Starting phenix.real_space_refine on Sun Aug 24 08:52:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wa5_37391/08_2025/8wa5_37391.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wa5_37391/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8wa5_37391/08_2025/8wa5_37391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wa5_37391/08_2025/8wa5_37391.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wa5_37391/08_2025/8wa5_37391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wa5_37391/08_2025/8wa5_37391.map" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.85, per 1000 atoms: 0.19 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: 0.64 Conformation dependent library (CDL) restraints added in 400.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.28 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: 1.72 Time building geometry restraints manager: 0.90 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: 4.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 8.900 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.370 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.010 0.000 ARG A 428 TYR 0.016 0.001 TYR A 802 PHE 0.025 0.001 PHE A 300 TRP 0.010 0.001 TRP A 401 HIS 0.003 0.001 HIS A 629 Details of bonding type rmsd covalent geometry : bond 0.00416 (10146) covalent geometry : angle 1.10023 (13786) SS BOND : bond 0.00087 ( 3) SS BOND : angle 0.56766 ( 6) hydrogen bonds : bond 0.13561 ( 521) hydrogen bonds : angle 5.87659 ( 1515) Misc. bond : bond 0.11946 ( 1) link_NAG-ASN : bond 0.00577 ( 5) link_NAG-ASN : angle 2.39806 ( 15) *********************** 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 : 0.309 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: 0.6163 time to fit residues: 82.5097 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 : 0.238 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.0970 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.144485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.109631 restraints weight = 11090.476| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.79 r_work: 0.3134 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.0829 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= 0.158 Angle : 0.814 30.698 13807 Z= 0.352 Chirality : 0.046 0.393 1571 Planarity : 0.005 0.050 1761 Dihedral : 8.176 166.689 1575 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.95 % Allowed : 12.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.23), residues: 1245 helix: 1.78 (0.21), residues: 588 sheet: 0.05 (0.42), residues: 141 loop : -0.09 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 428 TYR 0.022 0.002 TYR A 802 PHE 0.029 0.002 PHE A 300 TRP 0.011 0.002 TRP A 915 HIS 0.005 0.001 HIS A 629 Details of bonding type rmsd covalent geometry : bond 0.00372 (10146) covalent geometry : angle 0.80821 (13786) SS BOND : bond 0.00236 ( 3) SS BOND : angle 0.87090 ( 6) hydrogen bonds : bond 0.04705 ( 521) hydrogen bonds : angle 4.72396 ( 1515) Misc. bond : bond 0.00243 ( 1) link_NAG-ASN : bond 0.00446 ( 5) link_NAG-ASN : angle 2.92909 ( 15) *********************** 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 155 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 113 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: A 54 GLN cc_start: 0.7274 (OUTLIER) cc_final: 0.6455 (mt0) REVERT: A 103 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.8002 (ttp-170) REVERT: A 171 LYS cc_start: 0.7131 (ttmt) cc_final: 0.6885 (ttmm) REVERT: A 216 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8012 (pt0) REVERT: A 414 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.8222 (p0) REVERT: A 428 ARG cc_start: 0.7267 (mtm-85) cc_final: 0.7059 (mtm-85) REVERT: A 560 ARG cc_start: 0.7675 (mtm-85) cc_final: 0.7339 (mtm-85) REVERT: A 650 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8192 (p) REVERT: A 677 MET cc_start: 0.7795 (mmp) cc_final: 0.7546 (mmt) REVERT: A 772 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8389 (tt0) REVERT: A 865 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8023 (mt0) REVERT: A 933 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8891 (tp) REVERT: B 115 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.6887 (ptt90) outliers start: 42 outliers final: 10 residues processed: 140 average time/residue: 0.5795 time to fit residues: 86.3932 Evaluate side-chains 125 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 865 GLN 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 44 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.145105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.110113 restraints weight = 11045.471| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.83 r_work: 0.3137 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1028 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= 0.130 Angle : 0.776 30.195 13807 Z= 0.330 Chirality : 0.044 0.305 1571 Planarity : 0.004 0.045 1761 Dihedral : 7.916 166.876 1571 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.76 % Allowed : 13.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.24), residues: 1245 helix: 1.92 (0.21), residues: 588 sheet: 0.16 (0.42), residues: 136 loop : -0.11 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 428 TYR 0.018 0.001 TYR A 802 PHE 0.028 0.002 PHE A 300 TRP 0.008 0.001 TRP A 915 HIS 0.004 0.001 HIS A 629 Details of bonding type rmsd covalent geometry : bond 0.00299 (10146) covalent geometry : angle 0.77095 (13786) SS BOND : bond 0.00213 ( 3) SS BOND : angle 0.70958 ( 6) hydrogen bonds : bond 0.04169 ( 521) hydrogen bonds : angle 4.48248 ( 1515) Misc. bond : bond 0.00140 ( 1) link_NAG-ASN : bond 0.00253 ( 5) link_NAG-ASN : angle 2.71861 ( 15) *********************** 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: 40 poor density : 115 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 171 LYS cc_start: 0.7117 (ttmt) cc_final: 0.6877 (ttmm) REVERT: A 414 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.8261 (p0) REVERT: A 428 ARG cc_start: 0.7104 (mtm-85) cc_final: 0.6876 (mtm-85) REVERT: A 560 ARG cc_start: 0.7666 (mtm-85) cc_final: 0.7397 (mtm-85) REVERT: A 677 MET cc_start: 0.7881 (mmp) cc_final: 0.7618 (mmt) REVERT: A 682 MET cc_start: 0.8037 (mtm) cc_final: 0.7737 (ttm) REVERT: A 844 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7878 (mtt-85) REVERT: A 865 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7999 (mt0) REVERT: A 933 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8890 (tp) REVERT: B 84 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8440 (pt) REVERT: B 115 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.6855 (ptt90) REVERT: B 287 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8449 (tttp) outliers start: 40 outliers final: 13 residues processed: 141 average time/residue: 0.6260 time to fit residues: 93.7280 Evaluate side-chains 128 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 526 ARG Chi-restraints excluded: chain A residue 656 ARG 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 Chi-restraints excluded: chain B residue 287 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 80 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 5 optimal weight: 0.0570 chunk 11 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 123 optimal weight: 0.7980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 884 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.144847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.110278 restraints weight = 11219.467| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.85 r_work: 0.3137 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10155 Z= 0.121 Angle : 0.771 30.181 13807 Z= 0.326 Chirality : 0.043 0.279 1571 Planarity : 0.004 0.045 1761 Dihedral : 7.685 168.488 1570 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.48 % Allowed : 13.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.24), residues: 1245 helix: 1.98 (0.21), residues: 588 sheet: 0.22 (0.42), residues: 135 loop : -0.10 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 428 TYR 0.017 0.001 TYR A 802 PHE 0.028 0.001 PHE A 300 TRP 0.008 0.001 TRP A 401 HIS 0.003 0.001 HIS A 629 Details of bonding type rmsd covalent geometry : bond 0.00277 (10146) covalent geometry : angle 0.76529 (13786) SS BOND : bond 0.00200 ( 3) SS BOND : angle 0.64084 ( 6) hydrogen bonds : bond 0.03956 ( 521) hydrogen bonds : angle 4.39675 ( 1515) Misc. bond : bond 0.00079 ( 1) link_NAG-ASN : bond 0.00235 ( 5) link_NAG-ASN : angle 2.93045 ( 15) *********************** 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 147 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 110 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7705 (mm-40) REVERT: A 171 LYS cc_start: 0.7060 (ttmt) cc_final: 0.6797 (ttmm) REVERT: A 414 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8294 (p0) REVERT: A 560 ARG cc_start: 0.7658 (mtm-85) cc_final: 0.7411 (mtm-85) REVERT: A 650 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.8145 (p) REVERT: A 677 MET cc_start: 0.7853 (mmp) cc_final: 0.7603 (mmt) REVERT: A 682 MET cc_start: 0.8107 (mtm) cc_final: 0.7806 (ttm) REVERT: A 772 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8352 (tt0) REVERT: A 844 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7887 (mtt-85) REVERT: A 865 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7993 (mt0) REVERT: A 1031 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8405 (mt) REVERT: B 84 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8377 (pt) REVERT: B 115 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7174 (ptt90) outliers start: 37 outliers final: 16 residues processed: 135 average time/residue: 0.6512 time to fit residues: 93.2779 Evaluate side-chains 127 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLN 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 437 CYS Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 656 ARG 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 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 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 90 optimal weight: 1.9990 chunk 102 optimal weight: 0.3980 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.142985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.108250 restraints weight = 11154.212| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.81 r_work: 0.3110 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 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 : 0.004 0.046 10155 Z= 0.150 Angle : 0.787 30.415 13807 Z= 0.339 Chirality : 0.045 0.273 1571 Planarity : 0.004 0.046 1761 Dihedral : 7.760 171.150 1570 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.67 % Allowed : 13.55 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.23), residues: 1245 helix: 1.90 (0.21), residues: 586 sheet: 0.09 (0.41), residues: 139 loop : -0.16 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 428 TYR 0.020 0.002 TYR A 802 PHE 0.029 0.002 PHE A 300 TRP 0.009 0.002 TRP A 401 HIS 0.004 0.001 HIS A 629 Details of bonding type rmsd covalent geometry : bond 0.00356 (10146) covalent geometry : angle 0.78177 (13786) SS BOND : bond 0.00250 ( 3) SS BOND : angle 0.81627 ( 6) hydrogen bonds : bond 0.04398 ( 521) hydrogen bonds : angle 4.48107 ( 1515) Misc. bond : bond 0.00101 ( 1) link_NAG-ASN : bond 0.00231 ( 5) link_NAG-ASN : angle 2.81708 ( 15) *********************** 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 144 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 105 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8438 (pt0) REVERT: A 414 ASP cc_start: 0.8625 (OUTLIER) cc_final: 0.8404 (p0) REVERT: A 560 ARG cc_start: 0.7708 (mtm-85) cc_final: 0.7492 (mtm-85) REVERT: A 650 VAL cc_start: 0.8549 (OUTLIER) cc_final: 0.8175 (p) REVERT: A 677 MET cc_start: 0.7831 (mmp) cc_final: 0.7593 (mmt) REVERT: A 772 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8405 (tt0) REVERT: A 844 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7905 (mtt-85) REVERT: A 865 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8074 (mt0) REVERT: A 1031 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8503 (mt) REVERT: B 78 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8347 (mmtm) REVERT: B 84 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8540 (pt) REVERT: B 115 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.6842 (ptt90) outliers start: 39 outliers final: 18 residues processed: 133 average time/residue: 0.6439 time to fit residues: 91.0898 Evaluate side-chains 134 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 366 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 457 ILE Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 656 ARG 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 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 78 LYS 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 24 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 119 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.143295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.108946 restraints weight = 11229.828| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.82 r_work: 0.3115 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1507 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= 0.139 Angle : 0.781 30.389 13807 Z= 0.333 Chirality : 0.044 0.261 1571 Planarity : 0.004 0.045 1761 Dihedral : 7.694 170.834 1570 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.76 % Allowed : 13.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.23), residues: 1245 helix: 1.96 (0.21), residues: 586 sheet: 0.11 (0.41), residues: 139 loop : -0.15 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 428 TYR 0.018 0.001 TYR A 802 PHE 0.029 0.002 PHE A 300 TRP 0.010 0.001 TRP A 401 HIS 0.004 0.001 HIS A 629 Details of bonding type rmsd covalent geometry : bond 0.00327 (10146) covalent geometry : angle 0.77393 (13786) SS BOND : bond 0.00226 ( 3) SS BOND : angle 0.71403 ( 6) hydrogen bonds : bond 0.04190 ( 521) hydrogen bonds : angle 4.43587 ( 1515) Misc. bond : bond 0.00093 ( 1) link_NAG-ASN : bond 0.00258 ( 5) link_NAG-ASN : angle 3.17565 ( 15) *********************** 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 147 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 107 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.6848 (mt0) REVERT: A 171 LYS cc_start: 0.7101 (OUTLIER) cc_final: 0.6677 (ttmt) REVERT: A 216 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8463 (pt0) REVERT: A 650 VAL cc_start: 0.8536 (OUTLIER) cc_final: 0.8159 (p) REVERT: A 677 MET cc_start: 0.7855 (mmp) cc_final: 0.7603 (mmt) REVERT: A 772 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8403 (tt0) REVERT: A 844 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7912 (mtp-110) REVERT: A 865 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8071 (mt0) REVERT: A 1031 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8439 (mt) REVERT: B 115 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.6793 (ptt90) REVERT: B 289 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.7580 (mm-40) outliers start: 40 outliers final: 17 residues processed: 132 average time/residue: 0.6009 time to fit residues: 84.3401 Evaluate side-chains 129 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 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 379 THR Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 656 ARG 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 22 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 102 optimal weight: 0.2980 chunk 122 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 2 optimal weight: 0.0770 chunk 88 optimal weight: 0.7980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.144412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.109953 restraints weight = 11180.776| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.88 r_work: 0.3134 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1524 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= 0.114 Angle : 0.772 30.211 13807 Z= 0.325 Chirality : 0.043 0.252 1571 Planarity : 0.004 0.046 1761 Dihedral : 7.442 170.859 1570 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.20 % Allowed : 14.39 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.24), residues: 1245 helix: 2.07 (0.22), residues: 586 sheet: 0.31 (0.41), residues: 137 loop : -0.09 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 850 TYR 0.015 0.001 TYR A 802 PHE 0.028 0.001 PHE A 300 TRP 0.009 0.001 TRP A 401 HIS 0.003 0.001 HIS B 227 Details of bonding type rmsd covalent geometry : bond 0.00260 (10146) covalent geometry : angle 0.76768 (13786) SS BOND : bond 0.00184 ( 3) SS BOND : angle 0.55606 ( 6) hydrogen bonds : bond 0.03794 ( 521) hydrogen bonds : angle 4.32439 ( 1515) Misc. bond : bond 0.00064 ( 1) link_NAG-ASN : bond 0.00272 ( 5) link_NAG-ASN : angle 2.66530 ( 15) *********************** 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 137 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LYS cc_start: 0.7044 (OUTLIER) cc_final: 0.6604 (ttmt) REVERT: A 650 VAL cc_start: 0.8538 (OUTLIER) cc_final: 0.8139 (m) REVERT: A 677 MET cc_start: 0.7804 (mmp) cc_final: 0.7544 (mmt) REVERT: A 844 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7869 (mtt-85) REVERT: A 865 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7993 (mt0) REVERT: A 1031 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8407 (mt) REVERT: B 78 LYS cc_start: 0.8672 (mmpt) cc_final: 0.8336 (mmtm) REVERT: B 115 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7151 (ptt90) REVERT: B 289 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.7621 (mm-40) outliers start: 34 outliers final: 17 residues processed: 125 average time/residue: 0.6782 time to fit residues: 89.8471 Evaluate side-chains 125 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 437 CYS Chi-restraints excluded: chain A residue 457 ILE 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 656 ARG Chi-restraints excluded: chain A residue 680 LYS 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 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 47 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3689 r_free = 0.3689 target = 0.142891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.108259 restraints weight = 11022.841| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.83 r_work: 0.3112 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10155 Z= 0.142 Angle : 0.791 30.373 13807 Z= 0.339 Chirality : 0.045 0.236 1571 Planarity : 0.005 0.055 1761 Dihedral : 7.506 172.606 1570 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.20 % Allowed : 14.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.24), residues: 1245 helix: 1.98 (0.21), residues: 586 sheet: 0.33 (0.42), residues: 136 loop : -0.12 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 850 TYR 0.020 0.001 TYR A 802 PHE 0.029 0.002 PHE A 300 TRP 0.010 0.001 TRP A 401 HIS 0.004 0.001 HIS A 629 Details of bonding type rmsd covalent geometry : bond 0.00336 (10146) covalent geometry : angle 0.78363 (13786) SS BOND : bond 0.00229 ( 3) SS BOND : angle 0.73332 ( 6) hydrogen bonds : bond 0.04208 ( 521) hydrogen bonds : angle 4.42521 ( 1515) Misc. bond : bond 0.00085 ( 1) link_NAG-ASN : bond 0.00338 ( 5) link_NAG-ASN : angle 3.42083 ( 15) *********************** 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 133 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.6825 (mt0) REVERT: A 171 LYS cc_start: 0.7114 (OUTLIER) cc_final: 0.6673 (ttmt) REVERT: A 650 VAL cc_start: 0.8560 (OUTLIER) cc_final: 0.8176 (p) REVERT: A 677 MET cc_start: 0.7871 (mmp) cc_final: 0.7607 (mmt) REVERT: A 682 MET cc_start: 0.8401 (mtm) cc_final: 0.8025 (mtp) REVERT: A 844 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7874 (mtt-85) REVERT: A 865 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8067 (mt0) REVERT: A 1031 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8475 (mt) REVERT: B 78 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8354 (mmtm) REVERT: B 115 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.6833 (ptt90) REVERT: B 289 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.7624 (mm-40) outliers start: 34 outliers final: 18 residues processed: 120 average time/residue: 0.6684 time to fit residues: 85.2920 Evaluate side-chains 125 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 200 VAL 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 379 THR Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 656 ARG 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 A residue 1031 LEU Chi-restraints excluded: chain B residue 78 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 105 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 0.0030 chunk 25 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3699 r_free = 0.3699 target = 0.143736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.109382 restraints weight = 11148.214| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.78 r_work: 0.3127 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10155 Z= 0.123 Angle : 0.776 30.276 13807 Z= 0.329 Chirality : 0.044 0.234 1571 Planarity : 0.004 0.048 1761 Dihedral : 7.364 172.343 1570 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.73 % Allowed : 14.86 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.24), residues: 1245 helix: 2.04 (0.22), residues: 586 sheet: 0.28 (0.42), residues: 138 loop : -0.10 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 850 TYR 0.017 0.001 TYR A 802 PHE 0.029 0.001 PHE A 300 TRP 0.010 0.001 TRP A 401 HIS 0.004 0.001 HIS A 629 Details of bonding type rmsd covalent geometry : bond 0.00284 (10146) covalent geometry : angle 0.76970 (13786) SS BOND : bond 0.00195 ( 3) SS BOND : angle 0.61067 ( 6) hydrogen bonds : bond 0.03929 ( 521) hydrogen bonds : angle 4.35253 ( 1515) Misc. bond : bond 0.00072 ( 1) link_NAG-ASN : bond 0.00332 ( 5) link_NAG-ASN : angle 3.02717 ( 15) *********************** 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 129 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 LYS cc_start: 0.7067 (OUTLIER) cc_final: 0.6620 (ttmt) REVERT: A 650 VAL cc_start: 0.8524 (OUTLIER) cc_final: 0.8128 (m) REVERT: A 677 MET cc_start: 0.7818 (mmp) cc_final: 0.7546 (mmt) REVERT: A 682 MET cc_start: 0.8332 (mtm) cc_final: 0.7964 (mtp) REVERT: A 844 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7873 (mtt-85) REVERT: A 865 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7997 (mt0) REVERT: A 1031 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8425 (mt) REVERT: B 78 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8316 (mmtm) REVERT: B 115 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7176 (ptt90) outliers start: 29 outliers final: 18 residues processed: 120 average time/residue: 0.6726 time to fit residues: 85.6786 Evaluate side-chains 124 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 457 ILE Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 656 ARG Chi-restraints excluded: chain A residue 680 LYS 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 A residue 1031 LEU Chi-restraints excluded: chain B residue 78 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 43 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 120 optimal weight: 0.0370 chunk 57 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 54 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 = 0.3701 r_free = 0.3701 target = 0.143783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.109757 restraints weight = 10990.096| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.76 r_work: 0.3125 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10155 Z= 0.125 Angle : 0.777 30.280 13807 Z= 0.331 Chirality : 0.044 0.223 1571 Planarity : 0.004 0.062 1761 Dihedral : 7.349 172.337 1570 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.63 % Allowed : 15.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.24), residues: 1245 helix: 2.03 (0.22), residues: 586 sheet: 0.30 (0.42), residues: 137 loop : -0.11 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 850 TYR 0.017 0.001 TYR A 802 PHE 0.028 0.001 PHE A 300 TRP 0.012 0.001 TRP A 401 HIS 0.004 0.001 HIS A 629 Details of bonding type rmsd covalent geometry : bond 0.00289 (10146) covalent geometry : angle 0.77175 (13786) SS BOND : bond 0.00202 ( 3) SS BOND : angle 0.62570 ( 6) hydrogen bonds : bond 0.03958 ( 521) hydrogen bonds : angle 4.36260 ( 1515) Misc. bond : bond 0.00072 ( 1) link_NAG-ASN : bond 0.00301 ( 5) link_NAG-ASN : angle 2.91024 ( 15) ********************** 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 124 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 LYS cc_start: 0.7088 (OUTLIER) cc_final: 0.6837 (ttmm) REVERT: A 650 VAL cc_start: 0.8545 (OUTLIER) cc_final: 0.8150 (m) REVERT: A 677 MET cc_start: 0.7830 (mmp) cc_final: 0.7558 (mmt) REVERT: A 682 MET cc_start: 0.8320 (mtm) cc_final: 0.7997 (mtp) REVERT: A 844 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7880 (mtt-85) REVERT: A 865 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8007 (mt0) REVERT: A 1031 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8424 (mt) REVERT: B 78 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8340 (mmtm) REVERT: B 115 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.6789 (ptt90) outliers start: 28 outliers final: 17 residues processed: 115 average time/residue: 0.6584 time to fit residues: 80.2726 Evaluate side-chains 119 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 457 ILE Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 656 ARG Chi-restraints excluded: chain A residue 680 LYS 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 943 VAL Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain B residue 78 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 105 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.143357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.108905 restraints weight = 11099.947| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.78 r_work: 0.3123 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10155 Z= 0.130 Angle : 0.784 30.296 13807 Z= 0.334 Chirality : 0.044 0.222 1571 Planarity : 0.004 0.062 1761 Dihedral : 7.382 171.996 1570 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.73 % Allowed : 15.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.24), residues: 1245 helix: 2.01 (0.21), residues: 586 sheet: 0.22 (0.42), residues: 138 loop : -0.10 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 850 TYR 0.018 0.001 TYR A 802 PHE 0.028 0.001 PHE A 300 TRP 0.011 0.001 TRP A 401 HIS 0.003 0.001 HIS B 227 Details of bonding type rmsd covalent geometry : bond 0.00303 (10146) covalent geometry : angle 0.77857 (13786) SS BOND : bond 0.00212 ( 3) SS BOND : angle 0.66760 ( 6) hydrogen bonds : bond 0.04021 ( 521) hydrogen bonds : angle 4.38702 ( 1515) Misc. bond : bond 0.00078 ( 1) link_NAG-ASN : bond 0.00292 ( 5) link_NAG-ASN : angle 2.84660 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3750.51 seconds wall clock time: 64 minutes 25.17 seconds (3865.17 seconds total)