Starting phenix.real_space_refine on Thu Aug 6 02:34:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k31_62003/08_2026/9k31_62003.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k31_62003/08_2026/9k31_62003.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k31_62003/08_2026/9k31_62003.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k31_62003/08_2026/9k31_62003.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k31_62003/08_2026/9k31_62003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k31_62003/08_2026/9k31_62003.map" } resolution = 2.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 357 5.49 5 Mg 5 5.21 5 S 19 5.16 5 C 6702 2.51 5 N 2467 2.21 5 O 3376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12928 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5284 Classifications: {'peptide': 665} Link IDs: {'PTRANS': 38, 'TRANS': 626} Chain: "B" Number of atoms: 6412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 6412 Classifications: {'RNA': 298} Modifications used: {'rna2p_pur': 25, 'rna2p_pyr': 12, 'rna3p_pur': 150, 'rna3p_pyr': 111} Link IDs: {'rna2p': 37, 'rna3p': 260} Chain breaks: 3 Chain: "C" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 724 Classifications: {'DNA': 36} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 35} Chain: "D" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 479 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain breaks: 2 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4, 'water': 21} Link IDs: {None: 24} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2592 SG CYS A 323 67.534 65.470 67.489 1.00 85.16 S ATOM 2615 SG CYS A 326 69.522 66.848 64.854 1.00 88.39 S ATOM 2854 SG CYS A 358 65.603 66.586 64.244 1.00 82.07 S ATOM 2880 SG CYS A 361 67.427 63.602 64.015 1.00 82.91 S ATOM 806 SG CYS A 107 31.575 60.202 100.344 1.00 69.02 S ATOM 891 SG CYS A 118 27.987 60.683 99.857 1.00 70.60 S ATOM 1770 SG CYS A 227 30.303 63.863 100.456 1.00 69.74 S Time building chain proxies: 2.74, per 1000 atoms: 0.21 Number of scatterers: 12928 At special positions: 0 Unit cell: (92.2011, 122.935, 141.183, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 19 16.00 P 357 15.00 Mg 5 11.99 O 3376 8.00 N 2467 7.00 C 6702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 220.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 702 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 326 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 323 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 358 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 361 " pdb=" ZN A 703 " pdb="ZN ZN A 703 " - pdb=" ND1 HIS A 230 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 227 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 107 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 118 " Number of angles added : 9 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1236 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 6 sheets defined 35.3% alpha, 13.7% beta 138 base pairs and 229 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 46 through 60 Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.784A pdb=" N THR A 77 " --> pdb=" O GLY A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 127 Processing helix chain 'A' and resid 128 through 138 removed outlier: 3.641A pdb=" N ILE A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 150 removed outlier: 4.090A pdb=" N PHE A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 154 removed outlier: 3.551A pdb=" N VAL A 154 " --> pdb=" O LEU A 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 151 through 154' Processing helix chain 'A' and resid 161 through 167 removed outlier: 3.939A pdb=" N ALA A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 180 removed outlier: 3.897A pdb=" N ALA A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Proline residue: A 175 - end of helix removed outlier: 3.603A pdb=" N VAL A 179 " --> pdb=" O PRO A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 198 Processing helix chain 'A' and resid 201 through 213 removed outlier: 3.692A pdb=" N SER A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 237 removed outlier: 5.421A pdb=" N HIS A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 266 removed outlier: 3.545A pdb=" N VAL A 261 " --> pdb=" O ASP A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 292 removed outlier: 4.089A pdb=" N THR A 291 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA A 292 " --> pdb=" O ARG A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 Processing helix chain 'A' and resid 310 through 320 Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 358 through 366 Processing helix chain 'A' and resid 397 through 406 removed outlier: 3.553A pdb=" N THR A 404 " --> pdb=" O TYR A 400 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASP A 405 " --> pdb=" O MET A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 419 Processing helix chain 'A' and resid 428 through 440 removed outlier: 3.777A pdb=" N ARG A 438 " --> pdb=" O PHE A 434 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP A 439 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 453 removed outlier: 3.546A pdb=" N ALA A 450 " --> pdb=" O PHE A 446 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 451 " --> pdb=" O VAL A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 515 removed outlier: 3.671A pdb=" N VAL A 512 " --> pdb=" O PHE A 509 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA A 513 " --> pdb=" O LYS A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 539 removed outlier: 3.583A pdb=" N THR A 523 " --> pdb=" O ARG A 519 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 554 removed outlier: 3.517A pdb=" N LEU A 551 " --> pdb=" O ALA A 548 " (cutoff:3.500A) Proline residue: A 552 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 423 through 425 removed outlier: 6.571A pdb=" N GLN A 8 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N VAL A 276 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU A 10 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE A 35 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ALA A 25 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL A 33 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N GLY A 27 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLU A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 339 through 342 Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 488 Processing sheet with id=AA4, first strand: chain 'A' and resid 571 through 574 removed outlier: 3.531A pdb=" N HIS A 577 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 597 through 604 removed outlier: 6.666A pdb=" N THR A 589 " --> pdb=" O THR A 624 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR A 624 " --> pdb=" O THR A 589 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL A 591 " --> pdb=" O VAL A 622 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 630 through 632 removed outlier: 6.698A pdb=" N THR A 650 " --> pdb=" O THR A 641 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ASN A 643 " --> pdb=" O THR A 648 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR A 648 " --> pdb=" O ASN A 643 " (cutoff:3.500A) 170 hydrogen bonds defined for protein. 459 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 363 hydrogen bonds 646 hydrogen bond angles 0 basepair planarities 138 basepair parallelities 229 stacking parallelities Total time for adding SS restraints: 3.41 Time building geometry restraints manager: 0.98 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: 2127 1.34 - 1.46: 5461 1.46 - 1.58: 5593 1.58 - 1.70: 712 1.70 - 1.82: 24 Bond restraints: 13917 Sorted by residual: bond pdb=" C THR A 541 " pdb=" N PRO A 542 " ideal model delta sigma weight residual 1.331 1.373 -0.042 8.70e-03 1.32e+04 2.35e+01 bond pdb=" C ILE A 554 " pdb=" N PRO A 555 " ideal model delta sigma weight residual 1.332 1.375 -0.043 8.90e-03 1.26e+04 2.33e+01 bond pdb=" C LYS A 553 " pdb=" N ILE A 554 " ideal model delta sigma weight residual 1.329 1.357 -0.028 7.30e-03 1.88e+04 1.45e+01 bond pdb=" C ALA A 91 " pdb=" N PRO A 92 " ideal model delta sigma weight residual 1.331 1.376 -0.045 1.27e-02 6.20e+03 1.23e+01 bond pdb=" NE ARG A 26 " pdb=" CZ ARG A 26 " ideal model delta sigma weight residual 1.326 1.364 -0.038 1.10e-02 8.26e+03 1.20e+01 ... (remaining 13912 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 17616 1.86 - 3.73: 2642 3.73 - 5.59: 265 5.59 - 7.45: 21 7.45 - 9.32: 2 Bond angle restraints: 20546 Sorted by residual: angle pdb=" O4' G B -8 " pdb=" C1' G B -8 " pdb=" N9 G B -8 " ideal model delta sigma weight residual 108.20 113.35 -5.15 8.00e-01 1.56e+00 4.15e+01 angle pdb=" C2' G B 288 " pdb=" C1' G B 288 " pdb=" N9 G B 288 " ideal model delta sigma weight residual 112.00 118.01 -6.01 1.10e+00 8.26e-01 2.98e+01 angle pdb=" N PHE A 231 " pdb=" CA PHE A 231 " pdb=" CB PHE A 231 " ideal model delta sigma weight residual 110.01 117.28 -7.27 1.45e+00 4.76e-01 2.52e+01 angle pdb=" CA PHE A 180 " pdb=" CB PHE A 180 " pdb=" CG PHE A 180 " ideal model delta sigma weight residual 113.80 118.74 -4.94 1.00e+00 1.00e+00 2.44e+01 angle pdb=" CA ASP A 130 " pdb=" CB ASP A 130 " pdb=" CG ASP A 130 " ideal model delta sigma weight residual 112.60 117.43 -4.83 1.00e+00 1.00e+00 2.34e+01 ... (remaining 20541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.20: 7091 20.20 - 40.40: 813 40.40 - 60.61: 380 60.61 - 80.81: 310 80.81 - 101.01: 5 Dihedral angle restraints: 8599 sinusoidal: 6690 harmonic: 1909 Sorted by residual: dihedral pdb=" O4' G B 325 " pdb=" C1' G B 325 " pdb=" N9 G B 325 " pdb=" C4 G B 325 " ideal model delta sinusoidal sigma weight residual 254.00 173.69 80.31 1 1.70e+01 3.46e-03 2.76e+01 dihedral pdb=" CA PHE A 14 " pdb=" C PHE A 14 " pdb=" N GLY A 15 " pdb=" CA GLY A 15 " ideal model delta harmonic sigma weight residual 180.00 155.11 24.89 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" O4' A B 198 " pdb=" C2' A B 198 " pdb=" C1' A B 198 " pdb=" C3' A B 198 " ideal model delta sinusoidal sigma weight residual 25.00 -7.04 32.04 1 8.00e+00 1.56e-02 2.29e+01 ... (remaining 8596 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 2177 0.134 - 0.267: 319 0.267 - 0.401: 0 0.401 - 0.534: 0 0.534 - 0.668: 8 Chirality restraints: 2504 Sorted by residual: chirality pdb=" P DA C -11 " pdb=" OP1 DA C -11 " pdb=" OP2 DA C -11 " pdb=" O5' DA C -11 " both_signs ideal model delta sigma weight residual True 2.34 -3.00 -0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" P DA D -9 " pdb=" OP1 DA D -9 " pdb=" OP2 DA D -9 " pdb=" O5' DA D -9 " both_signs ideal model delta sigma weight residual True 2.34 -2.99 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" P DC D -1 " pdb=" OP1 DC D -1 " pdb=" OP2 DC D -1 " pdb=" O5' DC D -1 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.65 2.00e-01 2.50e+01 1.04e+01 ... (remaining 2501 not shown) Planarity restraints: 1328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A B 127 " -0.013 2.00e-02 2.50e+03 1.31e-02 4.69e+00 pdb=" N9 A B 127 " 0.007 2.00e-02 2.50e+03 pdb=" C8 A B 127 " 0.000 2.00e-02 2.50e+03 pdb=" N7 A B 127 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A B 127 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A B 127 " 0.016 2.00e-02 2.50e+03 pdb=" N6 A B 127 " -0.003 2.00e-02 2.50e+03 pdb=" N1 A B 127 " -0.032 2.00e-02 2.50e+03 pdb=" C2 A B 127 " 0.019 2.00e-02 2.50e+03 pdb=" N3 A B 127 " 0.002 2.00e-02 2.50e+03 pdb=" C4 A B 127 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 2 " -0.009 2.00e-02 2.50e+03 1.19e-02 3.18e+00 pdb=" N1 U B 2 " 0.005 2.00e-02 2.50e+03 pdb=" C2 U B 2 " 0.017 2.00e-02 2.50e+03 pdb=" O2 U B 2 " 0.003 2.00e-02 2.50e+03 pdb=" N3 U B 2 " -0.026 2.00e-02 2.50e+03 pdb=" C4 U B 2 " 0.014 2.00e-02 2.50e+03 pdb=" O4 U B 2 " -0.001 2.00e-02 2.50e+03 pdb=" C5 U B 2 " -0.003 2.00e-02 2.50e+03 pdb=" C6 U B 2 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B -8 " -0.023 2.00e-02 2.50e+03 9.64e-03 2.79e+00 pdb=" N9 G B -8 " 0.020 2.00e-02 2.50e+03 pdb=" C8 G B -8 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G B -8 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G B -8 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G B -8 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G B -8 " -0.005 2.00e-02 2.50e+03 pdb=" N1 G B -8 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G B -8 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G B -8 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G B -8 " 0.008 2.00e-02 2.50e+03 pdb=" C4 G B -8 " 0.006 2.00e-02 2.50e+03 ... (remaining 1325 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 191 2.61 - 3.18: 8960 3.18 - 3.76: 22750 3.76 - 4.33: 33254 4.33 - 4.90: 44924 Nonbonded interactions: 110079 Sorted by model distance: nonbonded pdb="MG MG B 403 " pdb=" O HOH B 501 " model vdw 2.042 2.170 nonbonded pdb=" OP2 A B 127 " pdb="MG MG B 402 " model vdw 2.051 2.170 nonbonded pdb="MG MG B 402 " pdb=" O HOH B 512 " model vdw 2.051 2.170 nonbonded pdb="MG MG B 404 " pdb=" O HOH B 507 " model vdw 2.054 2.170 nonbonded pdb="MG MG B 404 " pdb=" O HOH B 510 " model vdw 2.057 2.170 ... (remaining 110074 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.340 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 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 : 0.011 0.061 13925 Z= 0.805 Angle : 1.313 12.712 20555 Z= 0.961 Chirality : 0.087 0.668 2504 Planarity : 0.004 0.041 1328 Dihedral : 21.483 101.008 7363 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 0.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.36 % Allowed : 9.21 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.27), residues: 663 helix: -1.74 (0.30), residues: 177 sheet: -0.27 (0.65), residues: 66 loop : -1.14 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 302 TYR 0.012 0.002 TYR A 94 PHE 0.008 0.001 PHE A 231 TRP 0.014 0.002 TRP A 378 HIS 0.002 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.01125 / 0.81 (13917) covalent geometry : angle 1.30433 / 0.96 (20546) hydrogen bonds : bond 0.19266 / 13.38 ( 533) hydrogen bonds : angle 5.68665 / 3.95 ( 1105) metal coordination : bond 0.01512 / 0.89 ( 8) metal coordination : angle 7.48292 / 4.16 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 57 average time/residue: 0.9978 time to fit residues: 60.1597 Evaluate side-chains 36 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 0.0570 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 overall best weight: 0.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 GLN A 417 GLN A 601 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.091281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.069202 restraints weight = 27070.595| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.53 r_work: 0.3127 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13925 Z= 0.153 Angle : 0.593 9.731 20555 Z= 0.359 Chirality : 0.042 0.238 2504 Planarity : 0.005 0.032 1328 Dihedral : 21.980 98.749 6040 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.44 % Allowed : 14.08 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.30), residues: 663 helix: -0.13 (0.37), residues: 184 sheet: 0.15 (0.64), residues: 70 loop : -0.70 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 460 TYR 0.013 0.002 TYR A 430 PHE 0.010 0.001 PHE A 446 TRP 0.014 0.001 TRP A 378 HIS 0.002 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.15 (13917) covalent geometry : angle 0.58320 / 0.36 (20546) hydrogen bonds : bond 0.07900 / 5.64 ( 533) hydrogen bonds : angle 3.54062 / 2.48 ( 1105) metal coordination : bond 0.00785 / 0.38 ( 8) metal coordination : angle 5.19511 / 2.99 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.8850 (ttm-80) cc_final: 0.8599 (mtm-85) REVERT: A 260 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8731 (tmtm) outliers start: 8 outliers final: 3 residues processed: 40 average time/residue: 1.0440 time to fit residues: 44.3791 Evaluate side-chains 37 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 458 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 GLN A 426 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.084840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.062157 restraints weight = 26999.883| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.53 r_work: 0.2932 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 13925 Z= 0.227 Angle : 0.615 7.817 20555 Z= 0.354 Chirality : 0.045 0.239 2504 Planarity : 0.006 0.059 1328 Dihedral : 22.135 97.441 6040 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.90 % Allowed : 15.16 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.30), residues: 663 helix: 0.11 (0.38), residues: 186 sheet: 0.22 (0.63), residues: 75 loop : -0.77 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 620 TYR 0.020 0.003 TYR A 592 PHE 0.013 0.002 PHE A 546 TRP 0.008 0.002 TRP A 246 HIS 0.006 0.001 HIS A 577 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.23 (13917) covalent geometry : angle 0.60801 / 0.35 (20546) hydrogen bonds : bond 0.07700 / 5.42 ( 533) hydrogen bonds : angle 3.28122 / 2.27 ( 1105) metal coordination : bond 0.00442 / 0.26 ( 8) metal coordination : angle 4.32607 / 2.61 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 39 average time/residue: 0.8596 time to fit residues: 35.5907 Evaluate side-chains 40 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 458 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 38 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.084005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.061454 restraints weight = 26975.836| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.53 r_work: 0.2915 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 13925 Z= 0.277 Angle : 0.642 7.557 20555 Z= 0.362 Chirality : 0.047 0.259 2504 Planarity : 0.006 0.059 1328 Dihedral : 22.229 96.640 6040 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.81 % Allowed : 15.52 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.31), residues: 663 helix: 0.09 (0.38), residues: 186 sheet: 0.21 (0.60), residues: 85 loop : -0.80 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 639 TYR 0.016 0.003 TYR A 94 PHE 0.011 0.002 PHE A 546 TRP 0.010 0.002 TRP A 300 HIS 0.004 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.28 (13917) covalent geometry : angle 0.63659 / 0.36 (20546) hydrogen bonds : bond 0.07760 / 5.49 ( 533) hydrogen bonds : angle 3.21987 / 2.22 ( 1105) metal coordination : bond 0.00448 / 0.26 ( 8) metal coordination : angle 4.08191 / 2.47 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.9063 (tpp80) cc_final: 0.8672 (mtt-85) outliers start: 10 outliers final: 6 residues processed: 41 average time/residue: 0.9429 time to fit residues: 41.1071 Evaluate side-chains 41 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 621 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 90 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 35 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.085415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.062937 restraints weight = 26967.273| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.53 r_work: 0.2954 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13925 Z= 0.167 Angle : 0.533 6.532 20555 Z= 0.317 Chirality : 0.039 0.264 2504 Planarity : 0.005 0.055 1328 Dihedral : 22.253 96.840 6040 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.99 % Allowed : 16.25 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.31), residues: 663 helix: 0.32 (0.39), residues: 186 sheet: 0.47 (0.60), residues: 83 loop : -0.77 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 639 TYR 0.014 0.002 TYR A 592 PHE 0.009 0.001 PHE A 546 TRP 0.009 0.001 TRP A 439 HIS 0.003 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.17 (13917) covalent geometry : angle 0.52679 / 0.32 (20546) hydrogen bonds : bond 0.06515 / 4.63 ( 533) hydrogen bonds : angle 3.07685 / 2.11 ( 1105) metal coordination : bond 0.00258 / 0.15 ( 8) metal coordination : angle 3.92080 / 2.33 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.9060 (tpp80) cc_final: 0.8675 (mtt-85) REVERT: A 269 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7015 (ttp-110) REVERT: A 600 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.7932 (mtt) REVERT: A 601 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8494 (tt0) outliers start: 11 outliers final: 6 residues processed: 43 average time/residue: 1.0147 time to fit residues: 46.1305 Evaluate side-chains 45 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 601 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 56 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.085853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.063449 restraints weight = 26878.220| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.54 r_work: 0.2968 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13925 Z= 0.152 Angle : 0.514 7.039 20555 Z= 0.308 Chirality : 0.038 0.264 2504 Planarity : 0.005 0.053 1328 Dihedral : 22.236 96.261 6040 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.99 % Allowed : 15.88 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.31), residues: 663 helix: 0.37 (0.39), residues: 186 sheet: 0.45 (0.60), residues: 83 loop : -0.72 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 620 TYR 0.014 0.002 TYR A 592 PHE 0.008 0.001 PHE A 546 TRP 0.008 0.001 TRP A 439 HIS 0.002 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 (13917) covalent geometry : angle 0.50846 / 0.31 (20546) hydrogen bonds : bond 0.06228 / 4.42 ( 533) hydrogen bonds : angle 3.03188 / 2.08 ( 1105) metal coordination : bond 0.00255 / 0.15 ( 8) metal coordination : angle 3.76212 / 2.23 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.9080 (tpp80) cc_final: 0.8746 (mtm-85) REVERT: A 269 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7050 (ttp-110) REVERT: A 576 ARG cc_start: 0.8727 (mtm-85) cc_final: 0.8477 (mpp-170) REVERT: A 600 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.7913 (mtt) REVERT: A 601 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8419 (tt0) outliers start: 11 outliers final: 6 residues processed: 43 average time/residue: 0.8636 time to fit residues: 39.3250 Evaluate side-chains 45 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 601 GLN Chi-restraints excluded: chain A residue 621 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 28 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 76 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 chunk 15 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 87 optimal weight: 20.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.085082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.062634 restraints weight = 26678.783| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.52 r_work: 0.2951 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13925 Z= 0.185 Angle : 0.542 7.344 20555 Z= 0.317 Chirality : 0.040 0.267 2504 Planarity : 0.005 0.055 1328 Dihedral : 22.228 95.250 6039 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.62 % Allowed : 16.06 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.31), residues: 663 helix: 0.40 (0.39), residues: 186 sheet: 0.43 (0.59), residues: 83 loop : -0.72 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 639 TYR 0.023 0.002 TYR A 430 PHE 0.008 0.001 PHE A 226 TRP 0.007 0.001 TRP A 408 HIS 0.003 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.19 (13917) covalent geometry : angle 0.53595 / 0.32 (20546) hydrogen bonds : bond 0.06578 / 4.65 ( 533) hydrogen bonds : angle 3.01748 / 2.07 ( 1105) metal coordination : bond 0.00333 / 0.19 ( 8) metal coordination : angle 3.73802 / 2.25 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.9096 (tpp80) cc_final: 0.8696 (mtt-85) REVERT: A 269 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7071 (ttp-110) REVERT: A 576 ARG cc_start: 0.8728 (mtm-85) cc_final: 0.8477 (mpp-170) REVERT: A 601 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8457 (tt0) outliers start: 9 outliers final: 7 residues processed: 42 average time/residue: 0.8871 time to fit residues: 39.4541 Evaluate side-chains 46 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 601 GLN Chi-restraints excluded: chain A residue 621 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 18 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.084259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.061757 restraints weight = 26656.209| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.53 r_work: 0.2925 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 13925 Z= 0.248 Angle : 0.605 9.424 20555 Z= 0.343 Chirality : 0.044 0.273 2504 Planarity : 0.006 0.059 1328 Dihedral : 22.254 94.458 6039 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.17 % Allowed : 16.25 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.31), residues: 663 helix: 0.28 (0.38), residues: 186 sheet: 0.27 (0.58), residues: 83 loop : -0.75 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 620 TYR 0.015 0.002 TYR A 592 PHE 0.009 0.001 PHE A 226 TRP 0.008 0.002 TRP A 300 HIS 0.005 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.25 (13917) covalent geometry : angle 0.59989 / 0.34 (20546) hydrogen bonds : bond 0.07238 / 5.11 ( 533) hydrogen bonds : angle 3.06502 / 2.11 ( 1105) metal coordination : bond 0.00445 / 0.25 ( 8) metal coordination : angle 3.80874 / 2.31 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.9111 (tpp80) cc_final: 0.8766 (mtm-85) REVERT: A 269 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7095 (ttp-110) REVERT: A 601 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8506 (tt0) outliers start: 12 outliers final: 7 residues processed: 44 average time/residue: 0.9515 time to fit residues: 44.3783 Evaluate side-chains 45 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 601 GLN Chi-restraints excluded: chain A residue 621 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 55 optimal weight: 0.0870 chunk 40 optimal weight: 3.9990 chunk 88 optimal weight: 20.0000 chunk 8 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.085554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.063159 restraints weight = 26829.441| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.53 r_work: 0.2964 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13925 Z= 0.139 Angle : 0.517 9.025 20555 Z= 0.310 Chirality : 0.038 0.275 2504 Planarity : 0.005 0.054 1328 Dihedral : 22.293 94.967 6039 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.90 % Allowed : 17.87 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.32), residues: 663 helix: 0.40 (0.39), residues: 186 sheet: 0.40 (0.59), residues: 83 loop : -0.69 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 376 TYR 0.016 0.002 TYR A 592 PHE 0.008 0.001 PHE A 446 TRP 0.010 0.001 TRP A 439 HIS 0.002 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.14 (13917) covalent geometry : angle 0.51177 / 0.31 (20546) hydrogen bonds : bond 0.06315 / 4.48 ( 533) hydrogen bonds : angle 2.99214 / 2.05 ( 1105) metal coordination : bond 0.00255 / 0.15 ( 8) metal coordination : angle 3.69592 / 2.20 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 239 ARG cc_start: 0.9107 (tpp80) cc_final: 0.8701 (mtt-85) REVERT: A 576 ARG cc_start: 0.8731 (mtm-85) cc_final: 0.8485 (mpp-170) REVERT: A 601 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8456 (tt0) REVERT: A 668 ARG cc_start: 0.6382 (ppt170) cc_final: 0.6111 (pmt-80) outliers start: 5 outliers final: 5 residues processed: 40 average time/residue: 0.9938 time to fit residues: 42.3020 Evaluate side-chains 43 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 601 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 13 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 8 optimal weight: 0.0670 chunk 17 optimal weight: 0.4980 chunk 83 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 72 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 overall best weight: 2.5122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.085231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.062849 restraints weight = 26908.276| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.53 r_work: 0.2956 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13925 Z= 0.176 Angle : 0.543 11.377 20555 Z= 0.318 Chirality : 0.039 0.274 2504 Planarity : 0.005 0.055 1328 Dihedral : 22.262 94.639 6039 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.26 % Allowed : 17.69 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.32), residues: 663 helix: 0.39 (0.38), residues: 186 sheet: 0.42 (0.59), residues: 83 loop : -0.74 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 376 TYR 0.024 0.002 TYR A 430 PHE 0.008 0.001 PHE A 546 TRP 0.008 0.001 TRP A 408 HIS 0.003 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.18 (13917) covalent geometry : angle 0.53760 / 0.32 (20546) hydrogen bonds : bond 0.06433 / 4.54 ( 533) hydrogen bonds : angle 2.98918 / 2.05 ( 1105) metal coordination : bond 0.00306 / 0.17 ( 8) metal coordination : angle 3.69951 / 2.22 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 239 ARG cc_start: 0.9110 (tpp80) cc_final: 0.8772 (mtm-85) REVERT: A 269 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7055 (ttp-110) REVERT: A 576 ARG cc_start: 0.8727 (mtm-85) cc_final: 0.8483 (mpp-170) REVERT: A 601 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8490 (tt0) REVERT: A 639 ARG cc_start: 0.7811 (ttm-80) cc_final: 0.7499 (ttm-80) REVERT: A 668 ARG cc_start: 0.6454 (ppt170) cc_final: 0.6168 (pmt-80) outliers start: 7 outliers final: 5 residues processed: 42 average time/residue: 1.0389 time to fit residues: 46.1459 Evaluate side-chains 44 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 601 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 94 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.083275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.060822 restraints weight = 26766.843| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.53 r_work: 0.2905 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 13925 Z= 0.313 Angle : 0.672 10.420 20555 Z= 0.372 Chirality : 0.050 0.278 2504 Planarity : 0.006 0.062 1328 Dihedral : 22.325 91.357 6039 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.44 % Allowed : 17.87 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.31), residues: 663 helix: 0.15 (0.38), residues: 188 sheet: 0.26 (0.58), residues: 83 loop : -0.86 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 376 TYR 0.018 0.003 TYR A 94 PHE 0.011 0.002 PHE A 226 TRP 0.009 0.002 TRP A 300 HIS 0.006 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00613 / 0.31 (13917) covalent geometry : angle 0.66670 / 0.37 (20546) hydrogen bonds : bond 0.08217 / 5.78 ( 533) hydrogen bonds : angle 3.11671 / 2.14 ( 1105) metal coordination : bond 0.00612 / 0.33 ( 8) metal coordination : angle 4.04826 / 2.48 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4657.15 seconds wall clock time: 79 minutes 46.25 seconds (4786.25 seconds total)