Starting phenix.real_space_refine on Mon Jul 28 19:30:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x21_32954/07_2025/7x21_32954.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x21_32954/07_2025/7x21_32954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x21_32954/07_2025/7x21_32954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x21_32954/07_2025/7x21_32954.map" model { file = "/net/cci-nas-00/data/ceres_data/7x21_32954/07_2025/7x21_32954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x21_32954/07_2025/7x21_32954.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians K 2 8.98 5 Al 1 5.89 5 P 3 5.49 5 Mg 1 5.21 5 S 49 5.16 5 C 6558 2.51 5 N 1651 2.21 5 O 1898 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 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10167 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7662 Classifications: {'peptide': 986} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 35, 'TRANS': 950} Chain: "B" Number of atoms: 2255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2255 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 257} Chain: "A" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 118 Unusual residues: {' K': 2, ' MG': 1, 'ALF': 1, 'CLR': 2, 'PCW': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 114 Unusual residues: {'NAG': 1, 'PCW': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Time building chain proxies: 7.04, per 1000 atoms: 0.69 Number of scatterers: 10167 At special positions: 0 Unit cell: (122.84, 97.11, 173.47, 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 2 19.00 S 49 16.00 P 3 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1898 8.00 N 1651 7.00 C 6558 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 277 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG B 401 " - " ASN B 158 " Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 1.3 seconds 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2350 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 10 sheets defined 48.8% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 60 through 69 Processing helix chain 'A' and resid 77 through 89 removed outlier: 3.816A pdb=" N GLU A 83 " --> pdb=" O VAL A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 108 removed outlier: 3.685A pdb=" N GLN A 108 " --> pdb=" O LYS A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 113 through 134 Processing helix chain 'A' and resid 139 through 163 Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.513A pdb=" N SER A 174 " --> pdb=" O ALA A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.728A pdb=" N THR A 251 " --> pdb=" O PRO A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 276 Processing helix chain 'A' and resid 277 through 289 Processing helix chain 'A' and resid 294 through 325 Processing helix chain 'A' and resid 328 through 344 Processing helix chain 'A' and resid 347 through 365 Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.971A pdb=" N THR A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 374 through 379' Processing helix chain 'A' and resid 430 through 440 Processing helix chain 'A' and resid 462 through 476 Processing helix chain 'A' and resid 478 through 486 removed outlier: 4.364A pdb=" N ILE A 482 " --> pdb=" O ASP A 478 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 528 Processing helix chain 'A' and resid 543 through 559 Processing helix chain 'A' and resid 610 through 621 removed outlier: 3.546A pdb=" N ALA A 614 " --> pdb=" O THR A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 643 Processing helix chain 'A' and resid 652 through 660 Processing helix chain 'A' and resid 679 through 684 removed outlier: 3.681A pdb=" N ASP A 684 " --> pdb=" O MET A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 697 Processing helix chain 'A' and resid 706 through 719 removed outlier: 3.589A pdb=" N LEU A 711 " --> pdb=" O PRO A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 732 No H-bonds generated for 'chain 'A' and resid 730 through 732' Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 751 through 758 Processing helix chain 'A' and resid 767 through 809 removed outlier: 3.652A pdb=" N ALA A 794 " --> pdb=" O TYR A 790 " (cutoff:3.500A) Proline residue: A 801 - end of helix Processing helix chain 'A' and resid 815 through 825 removed outlier: 3.642A pdb=" N ILE A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 820 " --> pdb=" O THR A 816 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A 821 " --> pdb=" O ILE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 834 Processing helix chain 'A' and resid 835 through 837 No H-bonds generated for 'chain 'A' and resid 835 through 837' Processing helix chain 'A' and resid 858 through 868 removed outlier: 3.516A pdb=" N HIS A 868 " --> pdb=" O TYR A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 889 removed outlier: 3.715A pdb=" N MET A 872 " --> pdb=" O HIS A 868 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN A 888 " --> pdb=" O VAL A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 896 Processing helix chain 'A' and resid 898 through 903 Processing helix chain 'A' and resid 919 through 949 Processing helix chain 'A' and resid 955 through 960 Processing helix chain 'A' and resid 964 through 984 removed outlier: 4.044A pdb=" N TRP A 968 " --> pdb=" O ASN A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1002 Processing helix chain 'A' and resid 1004 through 1025 Processing helix chain 'A' and resid 1029 through 1034 Processing helix chain 'B' and resid 29 through 59 removed outlier: 3.596A pdb=" N TYR B 39 " --> pdb=" O ILE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 110 removed outlier: 4.127A pdb=" N TYR B 98 " --> pdb=" O ASP B 94 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA B 100 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N TYR B 101 " --> pdb=" O SER B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 115 through 119 removed outlier: 3.639A pdb=" N LYS B 118 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASP B 119 " --> pdb=" O ALA B 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 115 through 119' Processing helix chain 'B' and resid 152 through 157 removed outlier: 3.665A pdb=" N GLY B 157 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 207 No H-bonds generated for 'chain 'B' and resid 205 through 207' Processing helix chain 'B' and resid 218 through 223 Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 242 through 244 No H-bonds generated for 'chain 'B' and resid 242 through 244' Processing sheet with id=AA1, first strand: chain 'A' and resid 189 through 193 removed outlier: 11.892A pdb=" N GLN A 180 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N LYS A 206 " --> pdb=" O GLN A 180 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU A 182 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL A 202 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N CYS A 261 " --> pdb=" O LYS A 224 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS A 224 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N GLU A 263 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLY A 222 " --> pdb=" O GLU A 263 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR A 265 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N SER A 220 " --> pdb=" O THR A 265 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR A 267 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASP A 214 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N CYS A 223 " --> pdb=" O ARG A 239 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 209 through 210 removed outlier: 3.615A pdb=" N ASP A 209 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N CYS A 261 " --> pdb=" O LYS A 224 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS A 224 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N GLU A 263 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLY A 222 " --> pdb=" O GLU A 263 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR A 265 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N SER A 220 " --> pdb=" O THR A 265 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR A 267 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASP A 214 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 368 through 370 removed outlier: 6.789A pdb=" N VAL A 724 " --> pdb=" O ILE A 742 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ILE A 744 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL A 726 " --> pdb=" O ILE A 744 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N MET A 746 " --> pdb=" O VAL A 726 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N GLY A 728 " --> pdb=" O MET A 746 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ILE A 385 " --> pdb=" O ILE A 626 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL A 628 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N SER A 387 " --> pdb=" O VAL A 628 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL A 625 " --> pdb=" O ILE A 700 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N PHE A 702 " --> pdb=" O VAL A 625 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N MET A 627 " --> pdb=" O PHE A 702 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 408 through 411 removed outlier: 3.682A pdb=" N HIS A 402 " --> pdb=" O SER A 602 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N PHE A 567 " --> pdb=" O VAL A 598 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU A 600 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU A 565 " --> pdb=" O LEU A 600 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER A 602 " --> pdb=" O ARG A 563 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ARG A 563 " --> pdb=" O SER A 602 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 408 through 411 removed outlier: 3.682A pdb=" N HIS A 402 " --> pdb=" O SER A 602 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N CYS A 530 " --> pdb=" O PHE A 595 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N PHE A 597 " --> pdb=" O CYS A 530 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR A 532 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N GLY A 599 " --> pdb=" O THR A 532 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N MET A 534 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 12.486A pdb=" N LEU A 601 " --> pdb=" O MET A 534 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 444 through 445 Processing sheet with id=AA7, first strand: chain 'A' and resid 910 through 911 Processing sheet with id=AA8, first strand: chain 'B' and resid 77 through 79 Processing sheet with id=AA9, first strand: chain 'B' and resid 87 through 90 removed outlier: 3.775A pdb=" N PHE B 90 " --> pdb=" O GLU B 301 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 123 through 124 486 hydrogen bonds defined for protein. 1389 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: 3.94 Time building geometry restraints manager: 3.23 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: 3164 1.34 - 1.46: 1518 1.46 - 1.58: 5579 1.58 - 1.70: 6 1.70 - 1.82: 82 Bond restraints: 10349 Sorted by residual: bond pdb=" C11 PCW B 403 " pdb=" O3 PCW B 403 " ideal model delta sigma weight residual 1.326 1.454 -0.128 2.00e-02 2.50e+03 4.11e+01 bond pdb=" C11 PCW B 402 " pdb=" O3 PCW B 402 " ideal model delta sigma weight residual 1.326 1.454 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C11 PCW A1106 " pdb=" O3 PCW A1106 " ideal model delta sigma weight residual 1.326 1.453 -0.127 2.00e-02 2.50e+03 4.06e+01 bond pdb=" C31 PCW B 403 " pdb=" O2 PCW B 403 " ideal model delta sigma weight residual 1.333 1.459 -0.126 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C31 PCW B 402 " pdb=" O2 PCW B 402 " ideal model delta sigma weight residual 1.333 1.452 -0.119 2.00e-02 2.50e+03 3.55e+01 ... (remaining 10344 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.12: 14007 14.12 - 28.25: 4 28.25 - 42.37: 0 42.37 - 56.49: 0 56.49 - 70.61: 2 Bond angle restraints: 14013 Sorted by residual: angle pdb=" F1 ALF A1103 " pdb="AL ALF A1103 " pdb=" F2 ALF A1103 " ideal model delta sigma weight residual 108.68 179.29 -70.61 3.00e+00 1.11e-01 5.54e+02 angle pdb=" F3 ALF A1103 " pdb="AL ALF A1103 " pdb=" F4 ALF A1103 " ideal model delta sigma weight residual 109.63 179.11 -69.48 3.00e+00 1.11e-01 5.36e+02 angle pdb=" F2 ALF A1103 " pdb="AL ALF A1103 " pdb=" F4 ALF A1103 " ideal model delta sigma weight residual 110.21 89.63 20.58 3.00e+00 1.11e-01 4.71e+01 angle pdb=" F1 ALF A1103 " pdb="AL ALF A1103 " pdb=" F3 ALF A1103 " ideal model delta sigma weight residual 109.69 90.12 19.57 3.00e+00 1.11e-01 4.26e+01 angle pdb=" F2 ALF A1103 " pdb="AL ALF A1103 " pdb=" F3 ALF A1103 " ideal model delta sigma weight residual 109.59 90.09 19.50 3.00e+00 1.11e-01 4.23e+01 ... (remaining 14008 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.98: 6215 32.98 - 65.96: 140 65.96 - 98.94: 22 98.94 - 131.92: 3 131.92 - 164.91: 1 Dihedral angle restraints: 6381 sinusoidal: 2723 harmonic: 3658 Sorted by residual: dihedral pdb=" CB CYS B 159 " pdb=" SG CYS B 159 " pdb=" SG CYS B 175 " pdb=" CB CYS B 175 " ideal model delta sinusoidal sigma weight residual 93.00 139.15 -46.15 1 1.00e+01 1.00e-02 2.95e+01 dihedral pdb=" N PCW B 403 " pdb=" C4 PCW B 403 " pdb=" C5 PCW B 403 " pdb=" O4P PCW B 403 " ideal model delta sinusoidal sigma weight residual -66.66 98.25 -164.91 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" CA PHE B 296 " pdb=" C PHE B 296 " pdb=" N ASP B 297 " pdb=" CA ASP B 297 " ideal model delta harmonic sigma weight residual 180.00 158.30 21.70 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 6378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1386 0.064 - 0.129: 200 0.129 - 0.193: 5 0.193 - 0.257: 3 0.257 - 0.321: 3 Chirality restraints: 1597 Sorted by residual: chirality pdb=" C2 PCW A1106 " pdb=" C1 PCW A1106 " pdb=" C3 PCW A1106 " pdb=" O2 PCW A1106 " both_signs ideal model delta sigma weight residual False -2.32 -2.64 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" C1 NAG B 401 " pdb=" ND2 ASN B 158 " pdb=" C2 NAG B 401 " pdb=" O5 NAG B 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C2 PCW B 402 " pdb=" C1 PCW B 402 " pdb=" C3 PCW B 402 " pdb=" O2 PCW B 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.60 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 1594 not shown) Planarity restraints: 1761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 401 " -0.277 2.00e-02 2.50e+03 2.32e-01 6.75e+02 pdb=" C7 NAG B 401 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG B 401 " -0.180 2.00e-02 2.50e+03 pdb=" N2 NAG B 401 " 0.395 2.00e-02 2.50e+03 pdb=" O7 NAG B 401 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A1029 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.66e+00 pdb=" C TRP A1029 " 0.041 2.00e-02 2.50e+03 pdb=" O TRP A1029 " -0.015 2.00e-02 2.50e+03 pdb=" N TRP A1030 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 891 " -0.035 5.00e-02 4.00e+02 5.41e-02 4.67e+00 pdb=" N PRO A 892 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 892 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 892 " -0.030 5.00e-02 4.00e+02 ... (remaining 1758 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.58: 74 2.58 - 3.22: 9709 3.22 - 3.86: 20075 3.86 - 4.50: 27689 4.50 - 5.14: 43956 Nonbonded interactions: 101503 Sorted by model distance: nonbonded pdb=" F3 ALF A1103 " pdb="MG MG A1104 " model vdw 1.943 2.120 nonbonded pdb=" OD1 ASP A 729 " pdb="MG MG A1104 " model vdw 2.066 2.170 nonbonded pdb=" O THR A 390 " pdb="MG MG A1104 " model vdw 2.077 2.170 nonbonded pdb=" OD2 ASP A 823 " pdb=" O HOH A1201 " model vdw 2.142 3.040 nonbonded pdb=" OG SER A 955 " pdb=" OE1 GLU A1016 " model vdw 2.171 3.040 ... (remaining 101498 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.180 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 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 : 0.005 0.128 10353 Z= 0.247 Angle : 1.155 70.615 14022 Z= 0.452 Chirality : 0.046 0.321 1597 Planarity : 0.007 0.232 1760 Dihedral : 14.862 164.905 4022 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.23), residues: 1259 helix: 1.48 (0.22), residues: 527 sheet: -0.06 (0.41), residues: 140 loop : -0.67 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 968 HIS 0.002 0.001 HIS A 487 PHE 0.020 0.002 PHE B 236 TYR 0.017 0.002 TYR A 257 ARG 0.009 0.000 ARG A 397 Details of bonding type rmsd link_NAG-ASN : bond 0.00597 ( 1) link_NAG-ASN : angle 4.61785 ( 3) hydrogen bonds : bond 0.14634 ( 475) hydrogen bonds : angle 6.41471 ( 1389) SS BOND : bond 0.00217 ( 3) SS BOND : angle 0.82633 ( 6) covalent geometry : bond 0.00509 (10349) covalent geometry : angle 1.15302 (14013) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.0606 (tmm) cc_final: 0.0140 (mpp) REVERT: A 71 ASN cc_start: 0.6290 (t0) cc_final: 0.5696 (t0) REVERT: A 195 GLU cc_start: 0.6797 (mt-10) cc_final: 0.6393 (mt-10) REVERT: A 366 LYS cc_start: 0.6567 (mtmt) cc_final: 0.6322 (mtpt) REVERT: A 500 PHE cc_start: 0.5418 (p90) cc_final: 0.4792 (p90) REVERT: A 911 GLU cc_start: 0.7372 (tt0) cc_final: 0.7160 (tt0) REVERT: B 36 LEU cc_start: 0.7676 (mt) cc_final: 0.7475 (mt) REVERT: B 63 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7337 (mt-10) REVERT: B 114 ASP cc_start: 0.6179 (m-30) cc_final: 0.5694 (m-30) REVERT: B 203 MET cc_start: 0.3649 (tpt) cc_final: 0.2479 (mpp) REVERT: B 223 ASP cc_start: 0.6622 (m-30) cc_final: 0.6194 (m-30) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 1.2773 time to fit residues: 208.9281 Evaluate side-chains 120 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 97 optimal weight: 0.2980 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 0.4980 chunk 72 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 732 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.175903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.117505 restraints weight = 11049.551| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.92 r_work: 0.3011 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10353 Z= 0.114 Angle : 0.786 29.462 14022 Z= 0.341 Chirality : 0.043 0.278 1597 Planarity : 0.004 0.043 1760 Dihedral : 10.101 164.005 1640 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.75 % Allowed : 7.27 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.23), residues: 1259 helix: 1.64 (0.22), residues: 543 sheet: -0.23 (0.40), residues: 147 loop : -0.60 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 968 HIS 0.002 0.001 HIS A 505 PHE 0.011 0.001 PHE A 335 TYR 0.016 0.001 TYR A 881 ARG 0.003 0.000 ARG A 397 Details of bonding type rmsd link_NAG-ASN : bond 0.00390 ( 1) link_NAG-ASN : angle 2.81723 ( 3) hydrogen bonds : bond 0.04697 ( 475) hydrogen bonds : angle 4.91515 ( 1389) SS BOND : bond 0.00179 ( 3) SS BOND : angle 0.78464 ( 6) covalent geometry : bond 0.00242 (10349) covalent geometry : angle 0.78493 (14013) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 1.140 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.0628 (tmm) cc_final: 0.0186 (mpp) REVERT: A 134 ASN cc_start: 0.5947 (m110) cc_final: 0.5647 (m-40) REVERT: A 150 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7457 (tp) REVERT: A 182 LEU cc_start: 0.7381 (tp) cc_final: 0.7178 (tp) REVERT: A 195 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6618 (mt-10) REVERT: A 410 PHE cc_start: 0.6760 (m-80) cc_final: 0.6287 (m-80) REVERT: A 413 ASP cc_start: 0.6439 (OUTLIER) cc_final: 0.6188 (p0) REVERT: A 500 PHE cc_start: 0.5364 (p90) cc_final: 0.4825 (p90) REVERT: A 534 MET cc_start: 0.6065 (tpp) cc_final: 0.5535 (tpp) REVERT: A 601 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7042 (mp) REVERT: A 651 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.5885 (tp30) REVERT: A 695 THR cc_start: 0.7665 (m) cc_final: 0.7465 (p) REVERT: A 963 ARG cc_start: 0.6164 (mtm180) cc_final: 0.5897 (mtt-85) REVERT: B 36 LEU cc_start: 0.7725 (mt) cc_final: 0.7477 (mt) REVERT: B 114 ASP cc_start: 0.6397 (m-30) cc_final: 0.5978 (m-30) REVERT: B 173 LYS cc_start: 0.7327 (mmtp) cc_final: 0.6823 (mptp) REVERT: B 203 MET cc_start: 0.3796 (tpt) cc_final: 0.2614 (mpp) REVERT: B 223 ASP cc_start: 0.6616 (m-30) cc_final: 0.6065 (m-30) REVERT: B 236 PHE cc_start: 0.7018 (m-80) cc_final: 0.6781 (m-80) outliers start: 19 outliers final: 4 residues processed: 145 average time/residue: 1.2163 time to fit residues: 191.0688 Evaluate side-chains 128 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 846 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 78 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 70 optimal weight: 0.0670 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.175837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.119845 restraints weight = 11208.300| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.76 r_work: 0.3022 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10353 Z= 0.110 Angle : 0.769 29.741 14022 Z= 0.331 Chirality : 0.042 0.250 1597 Planarity : 0.004 0.042 1760 Dihedral : 9.835 171.454 1640 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.02 % Allowed : 9.84 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.23), residues: 1259 helix: 1.68 (0.22), residues: 547 sheet: -0.23 (0.41), residues: 138 loop : -0.67 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 968 HIS 0.002 0.001 HIS A 505 PHE 0.009 0.001 PHE A 935 TYR 0.015 0.001 TYR A 881 ARG 0.003 0.000 ARG A 397 Details of bonding type rmsd link_NAG-ASN : bond 0.00972 ( 1) link_NAG-ASN : angle 3.28451 ( 3) hydrogen bonds : bond 0.04477 ( 475) hydrogen bonds : angle 4.67062 ( 1389) SS BOND : bond 0.00271 ( 3) SS BOND : angle 0.63716 ( 6) covalent geometry : bond 0.00240 (10349) covalent geometry : angle 0.76721 (14013) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.0668 (tmm) cc_final: 0.0346 (pmm) REVERT: A 107 LYS cc_start: 0.7336 (OUTLIER) cc_final: 0.6856 (mttp) REVERT: A 134 ASN cc_start: 0.5943 (m110) cc_final: 0.5590 (m-40) REVERT: A 150 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7525 (tp) REVERT: A 182 LEU cc_start: 0.7502 (tp) cc_final: 0.7250 (tp) REVERT: A 195 GLU cc_start: 0.7025 (mt-10) cc_final: 0.6564 (mt-10) REVERT: A 410 PHE cc_start: 0.6761 (m-80) cc_final: 0.6347 (m-80) REVERT: A 500 PHE cc_start: 0.5358 (p90) cc_final: 0.4901 (p90) REVERT: A 534 MET cc_start: 0.6102 (tpp) cc_final: 0.5541 (tpp) REVERT: A 601 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7035 (mp) REVERT: A 603 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7387 (mtm) REVERT: A 651 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.5988 (tp30) REVERT: A 823 ASP cc_start: 0.7440 (m-30) cc_final: 0.7140 (m-30) REVERT: A 963 ARG cc_start: 0.6224 (mtm180) cc_final: 0.5961 (mtt-85) REVERT: B 36 LEU cc_start: 0.7799 (mt) cc_final: 0.7592 (mt) REVERT: B 87 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7058 (mt-10) REVERT: B 114 ASP cc_start: 0.6378 (m-30) cc_final: 0.5958 (m-30) REVERT: B 173 LYS cc_start: 0.7351 (mmtp) cc_final: 0.7004 (mptp) REVERT: B 203 MET cc_start: 0.3773 (tpt) cc_final: 0.2571 (mpp) REVERT: B 222 LYS cc_start: 0.6744 (mttp) cc_final: 0.6465 (mttp) REVERT: B 223 ASP cc_start: 0.6689 (m-30) cc_final: 0.6110 (m-30) outliers start: 22 outliers final: 5 residues processed: 141 average time/residue: 1.0897 time to fit residues: 167.3406 Evaluate side-chains 134 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain B residue 87 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 32 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 417 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.172356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.112597 restraints weight = 10964.884| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.83 r_work: 0.2942 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10353 Z= 0.176 Angle : 0.828 30.222 14022 Z= 0.367 Chirality : 0.045 0.267 1597 Planarity : 0.005 0.046 1760 Dihedral : 10.519 176.763 1640 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.85 % Allowed : 11.22 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.23), residues: 1259 helix: 1.39 (0.22), residues: 545 sheet: -0.06 (0.40), residues: 141 loop : -0.70 (0.24), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 968 HIS 0.003 0.001 HIS A 487 PHE 0.014 0.002 PHE A1021 TYR 0.023 0.002 TYR A 805 ARG 0.004 0.000 ARG A 397 Details of bonding type rmsd link_NAG-ASN : bond 0.00996 ( 1) link_NAG-ASN : angle 3.07372 ( 3) hydrogen bonds : bond 0.05656 ( 475) hydrogen bonds : angle 4.86896 ( 1389) SS BOND : bond 0.00362 ( 3) SS BOND : angle 0.93837 ( 6) covalent geometry : bond 0.00411 (10349) covalent geometry : angle 0.82691 (14013) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 1.190 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.0486 (tmm) cc_final: 0.0097 (pmm) REVERT: A 150 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7504 (tp) REVERT: A 182 LEU cc_start: 0.7434 (tp) cc_final: 0.7203 (tp) REVERT: A 195 GLU cc_start: 0.7068 (mt-10) cc_final: 0.6642 (mt-10) REVERT: A 216 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.6242 (tmm160) REVERT: A 500 PHE cc_start: 0.5283 (p90) cc_final: 0.4903 (p90) REVERT: A 534 MET cc_start: 0.6056 (tpp) cc_final: 0.5431 (tpp) REVERT: A 601 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7181 (mp) REVERT: A 603 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7677 (mtt) REVERT: A 651 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6048 (tp30) REVERT: A 844 MET cc_start: 0.7860 (mmm) cc_final: 0.7594 (mmm) REVERT: B 87 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7207 (mt-10) REVERT: B 114 ASP cc_start: 0.6435 (m-30) cc_final: 0.6047 (m-30) REVERT: B 203 MET cc_start: 0.3727 (tpt) cc_final: 0.2512 (mpp) REVERT: B 213 GLN cc_start: 0.8112 (mt0) cc_final: 0.7837 (mt0) REVERT: B 223 ASP cc_start: 0.6712 (m-30) cc_final: 0.6151 (m-30) REVERT: B 236 PHE cc_start: 0.7098 (m-80) cc_final: 0.6845 (m-80) outliers start: 31 outliers final: 13 residues processed: 141 average time/residue: 1.0503 time to fit residues: 161.9103 Evaluate side-chains 138 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 282 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 28 optimal weight: 3.9990 chunk 122 optimal weight: 0.0070 chunk 99 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 2 optimal weight: 0.0870 chunk 10 optimal weight: 0.9990 chunk 37 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 196 GLN A 417 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.175277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.116092 restraints weight = 11111.870| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.87 r_work: 0.2995 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10353 Z= 0.107 Angle : 0.766 30.137 14022 Z= 0.329 Chirality : 0.042 0.259 1597 Planarity : 0.004 0.042 1760 Dihedral : 10.004 173.362 1640 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.30 % Allowed : 12.05 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.23), residues: 1259 helix: 1.66 (0.22), residues: 547 sheet: -0.23 (0.41), residues: 148 loop : -0.61 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 968 HIS 0.002 0.001 HIS A 505 PHE 0.014 0.001 PHE A 335 TYR 0.015 0.001 TYR A 881 ARG 0.003 0.000 ARG A 397 Details of bonding type rmsd link_NAG-ASN : bond 0.01085 ( 1) link_NAG-ASN : angle 3.39569 ( 3) hydrogen bonds : bond 0.04378 ( 475) hydrogen bonds : angle 4.55409 ( 1389) SS BOND : bond 0.00204 ( 3) SS BOND : angle 0.62107 ( 6) covalent geometry : bond 0.00232 (10349) covalent geometry : angle 0.76500 (14013) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 1.200 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.0414 (tmm) cc_final: 0.0127 (pmm) REVERT: A 134 ASN cc_start: 0.5852 (m-40) cc_final: 0.5536 (m-40) REVERT: A 150 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7462 (tp) REVERT: A 182 LEU cc_start: 0.7445 (tp) cc_final: 0.7203 (tp) REVERT: A 195 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6621 (mt-10) REVERT: A 366 LYS cc_start: 0.6759 (mtpt) cc_final: 0.6231 (ptmt) REVERT: A 500 PHE cc_start: 0.5230 (p90) cc_final: 0.4736 (p90) REVERT: A 534 MET cc_start: 0.5910 (tpt) cc_final: 0.5360 (tpp) REVERT: A 601 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7054 (mp) REVERT: A 603 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7394 (mtm) REVERT: A 651 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.5939 (tp30) REVERT: A 823 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.7104 (t0) REVERT: A 963 ARG cc_start: 0.6187 (mtm180) cc_final: 0.5756 (mtt90) REVERT: B 114 ASP cc_start: 0.6387 (m-30) cc_final: 0.6013 (m-30) REVERT: B 173 LYS cc_start: 0.7234 (mmtp) cc_final: 0.6788 (mptp) REVERT: B 203 MET cc_start: 0.3651 (tpt) cc_final: 0.2444 (mpp) REVERT: B 213 GLN cc_start: 0.8013 (mt0) cc_final: 0.7748 (mt0) REVERT: B 222 LYS cc_start: 0.6573 (mttp) cc_final: 0.6216 (mttp) REVERT: B 223 ASP cc_start: 0.6724 (m-30) cc_final: 0.6152 (m-30) outliers start: 25 outliers final: 13 residues processed: 136 average time/residue: 1.1038 time to fit residues: 163.4996 Evaluate side-chains 135 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 282 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 62 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 39 optimal weight: 9.9990 chunk 36 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 417 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.174487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.117406 restraints weight = 11114.448| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.62 r_work: 0.2991 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10353 Z= 0.127 Angle : 0.780 29.620 14022 Z= 0.338 Chirality : 0.043 0.255 1597 Planarity : 0.004 0.042 1760 Dihedral : 10.065 167.821 1640 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.85 % Allowed : 12.24 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.23), residues: 1259 helix: 1.61 (0.22), residues: 547 sheet: -0.12 (0.41), residues: 143 loop : -0.58 (0.24), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 968 HIS 0.002 0.001 HIS A 487 PHE 0.011 0.001 PHE A1021 TYR 0.017 0.001 TYR A 805 ARG 0.003 0.000 ARG A 397 Details of bonding type rmsd link_NAG-ASN : bond 0.01005 ( 1) link_NAG-ASN : angle 3.28093 ( 3) hydrogen bonds : bond 0.04754 ( 475) hydrogen bonds : angle 4.57274 ( 1389) SS BOND : bond 0.00247 ( 3) SS BOND : angle 0.71116 ( 6) covalent geometry : bond 0.00286 (10349) covalent geometry : angle 0.77899 (14013) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 1.030 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.0320 (tmm) cc_final: 0.0068 (pmm) REVERT: A 107 LYS cc_start: 0.7191 (mptp) cc_final: 0.6689 (mttp) REVERT: A 134 ASN cc_start: 0.5956 (m-40) cc_final: 0.5612 (m-40) REVERT: A 150 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7505 (tp) REVERT: A 182 LEU cc_start: 0.7494 (tp) cc_final: 0.7275 (tp) REVERT: A 195 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6672 (mt-10) REVERT: A 216 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.6373 (tmm160) REVERT: A 366 LYS cc_start: 0.6821 (mtpt) cc_final: 0.6241 (ptmt) REVERT: A 534 MET cc_start: 0.5969 (tpt) cc_final: 0.5449 (tpp) REVERT: A 601 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7108 (mp) REVERT: A 603 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7453 (mtt) REVERT: A 651 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6015 (tp30) REVERT: A 963 ARG cc_start: 0.6246 (mtm180) cc_final: 0.5801 (mtt90) REVERT: B 114 ASP cc_start: 0.6452 (m-30) cc_final: 0.6072 (m-30) REVERT: B 173 LYS cc_start: 0.7278 (mmtp) cc_final: 0.6869 (mptp) REVERT: B 203 MET cc_start: 0.3642 (tpt) cc_final: 0.2468 (mpp) REVERT: B 213 GLN cc_start: 0.8066 (mt0) cc_final: 0.7803 (mt0) REVERT: B 222 LYS cc_start: 0.6701 (mttp) cc_final: 0.6421 (mttp) REVERT: B 223 ASP cc_start: 0.6773 (m-30) cc_final: 0.6196 (m-30) outliers start: 31 outliers final: 16 residues processed: 135 average time/residue: 1.1473 time to fit residues: 168.3939 Evaluate side-chains 134 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 282 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 94 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 115 optimal weight: 0.0570 chunk 43 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 overall best weight: 0.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 417 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.174824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.118132 restraints weight = 11181.101| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.86 r_work: 0.3029 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10353 Z= 0.120 Angle : 0.775 29.733 14022 Z= 0.335 Chirality : 0.042 0.256 1597 Planarity : 0.004 0.043 1760 Dihedral : 10.001 164.257 1640 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.58 % Allowed : 13.16 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.23), residues: 1259 helix: 1.63 (0.22), residues: 547 sheet: -0.05 (0.41), residues: 144 loop : -0.60 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 968 HIS 0.002 0.001 HIS A 505 PHE 0.010 0.001 PHE A 318 TYR 0.017 0.001 TYR A 805 ARG 0.004 0.000 ARG A 397 Details of bonding type rmsd link_NAG-ASN : bond 0.01038 ( 1) link_NAG-ASN : angle 3.31143 ( 3) hydrogen bonds : bond 0.04604 ( 475) hydrogen bonds : angle 4.51890 ( 1389) SS BOND : bond 0.00222 ( 3) SS BOND : angle 0.67671 ( 6) covalent geometry : bond 0.00270 (10349) covalent geometry : angle 0.77401 (14013) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 1.307 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.0344 (tmm) cc_final: 0.0049 (pmm) REVERT: A 107 LYS cc_start: 0.7143 (mptp) cc_final: 0.6630 (mttp) REVERT: A 134 ASN cc_start: 0.5964 (m-40) cc_final: 0.5671 (m-40) REVERT: A 150 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7497 (tp) REVERT: A 182 LEU cc_start: 0.7476 (tp) cc_final: 0.7238 (tp) REVERT: A 195 GLU cc_start: 0.6995 (mt-10) cc_final: 0.6599 (mt-10) REVERT: A 216 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.6318 (tmm160) REVERT: A 366 LYS cc_start: 0.6833 (mtpt) cc_final: 0.6285 (ptmt) REVERT: A 407 ASN cc_start: 0.6059 (OUTLIER) cc_final: 0.5740 (t0) REVERT: A 500 PHE cc_start: 0.5265 (p90) cc_final: 0.4782 (p90) REVERT: A 534 MET cc_start: 0.5922 (tpt) cc_final: 0.5426 (tpp) REVERT: A 601 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7067 (mp) REVERT: A 603 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7422 (mtm) REVERT: A 651 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.5974 (tp30) REVERT: A 963 ARG cc_start: 0.6283 (mtm180) cc_final: 0.5812 (mtt90) REVERT: B 114 ASP cc_start: 0.6430 (m-30) cc_final: 0.6045 (m-30) REVERT: B 173 LYS cc_start: 0.7261 (mmtp) cc_final: 0.6827 (mptp) REVERT: B 203 MET cc_start: 0.3718 (tpt) cc_final: 0.2578 (mpp) REVERT: B 213 GLN cc_start: 0.8054 (mt0) cc_final: 0.7793 (mt0) REVERT: B 222 LYS cc_start: 0.6712 (mttp) cc_final: 0.6410 (mttp) REVERT: B 223 ASP cc_start: 0.6724 (m-30) cc_final: 0.6156 (m-30) outliers start: 28 outliers final: 16 residues processed: 137 average time/residue: 1.3126 time to fit residues: 194.3400 Evaluate side-chains 135 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 407 ASN Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 282 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 99 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 114 optimal weight: 0.2980 chunk 70 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 417 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.175042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.118728 restraints weight = 11198.439| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.86 r_work: 0.3033 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10353 Z= 0.116 Angle : 0.774 29.716 14022 Z= 0.334 Chirality : 0.042 0.253 1597 Planarity : 0.004 0.042 1760 Dihedral : 9.928 160.057 1640 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.85 % Allowed : 13.25 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.23), residues: 1259 helix: 1.57 (0.22), residues: 553 sheet: 0.03 (0.42), residues: 134 loop : -0.62 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 968 HIS 0.002 0.001 HIS A 505 PHE 0.011 0.001 PHE A 243 TYR 0.016 0.001 TYR A 805 ARG 0.004 0.000 ARG A 397 Details of bonding type rmsd link_NAG-ASN : bond 0.01028 ( 1) link_NAG-ASN : angle 3.33034 ( 3) hydrogen bonds : bond 0.04509 ( 475) hydrogen bonds : angle 4.47453 ( 1389) SS BOND : bond 0.00213 ( 3) SS BOND : angle 0.66680 ( 6) covalent geometry : bond 0.00260 (10349) covalent geometry : angle 0.77249 (14013) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 1.296 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.0277 (tmm) cc_final: -0.0033 (pmm) REVERT: A 107 LYS cc_start: 0.7159 (mptp) cc_final: 0.6654 (mttp) REVERT: A 134 ASN cc_start: 0.5771 (m-40) cc_final: 0.5489 (m-40) REVERT: A 150 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7498 (tp) REVERT: A 182 LEU cc_start: 0.7487 (tp) cc_final: 0.7253 (tp) REVERT: A 195 GLU cc_start: 0.6936 (mt-10) cc_final: 0.6498 (mt-10) REVERT: A 216 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.6302 (tmm160) REVERT: A 366 LYS cc_start: 0.6873 (mtpt) cc_final: 0.6313 (ptmt) REVERT: A 407 ASN cc_start: 0.6062 (OUTLIER) cc_final: 0.5738 (t0) REVERT: A 500 PHE cc_start: 0.5266 (p90) cc_final: 0.4795 (p90) REVERT: A 502 LEU cc_start: 0.6163 (tp) cc_final: 0.5821 (tm) REVERT: A 534 MET cc_start: 0.5930 (tpt) cc_final: 0.5428 (tpp) REVERT: A 601 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7031 (mp) REVERT: A 603 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7383 (mtm) REVERT: A 651 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.5964 (tp30) REVERT: A 654 GLU cc_start: 0.6197 (OUTLIER) cc_final: 0.5560 (mt-10) REVERT: A 823 ASP cc_start: 0.7451 (OUTLIER) cc_final: 0.7043 (t0) REVERT: A 844 MET cc_start: 0.7853 (mmm) cc_final: 0.7578 (mmm) REVERT: A 963 ARG cc_start: 0.6266 (mtm180) cc_final: 0.5784 (mtt90) REVERT: B 114 ASP cc_start: 0.6429 (m-30) cc_final: 0.6024 (m-30) REVERT: B 173 LYS cc_start: 0.7246 (mmtp) cc_final: 0.6809 (mptp) REVERT: B 203 MET cc_start: 0.3725 (tpt) cc_final: 0.2640 (mpp) REVERT: B 213 GLN cc_start: 0.8076 (mt0) cc_final: 0.7833 (mt0) REVERT: B 222 LYS cc_start: 0.6714 (mttp) cc_final: 0.6285 (mttp) REVERT: B 223 ASP cc_start: 0.6758 (m-30) cc_final: 0.6168 (m-30) outliers start: 31 outliers final: 16 residues processed: 134 average time/residue: 1.5994 time to fit residues: 233.5621 Evaluate side-chains 137 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 407 ASN Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 282 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 33 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 76 optimal weight: 0.0000 chunk 19 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 417 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.175280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.117345 restraints weight = 11262.962| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.84 r_work: 0.2981 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10353 Z= 0.110 Angle : 0.768 29.796 14022 Z= 0.329 Chirality : 0.042 0.252 1597 Planarity : 0.004 0.042 1760 Dihedral : 9.786 158.260 1640 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.58 % Allowed : 13.62 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.23), residues: 1259 helix: 1.63 (0.22), residues: 552 sheet: -0.12 (0.42), residues: 138 loop : -0.59 (0.24), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 968 HIS 0.002 0.001 HIS A 505 PHE 0.010 0.001 PHE A 445 TYR 0.015 0.001 TYR A 805 ARG 0.005 0.000 ARG A 397 Details of bonding type rmsd link_NAG-ASN : bond 0.01034 ( 1) link_NAG-ASN : angle 3.39108 ( 3) hydrogen bonds : bond 0.04330 ( 475) hydrogen bonds : angle 4.41880 ( 1389) SS BOND : bond 0.00200 ( 3) SS BOND : angle 0.63122 ( 6) covalent geometry : bond 0.00242 (10349) covalent geometry : angle 0.76674 (14013) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.0083 (tmm) cc_final: -0.0166 (pmm) REVERT: A 107 LYS cc_start: 0.7132 (mptp) cc_final: 0.6627 (mttp) REVERT: A 134 ASN cc_start: 0.5527 (m-40) cc_final: 0.5288 (m-40) REVERT: A 150 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7471 (tp) REVERT: A 182 LEU cc_start: 0.7438 (tp) cc_final: 0.7209 (tp) REVERT: A 195 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6491 (mt-10) REVERT: A 216 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.6336 (tmm160) REVERT: A 285 LEU cc_start: 0.6752 (mt) cc_final: 0.6443 (mt) REVERT: A 366 LYS cc_start: 0.6832 (mtpt) cc_final: 0.6311 (ptmt) REVERT: A 407 ASN cc_start: 0.6016 (OUTLIER) cc_final: 0.5716 (t0) REVERT: A 500 PHE cc_start: 0.5207 (p90) cc_final: 0.4749 (p90) REVERT: A 502 LEU cc_start: 0.6093 (tp) cc_final: 0.5753 (tm) REVERT: A 534 MET cc_start: 0.5897 (tpt) cc_final: 0.5437 (tpp) REVERT: A 601 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.6982 (mp) REVERT: A 603 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7447 (mtm) REVERT: A 651 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6002 (tp30) REVERT: A 823 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.7058 (t0) REVERT: A 963 ARG cc_start: 0.6268 (mtm180) cc_final: 0.5795 (mtt90) REVERT: B 114 ASP cc_start: 0.6432 (m-30) cc_final: 0.6044 (m-30) REVERT: B 173 LYS cc_start: 0.7160 (mmtp) cc_final: 0.6716 (mptp) REVERT: B 203 MET cc_start: 0.3813 (tpt) cc_final: 0.2662 (mpp) REVERT: B 213 GLN cc_start: 0.8111 (mt0) cc_final: 0.7875 (mt0) REVERT: B 222 LYS cc_start: 0.6635 (mttp) cc_final: 0.6201 (mttp) REVERT: B 223 ASP cc_start: 0.6743 (m-30) cc_final: 0.6162 (m-30) outliers start: 28 outliers final: 16 residues processed: 138 average time/residue: 1.1527 time to fit residues: 174.0673 Evaluate side-chains 141 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 407 ASN Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 282 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 113 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 417 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.173467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.116195 restraints weight = 11169.442| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.97 r_work: 0.2954 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10353 Z= 0.141 Angle : 0.800 29.673 14022 Z= 0.349 Chirality : 0.044 0.259 1597 Planarity : 0.004 0.043 1760 Dihedral : 10.107 155.599 1640 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.58 % Allowed : 14.35 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.23), residues: 1259 helix: 1.45 (0.22), residues: 553 sheet: -0.02 (0.42), residues: 132 loop : -0.60 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 968 HIS 0.002 0.001 HIS A 57 PHE 0.011 0.002 PHE A1021 TYR 0.020 0.002 TYR A 805 ARG 0.005 0.000 ARG A 397 Details of bonding type rmsd link_NAG-ASN : bond 0.00976 ( 1) link_NAG-ASN : angle 3.26452 ( 3) hydrogen bonds : bond 0.04980 ( 475) hydrogen bonds : angle 4.56555 ( 1389) SS BOND : bond 0.00235 ( 3) SS BOND : angle 0.73308 ( 6) covalent geometry : bond 0.00327 (10349) covalent geometry : angle 0.79895 (14013) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 1.150 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.0193 (tmm) cc_final: -0.0092 (pmm) REVERT: A 107 LYS cc_start: 0.7121 (mptp) cc_final: 0.6612 (mttp) REVERT: A 134 ASN cc_start: 0.5569 (m-40) cc_final: 0.5310 (m-40) REVERT: A 150 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7484 (tp) REVERT: A 182 LEU cc_start: 0.7446 (tp) cc_final: 0.7213 (tp) REVERT: A 195 GLU cc_start: 0.6916 (mt-10) cc_final: 0.6478 (mt-10) REVERT: A 216 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.6341 (tmm160) REVERT: A 407 ASN cc_start: 0.6089 (OUTLIER) cc_final: 0.5791 (t0) REVERT: A 502 LEU cc_start: 0.6033 (tp) cc_final: 0.5759 (tm) REVERT: A 534 MET cc_start: 0.5867 (tpt) cc_final: 0.5384 (tpp) REVERT: A 601 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7037 (mp) REVERT: A 603 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7555 (mtt) REVERT: A 651 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6009 (tp30) REVERT: A 844 MET cc_start: 0.7846 (mmm) cc_final: 0.7560 (mmm) REVERT: A 963 ARG cc_start: 0.6278 (mtm180) cc_final: 0.5803 (mtt90) REVERT: B 114 ASP cc_start: 0.6458 (m-30) cc_final: 0.6065 (m-30) REVERT: B 173 LYS cc_start: 0.7220 (mmtp) cc_final: 0.6775 (mptp) REVERT: B 203 MET cc_start: 0.3767 (tpt) cc_final: 0.2632 (mpp) REVERT: B 213 GLN cc_start: 0.8100 (mt0) cc_final: 0.7820 (mm-40) REVERT: B 223 ASP cc_start: 0.6774 (m-30) cc_final: 0.6187 (m-30) REVERT: B 274 ARG cc_start: 0.7436 (mtt-85) cc_final: 0.7088 (mtt-85) outliers start: 28 outliers final: 19 residues processed: 135 average time/residue: 1.1205 time to fit residues: 166.0294 Evaluate side-chains 139 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 407 ASN Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 282 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 98 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 34 optimal weight: 0.0670 chunk 114 optimal weight: 0.0670 chunk 50 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 417 ASN B 208 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.175787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.119009 restraints weight = 11183.483| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.93 r_work: 0.3011 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 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 : 0.002 0.032 10353 Z= 0.103 Angle : 0.767 30.083 14022 Z= 0.328 Chirality : 0.042 0.250 1597 Planarity : 0.004 0.042 1760 Dihedral : 9.687 156.049 1640 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.39 % Allowed : 14.35 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.23), residues: 1259 helix: 1.75 (0.22), residues: 545 sheet: -0.02 (0.43), residues: 133 loop : -0.55 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 968 HIS 0.002 0.001 HIS A 505 PHE 0.010 0.001 PHE A 445 TYR 0.014 0.001 TYR A 881 ARG 0.004 0.000 ARG A 397 Details of bonding type rmsd link_NAG-ASN : bond 0.01029 ( 1) link_NAG-ASN : angle 3.44280 ( 3) hydrogen bonds : bond 0.04157 ( 475) hydrogen bonds : angle 4.38620 ( 1389) SS BOND : bond 0.00207 ( 3) SS BOND : angle 0.58379 ( 6) covalent geometry : bond 0.00222 (10349) covalent geometry : angle 0.76515 (14013) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10163.75 seconds wall clock time: 178 minutes 38.76 seconds (10718.76 seconds total)