Starting phenix.real_space_refine on Wed Mar 4 10:54:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k31_62003/03_2026/9k31_62003.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k31_62003/03_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_62003/03_2026/9k31_62003.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k31_62003/03_2026/9k31_62003.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k31_62003/03_2026/9k31_62003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k31_62003/03_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 2.90, per 1000 atoms: 0.22 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: 1.00 Conformation dependent library (CDL) restraints added in 267.7 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: 1.97 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: 2.83 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: 3005 3.73 - 5.59: 262 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 - 0.132: 2019 0.132 - 0.263: 477 0.263 - 0.395: 0 0.395 - 0.526: 0 0.526 - 0.658: 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 2.35 -3.00 -0.66 2.00e-01 2.50e+01 1.08e+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 2.35 -2.99 -0.64 2.00e-01 2.50e+01 1.03e+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 2.35 -2.98 -0.64 2.00e-01 2.50e+01 1.01e+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: 1.470 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: 0.190 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.150 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:6.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 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= 0.720 Angle : 1.366 12.712 20555 Z= 0.867 Chirality : 0.096 0.658 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 covalent geometry : bond 0.01123 (13917) covalent geometry : angle 1.35755 (20546) hydrogen bonds : bond 0.19266 ( 533) hydrogen bonds : angle 5.68665 ( 1105) metal coordination : bond 0.01512 ( 8) metal coordination : angle 7.48292 ( 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 : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 57 average time/residue: 1.0202 time to fit residues: 61.3193 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 : 0.287 ------------------------------------------------------------------------------- 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: 2.9990 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... Flipped N/Q/H residues before XYZ refinement: A 417 GLN A 586 ASN A 601 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.091543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.069568 restraints weight = 27176.984| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.53 r_work: 0.3137 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13925 Z= 0.135 Angle : 0.574 9.506 20555 Z= 0.311 Chirality : 0.037 0.208 2504 Planarity : 0.004 0.035 1328 Dihedral : 22.017 102.444 6040 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % 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: -0.60 (0.30), residues: 663 helix: 0.08 (0.37), residues: 186 sheet: -0.02 (0.63), residues: 70 loop : -0.67 (0.27), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 637 TYR 0.011 0.002 TYR A 430 PHE 0.008 0.001 PHE A 35 TRP 0.010 0.001 TRP A 378 HIS 0.004 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00275 (13917) covalent geometry : angle 0.56501 (20546) hydrogen bonds : bond 0.05686 ( 533) hydrogen bonds : angle 3.32346 ( 1105) metal coordination : bond 0.00232 ( 8) metal coordination : angle 4.96231 ( 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 45 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.8966 (mtm-85) cc_final: 0.8501 (mtt180) REVERT: A 260 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8737 (tmtm) outliers start: 7 outliers final: 2 residues processed: 43 average time/residue: 0.9585 time to fit residues: 43.6131 Evaluate side-chains 37 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 24 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 93 optimal weight: 8.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.085798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.063252 restraints weight = 27080.055| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.54 r_work: 0.2961 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13925 Z= 0.189 Angle : 0.547 6.966 20555 Z= 0.294 Chirality : 0.036 0.195 2504 Planarity : 0.004 0.046 1328 Dihedral : 22.084 98.055 6040 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.90 % Allowed : 15.52 % Favored : 83.57 % 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: -0.44 (0.30), residues: 663 helix: 0.34 (0.38), residues: 186 sheet: 0.43 (0.62), residues: 73 loop : -0.72 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 639 TYR 0.012 0.002 TYR A 94 PHE 0.010 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 covalent geometry : bond 0.00389 (13917) covalent geometry : angle 0.54031 (20546) hydrogen bonds : bond 0.05581 ( 533) hydrogen bonds : angle 3.00668 ( 1105) metal coordination : bond 0.00241 ( 8) metal coordination : angle 3.97806 ( 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 43 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.8987 (mtm-85) cc_final: 0.8317 (mtt-85) REVERT: A 600 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.7886 (mtt) REVERT: A 639 ARG cc_start: 0.7899 (ttm-80) cc_final: 0.7696 (ttm-80) outliers start: 5 outliers final: 3 residues processed: 40 average time/residue: 1.1044 time to fit residues: 46.4408 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 : 0.305 ------------------------------------------------------------------------------- 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 458 LEU Chi-restraints excluded: chain A residue 600 MET 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: 30.0000 chunk 58 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.083334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.060807 restraints weight = 27080.890| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.57 r_work: 0.2903 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 13925 Z= 0.359 Angle : 0.653 7.466 20555 Z= 0.345 Chirality : 0.044 0.229 2504 Planarity : 0.006 0.056 1328 Dihedral : 22.230 96.176 6039 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % 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: -0.55 (0.31), residues: 663 helix: 0.17 (0.38), residues: 187 sheet: 0.32 (0.59), residues: 83 loop : -0.76 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 620 TYR 0.018 0.002 TYR A 94 PHE 0.010 0.002 PHE A 546 TRP 0.011 0.002 TRP A 300 HIS 0.005 0.001 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00744 (13917) covalent geometry : angle 0.64737 (20546) hydrogen bonds : bond 0.07241 ( 533) hydrogen bonds : angle 3.08675 ( 1105) metal coordination : bond 0.00457 ( 8) metal coordination : angle 4.11808 ( 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 46 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.9031 (mtm-85) cc_final: 0.8598 (mtt180) REVERT: A 639 ARG cc_start: 0.7964 (ttm-80) cc_final: 0.7694 (ttm-80) outliers start: 10 outliers final: 6 residues processed: 40 average time/residue: 1.0486 time to fit residues: 44.2589 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 : 0.298 ------------------------------------------------------------------------------- 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 447 VAL Chi-restraints excluded: chain A residue 458 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 90 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.084490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.062084 restraints weight = 27024.880| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.54 r_work: 0.2935 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 13925 Z= 0.231 Angle : 0.571 7.180 20555 Z= 0.306 Chirality : 0.038 0.213 2504 Planarity : 0.005 0.056 1328 Dihedral : 22.225 94.362 6039 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.44 % Allowed : 17.51 % 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: -0.46 (0.31), residues: 663 helix: 0.27 (0.39), residues: 187 sheet: 0.44 (0.59), residues: 83 loop : -0.74 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 620 TYR 0.013 0.002 TYR A 430 PHE 0.009 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 covalent geometry : bond 0.00479 (13917) covalent geometry : angle 0.56470 (20546) hydrogen bonds : bond 0.05926 ( 533) hydrogen bonds : angle 2.99666 ( 1105) metal coordination : bond 0.00322 ( 8) metal coordination : angle 3.95196 ( 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 44 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.9027 (mtm-85) cc_final: 0.8369 (mtt-85) REVERT: A 269 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7095 (ttp-110) REVERT: A 620 ARG cc_start: 0.7500 (mtm-85) cc_final: 0.7134 (ptp90) outliers start: 8 outliers final: 5 residues processed: 39 average time/residue: 1.0531 time to fit residues: 43.4278 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 : 0.286 ------------------------------------------------------------------------------- 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 458 LEU 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: 0.6980 chunk 35 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.084973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.062604 restraints weight = 26834.987| |-----------------------------------------------------------------------------| 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: 0.2837 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13925 Z= 0.171 Angle : 0.545 7.366 20555 Z= 0.293 Chirality : 0.036 0.205 2504 Planarity : 0.005 0.054 1328 Dihedral : 22.231 95.405 6039 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.62 % Allowed : 17.15 % 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: -0.38 (0.31), residues: 663 helix: 0.36 (0.39), residues: 187 sheet: 0.50 (0.59), residues: 83 loop : -0.70 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 376 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 covalent geometry : bond 0.00356 (13917) covalent geometry : angle 0.53865 (20546) hydrogen bonds : bond 0.05545 ( 533) hydrogen bonds : angle 2.96265 ( 1105) metal coordination : bond 0.00217 ( 8) metal coordination : angle 3.85783 ( 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 44 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.9024 (mtm-85) cc_final: 0.8370 (mtt-85) REVERT: A 269 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7101 (ttp-110) REVERT: A 600 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.7355 (mmt) REVERT: A 639 ARG cc_start: 0.7957 (ttm-80) cc_final: 0.7402 (ttm-80) outliers start: 9 outliers final: 5 residues processed: 39 average time/residue: 1.0832 time to fit residues: 44.4558 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 : 0.279 ------------------------------------------------------------------------------- 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 458 LEU Chi-restraints excluded: chain A residue 600 MET 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: 9.9990 chunk 45 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.084024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.061707 restraints weight = 26744.734| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.53 r_work: 0.2926 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 13925 Z= 0.258 Angle : 0.586 7.192 20555 Z= 0.312 Chirality : 0.039 0.211 2504 Planarity : 0.005 0.056 1328 Dihedral : 22.224 93.810 6039 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.81 % Allowed : 17.33 % Favored : 80.87 % 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: 0.34 (0.38), residues: 187 sheet: 0.46 (0.59), residues: 83 loop : -0.71 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 376 TYR 0.013 0.002 TYR A 430 PHE 0.009 0.001 PHE A 546 TRP 0.008 0.001 TRP A 300 HIS 0.004 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00536 (13917) covalent geometry : angle 0.58083 (20546) hydrogen bonds : bond 0.06173 ( 533) hydrogen bonds : angle 2.93003 ( 1105) metal coordination : bond 0.00329 ( 8) metal coordination : angle 3.81613 ( 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 47 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.9028 (mtm-85) cc_final: 0.8401 (mtt-85) REVERT: A 269 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7078 (ttp-110) REVERT: A 601 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8534 (tt0) REVERT: A 639 ARG cc_start: 0.7977 (ttm-80) cc_final: 0.7355 (ttm-80) outliers start: 10 outliers final: 5 residues processed: 43 average time/residue: 1.0331 time to fit residues: 46.8814 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 : 0.284 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 78 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 44 optimal weight: 0.0770 chunk 68 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 overall best weight: 2.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.084677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.062323 restraints weight = 26621.639| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.53 r_work: 0.2944 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13925 Z= 0.183 Angle : 0.560 9.491 20555 Z= 0.300 Chirality : 0.036 0.203 2504 Planarity : 0.005 0.053 1328 Dihedral : 22.240 95.186 6039 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % 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: -0.37 (0.31), residues: 663 helix: 0.34 (0.38), residues: 187 sheet: 0.45 (0.59), residues: 83 loop : -0.67 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 376 TYR 0.012 0.002 TYR A 430 PHE 0.008 0.001 PHE A 546 TRP 0.009 0.001 TRP A 408 HIS 0.003 0.001 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00383 (13917) covalent geometry : angle 0.55436 (20546) hydrogen bonds : bond 0.05691 ( 533) hydrogen bonds : angle 2.93376 ( 1105) metal coordination : bond 0.00226 ( 8) metal coordination : angle 3.75724 ( 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 42 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.9027 (mtm-85) cc_final: 0.8563 (mtt180) REVERT: A 269 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7061 (ttp-110) REVERT: A 601 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8529 (tt0) REVERT: A 639 ARG cc_start: 0.7969 (ttm-80) cc_final: 0.7399 (ttm-80) outliers start: 7 outliers final: 5 residues processed: 38 average time/residue: 1.0798 time to fit residues: 43.2926 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 : 0.297 ------------------------------------------------------------------------------- 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 458 LEU Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 601 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 25 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 8 optimal weight: 0.2980 chunk 51 optimal weight: 0.1980 chunk 96 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.085011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.062651 restraints weight = 26793.936| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.53 r_work: 0.2952 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 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 0.091 13925 Z= 0.166 Angle : 0.549 8.575 20555 Z= 0.295 Chirality : 0.035 0.201 2504 Planarity : 0.004 0.053 1328 Dihedral : 22.234 95.500 6039 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % 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: -0.35 (0.31), residues: 663 helix: 0.33 (0.38), residues: 187 sheet: 0.50 (0.59), residues: 83 loop : -0.65 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 620 TYR 0.008 0.001 TYR A 94 PHE 0.007 0.001 PHE A 546 TRP 0.009 0.001 TRP A 408 HIS 0.002 0.001 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00350 (13917) covalent geometry : angle 0.54349 (20546) hydrogen bonds : bond 0.05514 ( 533) hydrogen bonds : angle 2.90594 ( 1105) metal coordination : bond 0.00213 ( 8) metal coordination : angle 3.72467 ( 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 43 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.9019 (mtm-85) cc_final: 0.8377 (mtt-85) REVERT: A 269 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7061 (ttp-110) REVERT: A 601 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8494 (tt0) REVERT: A 639 ARG cc_start: 0.7954 (ttm-80) cc_final: 0.7402 (ttm-80) outliers start: 8 outliers final: 5 residues processed: 39 average time/residue: 1.1114 time to fit residues: 45.6289 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 : 0.306 ------------------------------------------------------------------------------- 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 458 LEU Chi-restraints excluded: chain A residue 550 MET 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: 0.9980 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 0.0270 chunk 17 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 overall best weight: 3.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.084109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.061765 restraints weight = 26919.859| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.52 r_work: 0.2931 rms_B_bonded: 2.46 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: 0.8438 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 13925 Z= 0.246 Angle : 0.579 7.853 20555 Z= 0.309 Chirality : 0.038 0.207 2504 Planarity : 0.005 0.086 1328 Dihedral : 22.212 94.159 6039 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.62 % Allowed : 17.69 % 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: -0.42 (0.31), residues: 663 helix: 0.31 (0.38), residues: 187 sheet: 0.36 (0.58), residues: 83 loop : -0.69 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 620 TYR 0.012 0.002 TYR A 435 PHE 0.009 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 covalent geometry : bond 0.00510 (13917) covalent geometry : angle 0.57356 (20546) hydrogen bonds : bond 0.06080 ( 533) hydrogen bonds : angle 2.92885 ( 1105) metal coordination : bond 0.00318 ( 8) metal coordination : angle 3.75522 ( 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: 9 poor density : 35 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.9027 (mtm-85) cc_final: 0.8393 (mtt-85) REVERT: A 269 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7103 (ttp-110) REVERT: A 601 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8513 (tt0) REVERT: A 639 ARG cc_start: 0.7964 (ttm-80) cc_final: 0.7348 (ttm-80) REVERT: A 668 ARG cc_start: 0.6404 (ppt170) cc_final: 0.6067 (pmt-80) outliers start: 9 outliers final: 6 residues processed: 39 average time/residue: 1.0584 time to fit residues: 43.5219 Evaluate side-chains 42 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP 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 458 LEU Chi-restraints excluded: chain A residue 550 MET 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: 6.9990 chunk 66 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 53 optimal weight: 0.0570 chunk 48 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 overall best weight: 4.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.083221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.060889 restraints weight = 26827.400| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.55 r_work: 0.2909 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 13925 Z= 0.317 Angle : 0.634 9.161 20555 Z= 0.336 Chirality : 0.042 0.223 2504 Planarity : 0.006 0.058 1328 Dihedral : 22.289 92.113 6039 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.44 % Allowed : 18.23 % Favored : 80.32 % 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: -0.52 (0.31), residues: 663 helix: 0.23 (0.38), residues: 187 sheet: 0.27 (0.57), residues: 83 loop : -0.74 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 376 TYR 0.023 0.003 TYR A 430 PHE 0.010 0.002 PHE A 546 TRP 0.009 0.002 TRP A 300 HIS 0.004 0.001 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00660 (13917) covalent geometry : angle 0.62894 (20546) hydrogen bonds : bond 0.06882 ( 533) hydrogen bonds : angle 2.95637 ( 1105) metal coordination : bond 0.00408 ( 8) metal coordination : angle 3.94726 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4943.57 seconds wall clock time: 84 minutes 27.87 seconds (5067.87 seconds total)