THR A 262 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ALA A 217 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLN A 264 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASP A 211 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 365 through 367 removed outlier: 6.350A pdb=" N GLY A 740 " --> pdb=" O MET A 757 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU A 759 " --> pdb=" O GLY A 740 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ALA A 742 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL A 721 " --> pdb=" O ILE A 739 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N VAL A 741 " --> pdb=" O VAL A 721 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL A 723 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N MET A 743 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N GLY A 725 " --> pdb=" O MET A 743 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ILE A 382 " --> pdb=" O ILE A 623 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL A 625 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N SER A 384 " --> pdb=" O VAL A 625 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL A 622 " --> pdb=" O MET A 697 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N PHE A 699 " --> pdb=" O VAL A 622 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N MET A 624 " --> pdb=" O PHE A 699 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 405 through 408 removed outlier: 5.223A pdb=" N VAL A 397 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE A 601 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS A 399 " --> pdb=" O SER A 599 " (cutoff:3.500A) removed outlier: 9.216A pdb=" N LEU A 592 " --> pdb=" O TYR A 568 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N TYR A 568 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N PHE A 594 " --> pdb=" O GLN A 566 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N GLN A 566 " --> pdb=" O PHE A 594 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR A 503 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LYS A 485 " --> pdb=" O THR A 503 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 405 through 408 removed outlier: 5.223A pdb=" N VAL A 397 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE A 601 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS A 399 " --> pdb=" O SER A 599 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N CYS A 527 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N PHE A 594 " --> pdb=" O CYS A 527 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N SER A 529 " --> pdb=" O PHE A 594 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N GLY A 596 " --> pdb=" O SER A 529 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N LEU A 531 " --> pdb=" O GLY A 596 " (cutoff:3.500A) removed outlier: 12.328A pdb=" N VAL A 598 " --> pdb=" O LEU A 531 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 441 through 442 Processing sheet with id=AA7, first strand: chain 'A' and resid 907 through 908 Processing sheet with id=AA8, first strand: chain 'B' and resid 82 through 85 Processing sheet with id=AA9, first strand: chain 'B' and resid 95 through 99 542 hydrogen bonds defined for protein. 1515 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: 3.69 Time building geometry restraints manager: 2.89 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: 3173 1.34 - 1.46: 1696 1.46 - 1.58: 5176 1.58 - 1.70: 2 1.70 - 1.82: 99 Bond restraints: 10146 Sorted by residual: bond pdb=" C11 PCW B 301 " pdb=" O3 PCW B 301 " ideal model delta sigma weight residual 1.326 1.450 -0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" C31 PCW B 301 " pdb=" O2 PCW B 301 " ideal model delta sigma weight residual 1.333 1.454 -0.121 2.00e-02 2.50e+03 3.65e+01 bond pdb=" F3 ALF A1104 " pdb="AL ALF A1104 " ideal model delta sigma weight residual 1.685 1.800 -0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" F1 ALF A1104 " pdb="AL ALF A1104 " ideal model delta sigma weight residual 1.684 1.799 -0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" F2 ALF A1104 " pdb="AL ALF A1104 " ideal model delta sigma weight residual 1.685 1.798 -0.113 2.00e-02 2.50e+03 3.20e+01 ... (remaining 10141 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.16: 13779 14.16 - 28.32: 5 28.32 - 42.48: 0 42.48 - 56.64: 0 56.64 - 70.80: 2 Bond angle restraints: 13786 Sorted by residual: angle pdb=" F1 ALF A1104 " pdb="AL ALF A1104 " pdb=" F2 ALF A1104 " ideal model delta sigma weight residual 108.68 179.48 -70.80 3.00e+00 1.11e-01 5.57e+02 angle pdb=" F3 ALF A1104 " pdb="AL ALF A1104 " pdb=" F4 ALF A1104 " ideal model delta sigma weight residual 109.63 179.70 -70.07 3.00e+00 1.11e-01 5.46e+02 angle pdb=" F2 ALF A1104 " pdb="AL ALF A1104 " pdb=" F3 ALF A1104 " ideal model delta sigma weight residual 109.59 89.70 19.89 3.00e+00 1.11e-01 4.40e+01 angle pdb=" F2 ALF A1104 " pdb="AL ALF A1104 " pdb=" F4 ALF A1104 " ideal model delta sigma weight residual 110.21 90.39 19.82 3.00e+00 1.11e-01 4.36e+01 angle pdb=" F1 ALF A1104 " pdb="AL ALF A1104 " pdb=" F4 ALF A1104 " ideal model delta sigma weight residual 109.02 89.51 19.51 3.00e+00 1.11e-01 4.23e+01 ... (remaining 13781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.65: 6002 34.65 - 69.29: 192 69.29 - 103.94: 16 103.94 - 138.59: 0 138.59 - 173.24: 1 Dihedral angle restraints: 6211 sinusoidal: 2583 harmonic: 3628 Sorted by residual: dihedral pdb=" N PCW B 301 " pdb=" C4 PCW B 301 " pdb=" C5 PCW B 301 " pdb=" O4P PCW B 301 " ideal model delta sinusoidal sigma weight residual -66.66 106.58 -173.24 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CA LEU A 376 " pdb=" C LEU A 376 " pdb=" N GLY A 377 " pdb=" CA GLY A 377 " ideal model delta harmonic sigma weight residual 180.00 159.75 20.25 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA PHE A 764 " pdb=" C PHE A 764 " pdb=" N ALA A 765 " pdb=" CA ALA A 765 " ideal model delta harmonic sigma weight residual 180.00 162.37 17.63 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 6208 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1421 0.074 - 0.148: 143 0.148 - 0.222: 4 0.222 - 0.296: 2 0.296 - 0.370: 1 Chirality restraints: 1571 Sorted by residual: chirality pdb=" C1 NAG B 304 " pdb=" ND2 ASN B 221 " pdb=" C2 NAG B 304 " pdb=" O5 NAG B 304 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" C1 NAG B 306 " pdb=" ND2 ASN B 146 " pdb=" C2 NAG B 306 " pdb=" O5 NAG B 306 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ASN B 221 " pdb=" N ASN B 221 " pdb=" C ASN B 221 " pdb=" CB ASN B 221 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1568 not shown) Planarity restraints: 1766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 302 " -0.270 2.00e-02 2.50e+03 2.26e-01 6.40e+02 pdb=" C7 NAG B 302 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG B 302 " -0.180 2.00e-02 2.50e+03 pdb=" N2 NAG B 302 " 0.382 2.00e-02 2.50e+03 pdb=" O7 NAG B 302 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 303 " -0.175 2.00e-02 2.50e+03 1.45e-01 2.61e+02 pdb=" C7 NAG B 303 " 0.049 2.00e-02 2.50e+03 pdb=" C8 NAG B 303 " -0.129 2.00e-02 2.50e+03 pdb=" N2 NAG B 303 " 0.233 2.00e-02 2.50e+03 pdb=" O7 NAG B 303 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 304 " 0.056 2.00e-02 2.50e+03 4.56e-02 2.60e+01 pdb=" C7 NAG B 304 " -0.015 2.00e-02 2.50e+03 pdb=" C8 NAG B 304 " 0.042 2.00e-02 2.50e+03 pdb=" N2 NAG B 304 " -0.072 2.00e-02 2.50e+03 pdb=" O7 NAG B 304 " -0.011 2.00e-02 2.50e+03 ... (remaining 1763 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.57: 54 2.57 - 3.21: 9018 3.21 - 3.85: 20178 3.85 - 4.50: 27802 4.50 - 5.14: 43895 Nonbonded interactions: 100947 Sorted by model distance: nonbonded pdb=" F2 ALF A1104 " pdb="MG MG A1105 " model vdw 1.926 2.120 nonbonded pdb=" OD1 ASP A 726 " pdb="MG MG A1105 " model vdw 2.003 2.170 nonbonded pdb=" O THR A 387 " pdb="MG MG A1105 " model vdw 2.004 2.170 nonbonded pdb=" OD2 ASP A 385 " pdb="MG MG A1105 " model vdw 2.153 2.170 nonbonded pdb=" O PRO B 145 " pdb=" OG1 THR B 148 " model vdw 2.200 3.040 ... (remaining 100942 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: 5.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.180 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 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 0.124 10155 Z= 0.234 Angle : 1.102 70.797 13807 Z= 0.428 Chirality : 0.044 0.370 1571 Planarity : 0.008 0.226 1761 Dihedral : 16.205 173.237 3864 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.85 % Allowed : 15.99 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1245 helix: 1.94 (0.21), residues: 572 sheet: -0.13 (0.38), residues: 177 loop : -0.19 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 401 HIS 0.003 0.001 HIS A 629 PHE 0.025 0.001 PHE A 300 TYR 0.016 0.001 TYR A 802 ARG 0.010 0.000 ARG A 428 Details of bonding type rmsd link_NAG-ASN : bond 0.00577 ( 5) link_NAG-ASN : angle 2.39806 ( 15) hydrogen bonds : bond 0.13561 ( 521) hydrogen bonds : angle 5.87659 ( 1515) SS BOND : bond 0.00087 ( 3) SS BOND : angle 0.56766 ( 6) covalent geometry : bond 0.00416 (10146) covalent geometry : angle 1.10023 (13786) Misc. bond : bond 0.11946 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 ARG cc_start: 0.6777 (mtm-85) cc_final: 0.6537 (mtm-85) REVERT: A 677 MET cc_start: 0.6969 (mmp) cc_final: 0.6715 (mmt) outliers start: 9 outliers final: 6 residues processed: 126 average time/residue: 1.4545 time to fit residues: 195.4778 Evaluate side-chains 121 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain B residue 35 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 chunk 52 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 59 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.144317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.109467 restraints weight = 11037.272| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.78 r_work: 0.3128 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10155 Z= 0.162 Angle : 0.817 30.895 13807 Z= 0.354 Chirality : 0.046 0.379 1571 Planarity : 0.005 0.050 1761 Dihedral : 8.213 166.788 1575 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.14 % Allowed : 12.32 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.16 (0.23), residues: 1245 helix: 1.77 (0.21), residues: 588 sheet: 0.05 (0.42), residues: 141 loop : -0.10 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 915 HIS 0.005 0.001 HIS A 629 PHE 0.029 0.002 PHE A 300 TYR 0.023 0.002 TYR A 802 ARG 0.007 0.000 ARG A 428 Details of bonding type rmsd link_NAG-ASN : bond 0.00337 ( 5) link_NAG-ASN : angle 2.97287 ( 15) hydrogen bonds : bond 0.04728 ( 521) hydrogen bonds : angle 4.71584 ( 1515) SS BOND : bond 0.00238 ( 3) SS BOND : angle 0.87554 ( 6) covalent geometry : bond 0.00379 (10146) covalent geometry : angle 0.81167 (13786) Misc. bond : bond 0.00324 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 113 time to evaluate : 1.137 Fit side-chains revert: symmetry clash REVERT: A 54 GLN cc_start: 0.7292 (OUTLIER) cc_final: 0.6482 (mt0) REVERT: A 103 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7993 (ttp-170) REVERT: A 171 LYS cc_start: 0.7119 (ttmt) cc_final: 0.6875 (ttmm) REVERT: A 216 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8034 (pt0) REVERT: A 414 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.8225 (p0) REVERT: A 428 ARG cc_start: 0.7231 (mtm-85) cc_final: 0.7009 (mtm-85) REVERT: A 560 ARG cc_start: 0.7671 (mtm-85) cc_final: 0.7336 (mtm-85) REVERT: A 650 VAL cc_start: 0.8528 (OUTLIER) cc_final: 0.8174 (p) REVERT: A 677 MET cc_start: 0.7804 (mmp) cc_final: 0.7557 (mmt) REVERT: A 772 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8410 (tt0) REVERT: A 933 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8888 (tp) REVERT: B 115 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.6872 (ptt90) outliers start: 44 outliers final: 10 residues processed: 141 average time/residue: 1.3708 time to fit residues: 206.1123 Evaluate side-chains 125 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 115 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 103 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 865 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.144096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.108699 restraints weight = 11176.322| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.83 r_work: 0.3123 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10155 Z= 0.143 Angle : 0.787 30.223 13807 Z= 0.337 Chirality : 0.044 0.310 1571 Planarity : 0.004 0.047 1761 Dihedral : 8.002 168.494 1571 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.86 % Allowed : 13.17 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.24 (0.23), residues: 1245 helix: 1.87 (0.21), residues: 588 sheet: 0.14 (0.42), residues: 136 loop : -0.14 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 106 HIS 0.005 0.001 HIS A 629 PHE 0.029 0.002 PHE A 300 TYR 0.018 0.001 TYR A 802 ARG 0.004 0.000 ARG A 428 Details of bonding type rmsd link_NAG-ASN : bond 0.00355 ( 5) link_NAG-ASN : angle 2.71532 ( 15) hydrogen bonds : bond 0.04374 ( 521) hydrogen bonds : angle 4.52918 ( 1515) SS BOND : bond 0.00231 ( 3) SS BOND : angle 0.78644 ( 6) covalent geometry : bond 0.00335 (10146) covalent geometry : angle 0.78254 (13786) Misc. bond : bond 0.00197 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 114 time to evaluate : 1.290 Fit side-chains revert: symmetry clash REVERT: A 171 LYS cc_start: 0.7157 (ttmt) cc_final: 0.6912 (ttmm) REVERT: A 202 MET cc_start: 0.7492 (mmp) cc_final: 0.7288 (mtm) REVERT: A 414 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8289 (p0) REVERT: A 560 ARG cc_start: 0.7673 (mtm-85) cc_final: 0.7411 (mtm-85) REVERT: A 650 VAL cc_start: 0.8534 (OUTLIER) cc_final: 0.8190 (m) REVERT: A 677 MET cc_start: 0.7903 (mmp) cc_final: 0.7648 (mmt) REVERT: A 682 MET cc_start: 0.8036 (mtm) cc_final: 0.7734 (ttm) REVERT: A 844 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.7890 (mtt-85) REVERT: A 865 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8106 (mt0) REVERT: A 933 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8891 (tp) REVERT: B 84 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8482 (pt) REVERT: B 115 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.6810 (ptt90) outliers start: 41 outliers final: 11 residues processed: 141 average time/residue: 1.4198 time to fit residues: 213.1917 Evaluate side-chains 124 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 865 GLN Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 115 ARG Chi-restraints excluded: chain B residue 183 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 15 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 865 GLN A 884 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.142751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.108091 restraints weight = 11095.518| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.80 r_work: 0.3110 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10155 Z= 0.161 Angle : 0.801 30.451 13807 Z= 0.345 Chirality : 0.045 0.293 1571 Planarity : 0.005 0.048 1761 Dihedral : 7.991 171.299 1570 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.57 % Allowed : 13.55 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1245 helix: 1.84 (0.21), residues: 587 sheet: 0.06 (0.42), residues: 138 loop : -0.19 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 106 HIS 0.005 0.001 HIS A 629 PHE 0.029 0.002 PHE A 300 TYR 0.020 0.002 TYR A 802 ARG 0.009 0.000 ARG A 428 Details of bonding type rmsd link_NAG-ASN : bond 0.00244 ( 5) link_NAG-ASN : angle 3.10126 ( 15) hydrogen bonds : bond 0.04495 ( 521) hydrogen bonds : angle 4.51970 ( 1515) SS BOND : bond 0.00259 ( 3) SS BOND : angle 0.81026 ( 6) covalent geometry : bond 0.00383 (10146) covalent geometry : angle 0.79528 (13786) Misc. bond : bond 0.00125 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 108 time to evaluate : 1.188 Fit side-chains revert: symmetry clash REVERT: A 54 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.6760 (mt0) REVERT: A 171 LYS cc_start: 0.7209 (ttmt) cc_final: 0.6952 (ttmm) REVERT: A 216 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8400 (pt0) REVERT: A 314 THR cc_start: 0.8829 (t) cc_final: 0.8625 (p) REVERT: A 414 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.8341 (p0) REVERT: A 560 ARG cc_start: 0.7696 (mtm-85) cc_final: 0.7445 (mtm-85) REVERT: A 650 VAL cc_start: 0.8538 (OUTLIER) cc_final: 0.8180 (m) REVERT: A 677 MET cc_start: 0.7891 (mmp) cc_final: 0.7630 (mmt) REVERT: A 772 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8383 (tt0) REVERT: A 844 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7880 (mtt-85) REVERT: A 933 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8879 (tp) REVERT: A 1031 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8502 (mt) REVERT: B 84 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8476 (pt) REVERT: B 115 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.6827 (ptt90) outliers start: 38 outliers final: 15 residues processed: 131 average time/residue: 1.4250 time to fit residues: 199.1107 Evaluate side-chains 131 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 115 ARG Chi-restraints excluded: chain B residue 183 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 53 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 44 optimal weight: 0.0970 chunk 104 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.144267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.109907 restraints weight = 11081.941| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.81 r_work: 0.3123 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10155 Z= 0.123 Angle : 0.769 30.205 13807 Z= 0.326 Chirality : 0.043 0.293 1571 Planarity : 0.004 0.045 1761 Dihedral : 7.738 170.197 1570 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.82 % Allowed : 14.68 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.30 (0.23), residues: 1245 helix: 1.98 (0.21), residues: 586 sheet: 0.15 (0.41), residues: 140 loop : -0.17 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 401 HIS 0.004 0.001 HIS A 629 PHE 0.029 0.001 PHE A 300 TYR 0.016 0.001 TYR A 802 ARG 0.009 0.000 ARG A 428 Details of bonding type rmsd link_NAG-ASN : bond 0.00230 ( 5) link_NAG-ASN : angle 3.27313 ( 15) hydrogen bonds : bond 0.03982 ( 521) hydrogen bonds : angle 4.35466 ( 1515) SS BOND : bond 0.00204 ( 3) SS BOND : angle 0.62358 ( 6) covalent geometry : bond 0.00282 (10146) covalent geometry : angle 0.76193 (13786) Misc. bond : bond 0.00086 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 1.200 Fit side-chains revert: symmetry clash REVERT: A 171 LYS cc_start: 0.7056 (OUTLIER) cc_final: 0.6625 (ttmt) REVERT: A 202 MET cc_start: 0.7795 (ttm) cc_final: 0.7567 (ttm) REVERT: A 414 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8391 (p0) REVERT: A 560 ARG cc_start: 0.7665 (mtm-85) cc_final: 0.7453 (mtm-85) REVERT: A 677 MET cc_start: 0.7786 (mmp) cc_final: 0.7536 (mmt) REVERT: A 772 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8385 (tt0) REVERT: A 844 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7836 (mtt-85) REVERT: A 1031 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8413 (mt) REVERT: B 78 LYS cc_start: 0.8686 (mmpt) cc_final: 0.8335 (mmtm) REVERT: B 84 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8436 (pt) REVERT: B 115 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.6775 (ptt90) outliers start: 30 outliers final: 15 residues processed: 125 average time/residue: 1.4457 time to fit residues: 192.9052 Evaluate side-chains 126 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 115 ARG Chi-restraints excluded: chain B residue 183 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 60 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.142087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.107389 restraints weight = 11059.786| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.79 r_work: 0.3098 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10155 Z= 0.167 Angle : 0.804 30.582 13807 Z= 0.348 Chirality : 0.045 0.265 1571 Planarity : 0.005 0.047 1761 Dihedral : 7.925 173.395 1570 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.29 % Allowed : 14.49 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.18 (0.23), residues: 1245 helix: 1.86 (0.21), residues: 587 sheet: 0.13 (0.41), residues: 138 loop : -0.21 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 401 HIS 0.005 0.001 HIS A 629 PHE 0.030 0.002 PHE A 300 TYR 0.020 0.002 TYR A 802 ARG 0.010 0.000 ARG A 428 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 5) link_NAG-ASN : angle 3.01524 ( 15) hydrogen bonds : bond 0.04549 ( 521) hydrogen bonds : angle 4.46044 ( 1515) SS BOND : bond 0.00275 ( 3) SS BOND : angle 0.82832 ( 6) covalent geometry : bond 0.00398 (10146) covalent geometry : angle 0.79817 (13786) Misc. bond : bond 0.00113 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 LYS cc_start: 0.7173 (OUTLIER) cc_final: 0.6738 (ttmt) REVERT: A 314 THR cc_start: 0.8865 (t) cc_final: 0.8623 (p) REVERT: A 650 VAL cc_start: 0.8540 (OUTLIER) cc_final: 0.8179 (m) REVERT: A 677 MET cc_start: 0.7874 (mmp) cc_final: 0.7595 (mmt) REVERT: A 772 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8405 (tt0) REVERT: A 844 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.7894 (mtp-110) REVERT: A 1031 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8510 (mt) REVERT: B 84 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8576 (pt) REVERT: B 115 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.6843 (ptt90) REVERT: B 289 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.7563 (mm-40) outliers start: 35 outliers final: 15 residues processed: 134 average time/residue: 1.4073 time to fit residues: 201.1948 Evaluate side-chains 129 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 587 PHE Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 115 ARG Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 289 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 86 optimal weight: 1.9990 chunk 76 optimal weight: 0.0770 chunk 28 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 121 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 66 optimal weight: 0.3980 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.142635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.107914 restraints weight = 11210.345| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.81 r_work: 0.3107 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10155 Z= 0.144 Angle : 0.790 30.513 13807 Z= 0.337 Chirality : 0.044 0.259 1571 Planarity : 0.004 0.046 1761 Dihedral : 7.762 173.523 1570 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.39 % Allowed : 14.49 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.27 (0.23), residues: 1245 helix: 1.92 (0.21), residues: 587 sheet: 0.25 (0.42), residues: 137 loop : -0.18 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 401 HIS 0.004 0.001 HIS A 629 PHE 0.029 0.002 PHE A 300 TYR 0.018 0.001 TYR A 802 ARG 0.012 0.000 ARG A 850 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 5) link_NAG-ASN : angle 3.43443 ( 15) hydrogen bonds : bond 0.04228 ( 521) hydrogen bonds : angle 4.37829 ( 1515) SS BOND : bond 0.00230 ( 3) SS BOND : angle 0.72359 ( 6) covalent geometry : bond 0.00341 (10146) covalent geometry : angle 0.78248 (13786) Misc. bond : bond 0.00106 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 LYS cc_start: 0.7097 (OUTLIER) cc_final: 0.6656 (ttmt) REVERT: A 455 ILE cc_start: 0.8535 (mm) cc_final: 0.8298 (mm) REVERT: A 650 VAL cc_start: 0.8545 (OUTLIER) cc_final: 0.8182 (m) REVERT: A 677 MET cc_start: 0.7839 (mmp) cc_final: 0.7587 (mmt) REVERT: A 682 MET cc_start: 0.8394 (mtm) cc_final: 0.8032 (mtp) REVERT: A 772 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8400 (tt0) REVERT: A 844 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7876 (mtt-85) REVERT: A 865 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8113 (mt0) REVERT: A 1002 MET cc_start: 0.8913 (mtt) cc_final: 0.8676 (mtt) REVERT: A 1031 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8489 (mt) REVERT: B 78 LYS cc_start: 0.8698 (mmpt) cc_final: 0.8378 (mmtm) REVERT: B 115 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.6852 (ptt90) REVERT: B 289 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.7496 (mm-40) outliers start: 36 outliers final: 15 residues processed: 127 average time/residue: 1.4358 time to fit residues: 194.1521 Evaluate side-chains 126 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 587 PHE Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 865 GLN Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 115 ARG Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 289 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 80 optimal weight: 0.7980 chunk 59 optimal weight: 0.0980 chunk 44 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 43 optimal weight: 0.0870 chunk 45 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 0.0470 overall best weight: 0.2856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.145825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.111919 restraints weight = 11172.325| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.79 r_work: 0.3157 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10155 Z= 0.098 Angle : 0.751 30.051 13807 Z= 0.313 Chirality : 0.042 0.248 1571 Planarity : 0.004 0.051 1761 Dihedral : 7.294 173.038 1570 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.26 % Allowed : 15.43 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.46 (0.24), residues: 1245 helix: 2.21 (0.22), residues: 584 sheet: 0.16 (0.41), residues: 141 loop : -0.20 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 915 HIS 0.002 0.001 HIS A 629 PHE 0.028 0.001 PHE A 300 TYR 0.011 0.001 TYR A 802 ARG 0.013 0.000 ARG A 850 Details of bonding type rmsd link_NAG-ASN : bond 0.00350 ( 5) link_NAG-ASN : angle 2.77342 ( 15) hydrogen bonds : bond 0.03453 ( 521) hydrogen bonds : angle 4.16592 ( 1515) SS BOND : bond 0.00143 ( 3) SS BOND : angle 0.45657 ( 6) covalent geometry : bond 0.00212 (10146) covalent geometry : angle 0.74590 (13786) Misc. bond : bond 0.00047 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.6798 (mt0) REVERT: A 171 LYS cc_start: 0.6968 (OUTLIER) cc_final: 0.6526 (ttmt) REVERT: A 455 ILE cc_start: 0.8517 (mm) cc_final: 0.8290 (mp) REVERT: A 560 ARG cc_start: 0.7683 (mtm-85) cc_final: 0.7465 (mtm-85) REVERT: A 677 MET cc_start: 0.7759 (mmp) cc_final: 0.7519 (mmt) REVERT: A 865 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7958 (mt0) REVERT: A 1031 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8347 (mt) REVERT: B 78 LYS cc_start: 0.8667 (mmpt) cc_final: 0.8368 (mmtm) outliers start: 24 outliers final: 9 residues processed: 115 average time/residue: 1.6220 time to fit residues: 197.9546 Evaluate side-chains 109 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 587 PHE Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 865 GLN Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain B residue 106 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 107 optimal weight: 0.3980 chunk 89 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.143578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.108889 restraints weight = 11151.797| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.89 r_work: 0.3116 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10155 Z= 0.126 Angle : 0.777 30.309 13807 Z= 0.329 Chirality : 0.044 0.226 1571 Planarity : 0.004 0.056 1761 Dihedral : 7.381 174.170 1570 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.79 % Allowed : 16.37 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.43 (0.24), residues: 1245 helix: 2.09 (0.21), residues: 586 sheet: 0.29 (0.42), residues: 138 loop : -0.13 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 401 HIS 0.003 0.001 HIS A 629 PHE 0.028 0.001 PHE A 300 TYR 0.019 0.001 TYR A 802 ARG 0.013 0.000 ARG A 850 Details of bonding type rmsd link_NAG-ASN : bond 0.00284 ( 5) link_NAG-ASN : angle 2.73358 ( 15) hydrogen bonds : bond 0.03975 ( 521) hydrogen bonds : angle 4.27275 ( 1515) SS BOND : bond 0.00195 ( 3) SS BOND : angle 0.61803 ( 6) covalent geometry : bond 0.00293 (10146) covalent geometry : angle 0.77175 (13786) Misc. bond : bond 0.00070 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 LYS cc_start: 0.7034 (OUTLIER) cc_final: 0.6788 (ttmm) REVERT: A 455 ILE cc_start: 0.8513 (mm) cc_final: 0.8285 (mp) REVERT: A 677 MET cc_start: 0.7820 (mmp) cc_final: 0.7553 (mmt) REVERT: A 844 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7844 (mtt-85) REVERT: A 865 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8076 (mt0) REVERT: A 1031 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8454 (mt) REVERT: B 78 LYS cc_start: 0.8683 (mmpt) cc_final: 0.8352 (mmtm) outliers start: 19 outliers final: 9 residues processed: 113 average time/residue: 1.5689 time to fit residues: 189.5194 Evaluate side-chains 112 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 865 GLN Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 289 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 32 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 chunk 23 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 107 optimal weight: 0.0370 chunk 38 optimal weight: 0.9980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.144328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.109934 restraints weight = 11114.581| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.82 r_work: 0.3135 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10155 Z= 0.113 Angle : 0.766 30.338 13807 Z= 0.322 Chirality : 0.043 0.225 1571 Planarity : 0.004 0.059 1761 Dihedral : 7.285 173.243 1570 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.51 % Allowed : 16.75 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.47 (0.24), residues: 1245 helix: 2.14 (0.22), residues: 586 sheet: 0.29 (0.42), residues: 138 loop : -0.12 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 401 HIS 0.003 0.001 HIS A 629 PHE 0.028 0.001 PHE A 300 TYR 0.014 0.001 TYR A 802 ARG 0.014 0.000 ARG A 850 Details of bonding type rmsd link_NAG-ASN : bond 0.00284 ( 5) link_NAG-ASN : angle 2.57898 ( 15) hydrogen bonds : bond 0.03739 ( 521) hydrogen bonds : angle 4.21696 ( 1515) SS BOND : bond 0.00186 ( 3) SS BOND : angle 0.54415 ( 6) covalent geometry : bond 0.00256 (10146) covalent geometry : angle 0.76183 (13786) Misc. bond : bond 0.00068 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 LYS cc_start: 0.6996 (OUTLIER) cc_final: 0.6733 (ttmm) REVERT: A 455 ILE cc_start: 0.8555 (mm) cc_final: 0.8338 (mp) REVERT: A 677 MET cc_start: 0.7882 (mmp) cc_final: 0.7610 (mmt) REVERT: A 865 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.8002 (mt0) REVERT: A 1031 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8410 (mt) REVERT: B 78 LYS cc_start: 0.8667 (mmpt) cc_final: 0.8374 (mmtm) outliers start: 16 outliers final: 10 residues processed: 112 average time/residue: 1.4546 time to fit residues: 173.6646 Evaluate side-chains 109 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 587 PHE Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 865 GLN Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain B residue 106 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 121 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.142681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.107973 restraints weight = 11049.513| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.80 r_work: 0.3111 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10155 Z= 0.141 Angle : 0.787 30.376 13807 Z= 0.336 Chirality : 0.044 0.220 1571 Planarity : 0.005 0.060 1761 Dihedral : 7.403 172.420 1570 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.60 % Allowed : 16.84 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.38 (0.23), residues: 1245 helix: 2.03 (0.21), residues: 586 sheet: 0.30 (0.42), residues: 138 loop : -0.14 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 401 HIS 0.004 0.001 HIS A 629 PHE 0.028 0.002 PHE A 300 TYR 0.019 0.001 TYR A 802 ARG 0.015 0.000 ARG A 850 Details of bonding type rmsd link_NAG-ASN : bond 0.00281 ( 5) link_NAG-ASN : angle 2.74356 ( 15) hydrogen bonds : bond 0.04184 ( 521) hydrogen bonds : angle 4.33906 ( 1515) SS BOND : bond 0.00218 ( 3) SS BOND : angle 0.68306 ( 6) covalent geometry : bond 0.00333 (10146) covalent geometry : angle 0.78267 (13786) Misc. bond : bond 0.00095 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8688.33 seconds wall clock time: 150 minutes 52.90 seconds (9052.90 seconds total)