Starting phenix.real_space_refine on Fri Jul 3 08:12:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k31_62003/07_2026/9k31_62003.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k31_62003/07_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_62003/07_2026/9k31_62003.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k31_62003/07_2026/9k31_62003.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k31_62003/07_2026/9k31_62003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k31_62003/07_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-dev-6108/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: 2.66, 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: 0.91 Conformation dependent library (CDL) restraints added in 300.2 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: 1.57 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: 2.86 Time building geometry restraints manager: 1.32 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: 17256 1.86 - 3.73: 3004 3.73 - 5.59: 263 5.59 - 7.45: 21 7.45 - 9.32: 2 Bond angle restraints: 20546 Sorted by residual: angle pdb=" O3' G B 141 " pdb=" C3' G B 141 " pdb=" C2' G B 141 " ideal model delta sigma weight residual 109.50 118.82 -9.32 1.50e+00 4.44e-01 3.86e+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 angle pdb=" CA PHE A 509 " pdb=" CB PHE A 509 " pdb=" CG PHE A 509 " ideal model delta sigma weight residual 113.80 118.63 -4.83 1.00e+00 1.00e+00 2.33e+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: 2023 0.134 - 0.267: 473 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: 1.730 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.090 Find NCS groups from input model: 0.040 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:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.710 ------------------------------------------------------------------------------- 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= 0.779 Angle : 1.365 12.712 20555 Z= 0.965 Chirality : 0.097 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 0.01139 / 0.78 (13917) covalent geometry : angle 1.35671 / 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 : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 57 average time/residue: 0.8856 time to fit residues: 53.3320 Evaluate side-chains 35 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.091070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.069170 restraints weight = 27270.769| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.52 r_work: 0.3114 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13925 Z= 0.147 Angle : 0.573 9.951 20555 Z= 0.353 Chirality : 0.041 0.229 2504 Planarity : 0.004 0.034 1328 Dihedral : 22.004 100.638 6040 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.26 % Allowed : 14.44 % Favored : 84.30 % 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: -0.66 (0.30), residues: 663 helix: -0.07 (0.37), residues: 182 sheet: 0.08 (0.65), residues: 68 loop : -0.67 (0.27), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 668 TYR 0.014 0.002 TYR A 430 PHE 0.011 0.001 PHE A 446 TRP 0.015 0.001 TRP A 378 HIS 0.003 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.15 (13917) covalent geometry : angle 0.56239 / 0.35 (20546) hydrogen bonds : bond 0.07673 / 5.50 ( 533) hydrogen bonds : angle 3.55580 / 2.49 ( 1105) metal coordination : bond 0.00805 / 0.39 ( 8) metal coordination : angle 5.35520 / 3.09 ( 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 41 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.8897 (mtm-85) cc_final: 0.8247 (mtt-85) REVERT: A 260 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8684 (tmtm) outliers start: 7 outliers final: 2 residues processed: 40 average time/residue: 0.8795 time to fit residues: 37.4556 Evaluate side-chains 36 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.190 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 8 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 60 optimal weight: 0.0970 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.085298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.062594 restraints weight = 26962.584| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.55 r_work: 0.2937 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 13925 Z= 0.206 Angle : 0.552 7.459 20555 Z= 0.333 Chirality : 0.042 0.217 2504 Planarity : 0.005 0.052 1328 Dihedral : 22.138 100.838 6040 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.90 % Allowed : 14.98 % Favored : 84.12 % 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: -0.61 (0.30), residues: 663 helix: 0.15 (0.38), residues: 186 sheet: 0.15 (0.62), residues: 75 loop : -0.76 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 639 TYR 0.021 0.003 TYR A 592 PHE 0.011 0.001 PHE A 546 TRP 0.009 0.002 TRP A 246 HIS 0.003 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.21 (13917) covalent geometry : angle 0.54468 / 0.33 (20546) hydrogen bonds : bond 0.06979 / 4.94 ( 533) hydrogen bonds : angle 3.28407 / 2.26 ( 1105) metal coordination : bond 0.00396 / 0.23 ( 8) metal coordination : angle 4.30973 / 2.58 ( 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 41 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.8986 (mtm-85) cc_final: 0.8418 (mtt90) REVERT: A 600 MET cc_start: 0.8494 (mtt) cc_final: 0.8046 (mtt) REVERT: A 620 ARG cc_start: 0.7344 (mpp80) cc_final: 0.7067 (mtm180) outliers start: 5 outliers final: 4 residues processed: 38 average time/residue: 0.8812 time to fit residues: 35.4818 Evaluate side-chains 39 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 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: 10.0000 chunk 45 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 426 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.085204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.062659 restraints weight = 26887.696| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.53 r_work: 0.2942 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2060 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= 0.202 Angle : 0.528 6.966 20555 Z= 0.321 Chirality : 0.040 0.214 2504 Planarity : 0.005 0.053 1328 Dihedral : 22.191 99.433 6040 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.44 % Allowed : 15.70 % Favored : 82.85 % 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: -0.47 (0.31), residues: 663 helix: 0.23 (0.38), residues: 186 sheet: 0.47 (0.61), residues: 83 loop : -0.74 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 639 TYR 0.016 0.002 TYR A 592 PHE 0.010 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 0.00389 / 0.20 (13917) covalent geometry : angle 0.52149 / 0.32 (20546) hydrogen bonds : bond 0.06469 / 4.60 ( 533) hydrogen bonds : angle 3.16999 / 2.18 ( 1105) metal coordination : bond 0.00293 / 0.17 ( 8) metal coordination : angle 4.02181 / 2.41 ( 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 45 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.9004 (mtm-85) cc_final: 0.8462 (mtt90) REVERT: A 620 ARG cc_start: 0.7502 (mpp80) cc_final: 0.7224 (mtm180) REVERT: A 639 ARG cc_start: 0.8217 (ttm-80) cc_final: 0.7969 (ttm-80) outliers start: 8 outliers final: 6 residues processed: 40 average time/residue: 0.8361 time to fit residues: 35.4346 Evaluate side-chains 40 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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: 5.9990 chunk 23 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 35 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.084833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.062290 restraints weight = 26943.834| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.54 r_work: 0.2939 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 13925 Z= 0.200 Angle : 0.515 6.614 20555 Z= 0.314 Chirality : 0.040 0.208 2504 Planarity : 0.005 0.054 1328 Dihedral : 22.272 96.920 6040 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.81 % Allowed : 16.25 % Favored : 81.95 % 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: 0.39 (0.39), residues: 186 sheet: 0.55 (0.60), residues: 83 loop : -0.76 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 639 TYR 0.016 0.002 TYR A 592 PHE 0.009 0.001 PHE A 546 TRP 0.009 0.001 TRP A 300 HIS 0.003 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.20 (13917) covalent geometry : angle 0.50933 / 0.31 (20546) hydrogen bonds : bond 0.06376 / 4.52 ( 533) hydrogen bonds : angle 3.03920 / 2.09 ( 1105) metal coordination : bond 0.00393 / 0.22 ( 8) metal coordination : angle 3.79767 / 2.26 ( 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 45 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.9017 (mtm-85) cc_final: 0.8508 (mtt180) REVERT: A 600 MET cc_start: 0.8514 (mtt) cc_final: 0.7995 (mtt) REVERT: A 601 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8440 (tt0) REVERT: A 639 ARG cc_start: 0.8176 (ttm-80) cc_final: 0.7901 (ttm-80) outliers start: 10 outliers final: 6 residues processed: 40 average time/residue: 0.9262 time to fit residues: 39.2583 Evaluate side-chains 42 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 375 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 56 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3587 r_free = 0.3587 target = 0.085056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.062581 restraints weight = 26819.285| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.54 r_work: 0.2949 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13925 Z= 0.183 Angle : 0.505 7.035 20555 Z= 0.308 Chirality : 0.038 0.205 2504 Planarity : 0.005 0.054 1328 Dihedral : 22.281 95.664 6039 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.81 % Allowed : 16.06 % 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: -0.39 (0.31), residues: 663 helix: 0.42 (0.39), residues: 186 sheet: 0.53 (0.60), residues: 83 loop : -0.76 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 620 TYR 0.014 0.002 TYR A 592 PHE 0.007 0.001 PHE A 546 TRP 0.008 0.001 TRP A 300 HIS 0.003 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.18 (13917) covalent geometry : angle 0.49900 / 0.31 (20546) hydrogen bonds : bond 0.06146 / 4.36 ( 533) hydrogen bonds : angle 3.01464 / 2.07 ( 1105) metal coordination : bond 0.00299 / 0.17 ( 8) metal coordination : angle 3.73473 / 2.24 ( 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 47 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.9011 (mtm-85) cc_final: 0.8508 (mtt180) REVERT: A 269 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7065 (ttp-110) REVERT: A 639 ARG cc_start: 0.8178 (ttm-80) cc_final: 0.7905 (ttm-80) outliers start: 10 outliers final: 7 residues processed: 44 average time/residue: 0.7905 time to fit residues: 36.8655 Evaluate side-chains 45 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.3590 r_free = 0.3590 target = 0.085120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.062684 restraints weight = 26656.078| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.54 r_work: 0.2951 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2442 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= 0.182 Angle : 0.504 10.814 20555 Z= 0.307 Chirality : 0.038 0.203 2504 Planarity : 0.005 0.054 1328 Dihedral : 22.274 95.352 6039 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.17 % Allowed : 16.06 % 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: -0.36 (0.31), residues: 663 helix: 0.47 (0.39), residues: 186 sheet: 0.49 (0.59), residues: 83 loop : -0.74 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 376 TYR 0.015 0.002 TYR A 435 PHE 0.008 0.001 PHE A 546 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 0.00350 / 0.18 (13917) covalent geometry : angle 0.49838 / 0.31 (20546) hydrogen bonds : bond 0.06132 / 4.34 ( 533) hydrogen bonds : angle 2.99096 / 2.05 ( 1105) metal coordination : bond 0.00321 / 0.18 ( 8) metal coordination : angle 3.69783 / 2.22 ( 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 49 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.9013 (mtm-85) cc_final: 0.8339 (mtt-85) REVERT: A 269 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7057 (ttp-110) REVERT: A 601 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8426 (tt0) REVERT: A 639 ARG cc_start: 0.8159 (ttm-80) cc_final: 0.7834 (ttm-80) outliers start: 12 outliers final: 7 residues processed: 46 average time/residue: 0.8290 time to fit residues: 40.4356 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 : 0.192 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 78 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.084258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.061797 restraints weight = 26641.971| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.54 r_work: 0.2930 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2475 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 : 0.545 10.876 20555 Z= 0.327 Chirality : 0.040 0.214 2504 Planarity : 0.005 0.057 1328 Dihedral : 22.283 94.135 6039 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.81 % Allowed : 16.79 % Favored : 81.41 % 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: -0.45 (0.31), residues: 663 helix: 0.36 (0.38), residues: 187 sheet: 0.42 (0.59), residues: 83 loop : -0.77 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 620 TYR 0.013 0.002 TYR A 94 PHE 0.009 0.001 PHE A 226 TRP 0.008 0.002 TRP A 300 HIS 0.004 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.23 (13917) covalent geometry : angle 0.53991 / 0.33 (20546) hydrogen bonds : bond 0.06777 / 4.78 ( 533) hydrogen bonds : angle 3.03212 / 2.08 ( 1105) metal coordination : bond 0.00392 / 0.22 ( 8) metal coordination : angle 3.74488 / 2.27 ( 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 46 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.9022 (mtm-85) cc_final: 0.8340 (mtt-85) REVERT: A 269 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7086 (ttp-110) REVERT: A 601 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8516 (tt0) REVERT: A 639 ARG cc_start: 0.8158 (ttm-80) cc_final: 0.7830 (ttm-80) outliers start: 10 outliers final: 7 residues processed: 43 average time/residue: 0.8153 time to fit residues: 37.1421 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 : 0.291 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 88 optimal weight: 20.0000 chunk 8 optimal weight: 0.6980 chunk 51 optimal weight: 0.0870 chunk 96 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 overall best weight: 1.9362 ------------------------------------------------------------------------------- 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 = 0.3586 r_free = 0.3586 target = 0.084893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.062423 restraints weight = 26770.249| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.53 r_work: 0.2946 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13925 Z= 0.158 Angle : 0.505 11.210 20555 Z= 0.309 Chirality : 0.037 0.201 2504 Planarity : 0.005 0.054 1328 Dihedral : 22.320 95.630 6039 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.62 % Allowed : 16.97 % Favored : 81.41 % 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 (0.31), residues: 663 helix: 0.45 (0.38), residues: 187 sheet: 0.46 (0.59), residues: 83 loop : -0.73 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 620 TYR 0.012 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 0.00304 / 0.16 (13917) covalent geometry : angle 0.49942 / 0.31 (20546) hydrogen bonds : bond 0.06273 / 4.44 ( 533) hydrogen bonds : angle 2.99312 / 2.05 ( 1105) metal coordination : bond 0.00238 / 0.14 ( 8) metal coordination : angle 3.69298 / 2.22 ( 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 46 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.9020 (mtm-85) cc_final: 0.8357 (mtt-85) REVERT: A 269 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7064 (ttp-110) REVERT: A 601 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8511 (tt0) REVERT: A 639 ARG cc_start: 0.8138 (ttm-80) cc_final: 0.7791 (ttm-80) REVERT: A 668 ARG cc_start: 0.6379 (ppt170) cc_final: 0.6092 (pmt-80) outliers start: 9 outliers final: 7 residues processed: 43 average time/residue: 0.7924 time to fit residues: 36.0783 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 : 0.200 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 13 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 0.0870 chunk 17 optimal weight: 0.2980 chunk 83 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 72 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 overall best weight: 2.2764 ------------------------------------------------------------------------------- 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 = 0.3590 r_free = 0.3590 target = 0.085055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.062644 restraints weight = 26835.581| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.52 r_work: 0.2950 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2542 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= 0.171 Angle : 0.515 11.187 20555 Z= 0.313 Chirality : 0.038 0.200 2504 Planarity : 0.005 0.054 1328 Dihedral : 22.300 95.283 6039 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.44 % Allowed : 17.33 % 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: -0.39 (0.31), residues: 663 helix: 0.39 (0.38), residues: 187 sheet: 0.49 (0.59), residues: 83 loop : -0.73 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 620 TYR 0.015 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 577 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.17 (13917) covalent geometry : angle 0.50966 / 0.31 (20546) hydrogen bonds : bond 0.06158 / 4.37 ( 533) hydrogen bonds : angle 3.00959 / 2.06 ( 1105) metal coordination : bond 0.00267 / 0.16 ( 8) metal coordination : angle 3.64477 / 2.19 ( 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 44 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.9021 (mtm-85) cc_final: 0.8359 (mtt-85) REVERT: A 269 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7059 (ttp-110) REVERT: A 601 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8504 (tt0) REVERT: A 639 ARG cc_start: 0.8131 (ttm-80) cc_final: 0.7785 (ttm-80) REVERT: A 668 ARG cc_start: 0.6382 (ppt170) cc_final: 0.6098 (pmt-80) outliers start: 8 outliers final: 6 residues processed: 41 average time/residue: 0.8796 time to fit residues: 38.2246 Evaluate side-chains 44 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 621 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 94 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.083877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.061430 restraints weight = 26734.883| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.56 r_work: 0.2921 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 13925 Z= 0.256 Angle : 0.565 10.587 20555 Z= 0.336 Chirality : 0.042 0.217 2504 Planarity : 0.006 0.058 1328 Dihedral : 22.302 93.492 6039 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.81 % Allowed : 16.97 % 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: -0.49 (0.31), residues: 663 helix: 0.30 (0.38), residues: 187 sheet: 0.39 (0.58), residues: 83 loop : -0.78 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 376 TYR 0.021 0.002 TYR A 430 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 0.00501 / 0.26 (13917) covalent geometry : angle 0.55953 / 0.34 (20546) hydrogen bonds : bond 0.07071 / 4.98 ( 533) hydrogen bonds : angle 3.06322 / 2.10 ( 1105) metal coordination : bond 0.00449 / 0.25 ( 8) metal coordination : angle 3.81692 / 2.32 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4476.84 seconds wall clock time: 76 minutes 43.14 seconds (4603.14 seconds total)