Starting phenix.real_space_refine on Tue Feb 3 17:09:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w4s_65643/02_2026/9w4s_65643.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w4s_65643/02_2026/9w4s_65643.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w4s_65643/02_2026/9w4s_65643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w4s_65643/02_2026/9w4s_65643.map" model { file = "/net/cci-nas-00/data/ceres_data/9w4s_65643/02_2026/9w4s_65643.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w4s_65643/02_2026/9w4s_65643.cif" } resolution = 3.82 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= 0.016 sd= 0.477 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 57 5.49 5 S 31 5.16 5 C 3276 2.51 5 N 966 2.21 5 O 1145 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5478 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3265 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 378} Chain breaks: 1 Chain: "B" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 993 Classifications: {'peptide': 130} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 122} Chain breaks: 1 Chain: "C" Number of atoms: 1217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1217 Classifications: {'RNA': 57} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 4, 'rna3p_pur': 23, 'rna3p_pyr': 22} Link IDs: {'rna2p': 12, 'rna3p': 44} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 288 SG CYS A 306 56.334 46.404 60.493 1.00250.32 S ATOM 311 SG CYS A 309 53.891 44.383 62.764 1.00258.92 S ATOM 3966 SG CYS B 139 51.676 36.029 42.327 1.00315.33 S ATOM 3992 SG CYS B 142 52.771 35.877 38.541 1.00328.55 S ATOM 4065 SG CYS B 152 54.479 33.879 41.035 1.00350.92 S ATOM 4136 SG CYS B 161 49.611 51.203 31.116 1.00353.78 S ATOM 4163 SG CYS B 164 51.961 52.269 28.297 1.00388.90 S ATOM 4234 SG CYS B 174 48.186 53.403 28.320 1.00305.99 S Time building chain proxies: 1.23, per 1000 atoms: 0.22 Number of scatterers: 5478 At special positions: 0 Unit cell: (87.15, 97.11, 128.235, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 31 16.00 P 57 15.00 O 1145 8.00 N 966 7.00 C 3276 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: 0.35 Conformation dependent library (CDL) restraints added in 194.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 322 " pdb="ZN ZN A2001 " - pdb=" ND1 HIS A 328 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 309 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" ND1 HIS B 147 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 152 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 142 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 139 " pdb=" ZN B1002 " pdb="ZN ZN B1002 " - pdb=" NE2 HIS B 169 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 161 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 164 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 174 " Number of angles added : 7 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1002 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 5 sheets defined 41.6% alpha, 14.7% beta 9 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 274 through 287 removed outlier: 3.705A pdb=" N ASP A 287 " --> pdb=" O ARG A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 removed outlier: 3.838A pdb=" N ASN A 301 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 323 Processing helix chain 'A' and resid 325 through 344 removed outlier: 4.293A pdb=" N GLU A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER A 339 " --> pdb=" O LYS A 335 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU A 340 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 366 removed outlier: 3.937A pdb=" N HIS A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 389 removed outlier: 3.639A pdb=" N VAL A 375 " --> pdb=" O ASP A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 removed outlier: 3.679A pdb=" N ARG A 405 " --> pdb=" O SER A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 437 removed outlier: 3.813A pdb=" N ILE A 430 " --> pdb=" O PRO A 426 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ILE A 435 " --> pdb=" O LYS A 431 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU A 436 " --> pdb=" O VAL A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 490 Processing helix chain 'A' and resid 492 through 507 Processing helix chain 'A' and resid 511 through 515 removed outlier: 3.802A pdb=" N GLY A 515 " --> pdb=" O GLN A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 533 Processing helix chain 'A' and resid 550 through 557 removed outlier: 6.211A pdb=" N ASP A 555 " --> pdb=" O LYS A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 643 removed outlier: 3.591A pdb=" N TYR A 640 " --> pdb=" O LEU A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 665 Processing helix chain 'A' and resid 689 through 707 Processing helix chain 'B' and resid 111 through 115 removed outlier: 3.510A pdb=" N VAL B 115 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 174 Processing sheet with id=AA1, first strand: chain 'A' and resid 290 through 291 Processing sheet with id=AA2, first strand: chain 'A' and resid 395 through 399 removed outlier: 3.848A pdb=" N ASN A 414 " --> pdb=" O TYR A 399 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL A 413 " --> pdb=" O ARG A 468 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N SER A 470 " --> pdb=" O VAL A 413 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ILE A 415 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL A 456 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 559 through 563 removed outlier: 3.529A pdb=" N LYS A 569 " --> pdb=" O LYS A 560 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ILE A 562 " --> pdb=" O PHE A 567 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N PHE A 567 " --> pdb=" O ILE A 562 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 650 through 651 Processing sheet with id=AA5, first strand: chain 'B' and resid 64 through 75 removed outlier: 6.017A pdb=" N THR B 59 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N SER B 57 " --> pdb=" O PRO B 68 " (cutoff:3.500A) removed outlier: 10.858A pdb=" N VAL B 70 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 9.815A pdb=" N PHE B 55 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 12.023A pdb=" N VAL B 72 " --> pdb=" O PHE B 53 " (cutoff:3.500A) removed outlier: 10.773A pdb=" N PHE B 53 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N PHE B 53 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N PHE B 47 " --> pdb=" O PHE B 53 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N PHE B 55 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA B 41 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ARG B 61 " --> pdb=" O HIS B 39 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N HIS B 39 " --> pdb=" O ARG B 61 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B 108 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N LYS B 98 " --> pdb=" O SER B 106 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N SER B 106 " --> pdb=" O LYS B 98 " (cutoff:3.500A) 173 hydrogen bonds defined for protein. 468 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 32 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 0.60 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1024 1.33 - 1.45: 1625 1.45 - 1.57: 2912 1.57 - 1.70: 112 1.70 - 1.82: 41 Bond restraints: 5714 Sorted by residual: bond pdb=" C VAL A 497 " pdb=" O VAL A 497 " ideal model delta sigma weight residual 1.237 1.207 0.030 1.19e-02 7.06e+03 6.40e+00 bond pdb=" N PRO B 155 " pdb=" CA PRO B 155 " ideal model delta sigma weight residual 1.457 1.481 -0.024 1.31e-02 5.83e+03 3.49e+00 bond pdb=" CA CYS A 652 " pdb=" CB CYS A 652 " ideal model delta sigma weight residual 1.527 1.485 0.043 2.48e-02 1.63e+03 2.95e+00 bond pdb=" O5' C C 38 " pdb=" C5' C C 38 " ideal model delta sigma weight residual 1.420 1.440 -0.020 1.50e-02 4.44e+03 1.81e+00 bond pdb=" O5' U C 12 " pdb=" C5' U C 12 " ideal model delta sigma weight residual 1.420 1.440 -0.020 1.50e-02 4.44e+03 1.73e+00 ... (remaining 5709 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 7250 1.51 - 3.01: 619 3.01 - 4.52: 81 4.52 - 6.03: 27 6.03 - 7.53: 6 Bond angle restraints: 7983 Sorted by residual: angle pdb=" N GLY B 103 " pdb=" CA GLY B 103 " pdb=" C GLY B 103 " ideal model delta sigma weight residual 112.29 107.09 5.20 1.12e+00 7.97e-01 2.15e+01 angle pdb=" C ARG A 553 " pdb=" N MET A 554 " pdb=" CA MET A 554 " ideal model delta sigma weight residual 120.38 126.28 -5.90 1.37e+00 5.33e-01 1.85e+01 angle pdb=" C PRO A 347 " pdb=" N SER A 348 " pdb=" CA SER A 348 " ideal model delta sigma weight residual 121.03 127.41 -6.38 1.60e+00 3.91e-01 1.59e+01 angle pdb=" N LEU A 506 " pdb=" CA LEU A 506 " pdb=" C LEU A 506 " ideal model delta sigma weight residual 111.33 106.76 4.57 1.21e+00 6.83e-01 1.43e+01 angle pdb=" C GLU A 340 " pdb=" N LEU A 341 " pdb=" CA LEU A 341 " ideal model delta sigma weight residual 120.38 125.53 -5.15 1.37e+00 5.33e-01 1.41e+01 ... (remaining 7978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.77: 3096 21.77 - 43.54: 281 43.54 - 65.30: 133 65.30 - 87.07: 24 87.07 - 108.84: 2 Dihedral angle restraints: 3536 sinusoidal: 1993 harmonic: 1543 Sorted by residual: dihedral pdb=" CA SER B 120 " pdb=" C SER B 120 " pdb=" N GLU B 121 " pdb=" CA GLU B 121 " ideal model delta harmonic sigma weight residual -180.00 -150.07 -29.93 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA LEU A 344 " pdb=" C LEU A 344 " pdb=" N PRO A 345 " pdb=" CA PRO A 345 " ideal model delta harmonic sigma weight residual 180.00 -152.92 -27.08 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA ILE B 118 " pdb=" C ILE B 118 " pdb=" N GLY B 119 " pdb=" CA GLY B 119 " ideal model delta harmonic sigma weight residual -180.00 -156.41 -23.59 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 3533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 630 0.042 - 0.084: 199 0.084 - 0.126: 70 0.126 - 0.168: 24 0.168 - 0.210: 7 Chirality restraints: 930 Sorted by residual: chirality pdb=" CA ILE A 673 " pdb=" N ILE A 673 " pdb=" C ILE A 673 " pdb=" CB ILE A 673 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" C3' U C 12 " pdb=" C4' U C 12 " pdb=" O3' U C 12 " pdb=" C2' U C 12 " both_signs ideal model delta sigma weight residual False -2.48 -2.69 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB VAL A 653 " pdb=" CA VAL A 653 " pdb=" CG1 VAL A 653 " pdb=" CG2 VAL A 653 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 927 not shown) Planarity restraints: 804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 53 " -0.024 2.00e-02 2.50e+03 1.88e-02 6.19e+00 pdb=" CG PHE B 53 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE B 53 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE B 53 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 53 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 53 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 53 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 546 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C ILE A 546 " -0.033 2.00e-02 2.50e+03 pdb=" O ILE A 546 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU A 547 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 68 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO B 69 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 69 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 69 " -0.025 5.00e-02 4.00e+02 ... (remaining 801 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1103 2.78 - 3.31: 5252 3.31 - 3.84: 10796 3.84 - 4.37: 12355 4.37 - 4.90: 18371 Nonbonded interactions: 47877 Sorted by model distance: nonbonded pdb=" O LYS A 385 " pdb=" OG1 THR A 389 " model vdw 2.246 3.040 nonbonded pdb=" O SER A 384 " pdb=" OG1 THR A 388 " model vdw 2.261 3.040 nonbonded pdb=" O THR A 480 " pdb=" OG1 THR A 484 " model vdw 2.320 3.040 nonbonded pdb=" O4 U C 14 " pdb=" N4 C C 63 " model vdw 2.362 3.120 nonbonded pdb=" N ARG B 50 " pdb=" O2' C C 38 " model vdw 2.362 3.120 ... (remaining 47872 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 group one per residue 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: 0.100 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: 0.050 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.240 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5726 Z= 0.241 Angle : 0.947 8.500 7990 Z= 0.545 Chirality : 0.051 0.210 930 Planarity : 0.006 0.045 804 Dihedral : 19.636 108.837 2534 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 4.88 % Allowed : 14.23 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -1.94 (0.33), residues: 523 helix: -0.72 (0.33), residues: 182 sheet: -1.80 (0.58), residues: 62 loop : -1.51 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 654 TYR 0.019 0.002 TYR A 640 PHE 0.042 0.003 PHE B 53 TRP 0.012 0.002 TRP A 503 HIS 0.004 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 5714) covalent geometry : angle 0.93932 ( 7983) hydrogen bonds : bond 0.19463 ( 193) hydrogen bonds : angle 8.37503 ( 500) metal coordination : bond 0.01333 ( 12) metal coordination : angle 4.21956 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ARG cc_start: 0.9280 (tpt90) cc_final: 0.9046 (tpm170) REVERT: A 285 GLU cc_start: 0.9217 (tt0) cc_final: 0.8832 (tp30) REVERT: A 287 ASP cc_start: 0.9349 (m-30) cc_final: 0.8930 (p0) REVERT: A 304 TYR cc_start: 0.8983 (m-80) cc_final: 0.8454 (m-80) REVERT: A 314 GLU cc_start: 0.9470 (pm20) cc_final: 0.9214 (pm20) REVERT: A 316 ILE cc_start: 0.8316 (mt) cc_final: 0.7870 (tp) REVERT: A 377 GLN cc_start: 0.9703 (tt0) cc_final: 0.9461 (tp-100) REVERT: A 493 PHE cc_start: 0.7259 (t80) cc_final: 0.6591 (t80) REVERT: A 497 VAL cc_start: 0.8667 (OUTLIER) cc_final: 0.8340 (p) REVERT: A 500 PHE cc_start: 0.2624 (OUTLIER) cc_final: 0.0594 (t80) REVERT: A 537 LEU cc_start: 0.8777 (mt) cc_final: 0.8241 (tp) REVERT: A 631 GLN cc_start: 0.8494 (tt0) cc_final: 0.7819 (tp-100) REVERT: A 635 GLU cc_start: 0.8392 (pt0) cc_final: 0.8143 (pt0) REVERT: A 646 LEU cc_start: 0.8270 (mt) cc_final: 0.7936 (mt) REVERT: A 648 GLU cc_start: 0.9246 (mm-30) cc_final: 0.8785 (mp0) REVERT: A 654 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8310 (mmp-170) REVERT: A 673 ILE cc_start: 0.9156 (mt) cc_final: 0.8772 (tt) REVERT: A 675 ASP cc_start: 0.8546 (t70) cc_final: 0.7879 (t0) REVERT: B 51 MET cc_start: 0.1486 (ptt) cc_final: 0.1230 (ptt) REVERT: B 89 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7578 (mp0) REVERT: B 167 ILE cc_start: 0.9630 (OUTLIER) cc_final: 0.9379 (mm) outliers start: 23 outliers final: 3 residues processed: 119 average time/residue: 0.0982 time to fit residues: 13.8951 Evaluate side-chains 87 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 500 PHE Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 167 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 0.0770 chunk 56 optimal weight: 10.0000 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.0020 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 overall best weight: 1.3350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 HIS ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.124078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.095075 restraints weight = 29889.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.097806 restraints weight = 22128.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.099618 restraints weight = 17851.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.100870 restraints weight = 15230.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.101703 restraints weight = 13558.887| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 5726 Z= 0.163 Angle : 0.747 8.177 7990 Z= 0.388 Chirality : 0.043 0.169 930 Planarity : 0.006 0.041 804 Dihedral : 20.436 112.856 1464 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 4.46 % Allowed : 18.26 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -1.72 (0.35), residues: 523 helix: -0.46 (0.34), residues: 197 sheet: -1.73 (0.58), residues: 68 loop : -1.45 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 699 TYR 0.036 0.003 TYR A 695 PHE 0.033 0.003 PHE A 529 TRP 0.010 0.002 TRP A 503 HIS 0.004 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 5714) covalent geometry : angle 0.73860 ( 7983) hydrogen bonds : bond 0.06192 ( 193) hydrogen bonds : angle 6.64394 ( 500) metal coordination : bond 0.00609 ( 12) metal coordination : angle 3.95189 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ARG cc_start: 0.9207 (tpt90) cc_final: 0.8931 (tpm170) REVERT: A 285 GLU cc_start: 0.9170 (tt0) cc_final: 0.8705 (tp30) REVERT: A 287 ASP cc_start: 0.9191 (m-30) cc_final: 0.8649 (m-30) REVERT: A 312 HIS cc_start: 0.7209 (OUTLIER) cc_final: 0.6907 (m90) REVERT: A 631 GLN cc_start: 0.8695 (tt0) cc_final: 0.8099 (tp40) REVERT: A 646 LEU cc_start: 0.8279 (mt) cc_final: 0.7958 (mp) REVERT: A 648 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8786 (mp0) REVERT: A 656 GLN cc_start: 0.8474 (tm-30) cc_final: 0.8160 (tm-30) REVERT: A 673 ILE cc_start: 0.8927 (mt) cc_final: 0.8547 (tt) REVERT: A 675 ASP cc_start: 0.8498 (t70) cc_final: 0.8104 (t0) REVERT: B 51 MET cc_start: 0.2655 (ptt) cc_final: 0.2012 (ptt) REVERT: B 167 ILE cc_start: 0.9634 (OUTLIER) cc_final: 0.9319 (tt) outliers start: 21 outliers final: 11 residues processed: 92 average time/residue: 0.1141 time to fit residues: 12.5767 Evaluate side-chains 78 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 167 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 40 optimal weight: 0.0670 chunk 15 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 45 optimal weight: 0.2980 chunk 24 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.8724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.124813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.095709 restraints weight = 30653.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.098345 restraints weight = 22762.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.100025 restraints weight = 18405.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.101341 restraints weight = 15821.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.101794 restraints weight = 14106.196| |-----------------------------------------------------------------------------| r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5726 Z= 0.145 Angle : 0.721 8.870 7990 Z= 0.373 Chirality : 0.043 0.156 930 Planarity : 0.005 0.044 804 Dihedral : 20.268 109.251 1451 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 20.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 4.67 % Allowed : 18.90 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -1.48 (0.35), residues: 523 helix: -0.03 (0.35), residues: 197 sheet: -1.86 (0.57), residues: 68 loop : -1.44 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 699 TYR 0.044 0.003 TYR A 695 PHE 0.044 0.003 PHE A 529 TRP 0.009 0.002 TRP A 503 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 5714) covalent geometry : angle 0.71362 ( 7983) hydrogen bonds : bond 0.05262 ( 193) hydrogen bonds : angle 6.37696 ( 500) metal coordination : bond 0.00857 ( 12) metal coordination : angle 3.62476 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ARG cc_start: 0.9275 (tpt90) cc_final: 0.8980 (tpm170) REVERT: A 285 GLU cc_start: 0.9175 (tt0) cc_final: 0.8812 (tp30) REVERT: A 287 ASP cc_start: 0.9321 (m-30) cc_final: 0.8831 (m-30) REVERT: A 312 HIS cc_start: 0.7154 (OUTLIER) cc_final: 0.6917 (m90) REVERT: A 381 GLU cc_start: 0.9241 (mt-10) cc_final: 0.8897 (mt-10) REVERT: A 522 PHE cc_start: 0.8650 (t80) cc_final: 0.8197 (t80) REVERT: A 524 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9110 (mp) REVERT: A 631 GLN cc_start: 0.8706 (tt0) cc_final: 0.8253 (tp40) REVERT: A 648 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8888 (mp0) REVERT: A 673 ILE cc_start: 0.8930 (mt) cc_final: 0.8467 (tt) REVERT: B 51 MET cc_start: 0.2844 (ptt) cc_final: 0.2068 (ptp) REVERT: B 58 MET cc_start: 0.1086 (ptm) cc_final: 0.0620 (ttt) REVERT: B 167 ILE cc_start: 0.9641 (OUTLIER) cc_final: 0.9342 (tt) outliers start: 22 outliers final: 11 residues processed: 92 average time/residue: 0.1045 time to fit residues: 11.5585 Evaluate side-chains 78 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 502 TYR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 167 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 21 optimal weight: 8.9990 chunk 41 optimal weight: 0.7980 chunk 37 optimal weight: 30.0000 chunk 39 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 chunk 31 optimal weight: 7.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 GLN ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.124651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.095476 restraints weight = 31228.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.098167 restraints weight = 22995.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.099946 restraints weight = 18510.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.101146 restraints weight = 15830.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.102021 restraints weight = 14180.147| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5726 Z= 0.144 Angle : 0.698 7.535 7990 Z= 0.362 Chirality : 0.042 0.153 930 Planarity : 0.005 0.057 804 Dihedral : 20.105 108.237 1450 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.46 % Allowed : 20.81 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -1.37 (0.36), residues: 523 helix: 0.01 (0.35), residues: 201 sheet: -1.59 (0.61), residues: 58 loop : -1.46 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 405 TYR 0.036 0.003 TYR A 695 PHE 0.031 0.003 PHE A 493 TRP 0.040 0.002 TRP A 503 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 5714) covalent geometry : angle 0.69097 ( 7983) hydrogen bonds : bond 0.05052 ( 193) hydrogen bonds : angle 6.29953 ( 500) metal coordination : bond 0.00588 ( 12) metal coordination : angle 3.39901 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.9382 (pp20) cc_final: 0.9045 (pp20) REVERT: A 287 ASP cc_start: 0.9266 (m-30) cc_final: 0.8774 (m-30) REVERT: A 342 ARG cc_start: 0.9111 (ttt180) cc_final: 0.8772 (mtt90) REVERT: A 500 PHE cc_start: 0.2664 (OUTLIER) cc_final: 0.0344 (t80) REVERT: A 524 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9161 (mp) REVERT: A 631 GLN cc_start: 0.8800 (tt0) cc_final: 0.8359 (tp40) REVERT: A 646 LEU cc_start: 0.7618 (mt) cc_final: 0.7385 (mt) REVERT: A 648 GLU cc_start: 0.9249 (mm-30) cc_final: 0.8926 (mp0) REVERT: A 653 VAL cc_start: 0.8895 (OUTLIER) cc_final: 0.7309 (p) REVERT: A 673 ILE cc_start: 0.9006 (mt) cc_final: 0.8566 (tt) REVERT: B 51 MET cc_start: 0.3244 (ptt) cc_final: 0.2552 (ptp) REVERT: B 58 MET cc_start: 0.1441 (ptm) cc_final: 0.0768 (ttt) REVERT: B 167 ILE cc_start: 0.9658 (OUTLIER) cc_final: 0.9365 (tt) outliers start: 21 outliers final: 12 residues processed: 83 average time/residue: 0.0958 time to fit residues: 9.6512 Evaluate side-chains 78 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 500 PHE Chi-restraints excluded: chain A residue 502 TYR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 167 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 4 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 GLN ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.117508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.088370 restraints weight = 31581.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.090870 restraints weight = 24129.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.092536 restraints weight = 19837.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.093657 restraints weight = 17235.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.094493 restraints weight = 15572.273| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 5726 Z= 0.221 Angle : 0.782 8.159 7990 Z= 0.403 Chirality : 0.043 0.166 930 Planarity : 0.006 0.054 804 Dihedral : 20.306 113.235 1450 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 29.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 4.88 % Allowed : 21.02 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -1.42 (0.36), residues: 523 helix: 0.12 (0.36), residues: 204 sheet: -1.98 (0.58), residues: 63 loop : -1.52 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 286 TYR 0.025 0.003 TYR A 695 PHE 0.044 0.003 PHE A 529 TRP 0.042 0.003 TRP A 503 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 5714) covalent geometry : angle 0.77175 ( 7983) hydrogen bonds : bond 0.06354 ( 193) hydrogen bonds : angle 6.44468 ( 500) metal coordination : bond 0.01329 ( 12) metal coordination : angle 4.25510 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 ARG cc_start: 0.9253 (ttt180) cc_final: 0.9030 (tpp-160) REVERT: A 381 GLU cc_start: 0.9263 (mt-10) cc_final: 0.9031 (mt-10) REVERT: A 383 MET cc_start: 0.9443 (mmm) cc_final: 0.9197 (mpp) REVERT: A 433 LEU cc_start: 0.6887 (tp) cc_final: 0.6465 (mt) REVERT: A 500 PHE cc_start: 0.3287 (OUTLIER) cc_final: 0.0724 (t80) REVERT: A 631 GLN cc_start: 0.8888 (tt0) cc_final: 0.8414 (tp40) REVERT: A 637 LEU cc_start: 0.7306 (mt) cc_final: 0.6829 (mt) REVERT: A 646 LEU cc_start: 0.8287 (mt) cc_final: 0.7889 (mm) REVERT: A 648 GLU cc_start: 0.9308 (mm-30) cc_final: 0.9003 (mp0) REVERT: A 673 ILE cc_start: 0.9207 (mt) cc_final: 0.8841 (tt) REVERT: B 51 MET cc_start: 0.4133 (ptt) cc_final: 0.3562 (ptt) REVERT: B 58 MET cc_start: 0.1743 (ptm) cc_final: 0.0832 (ttt) REVERT: B 167 ILE cc_start: 0.9698 (pt) cc_final: 0.9433 (tt) outliers start: 23 outliers final: 14 residues processed: 86 average time/residue: 0.0811 time to fit residues: 8.5241 Evaluate side-chains 79 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 500 PHE Chi-restraints excluded: chain A residue 502 TYR Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 81 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 20 optimal weight: 40.0000 chunk 1 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.119378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.091595 restraints weight = 37469.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.092793 restraints weight = 28767.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.095408 restraints weight = 24711.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.096006 restraints weight = 21190.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.097190 restraints weight = 19413.748| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5726 Z= 0.204 Angle : 0.760 8.461 7990 Z= 0.396 Chirality : 0.044 0.203 930 Planarity : 0.006 0.042 804 Dihedral : 20.463 114.978 1448 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 30.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 4.46 % Allowed : 22.29 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -1.53 (0.36), residues: 523 helix: -0.14 (0.35), residues: 204 sheet: -2.15 (0.58), residues: 63 loop : -1.37 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 283 TYR 0.045 0.003 TYR A 695 PHE 0.051 0.003 PHE A 529 TRP 0.046 0.003 TRP A 503 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 5714) covalent geometry : angle 0.75253 ( 7983) hydrogen bonds : bond 0.06153 ( 193) hydrogen bonds : angle 6.66590 ( 500) metal coordination : bond 0.01181 ( 12) metal coordination : angle 3.66251 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 500 PHE cc_start: 0.3673 (OUTLIER) cc_final: 0.0671 (t80) REVERT: A 524 LEU cc_start: 0.9411 (mm) cc_final: 0.9143 (mp) REVERT: A 631 GLN cc_start: 0.8868 (tt0) cc_final: 0.8370 (tp-100) REVERT: A 637 LEU cc_start: 0.7257 (mt) cc_final: 0.6502 (mt) REVERT: A 646 LEU cc_start: 0.8403 (mt) cc_final: 0.8012 (mm) REVERT: A 648 GLU cc_start: 0.9284 (mm-30) cc_final: 0.9009 (mp0) REVERT: A 673 ILE cc_start: 0.9182 (mt) cc_final: 0.8763 (tt) REVERT: B 58 MET cc_start: 0.4002 (ptm) cc_final: 0.3384 (ttt) REVERT: B 167 ILE cc_start: 0.9681 (pt) cc_final: 0.9481 (tt) outliers start: 21 outliers final: 13 residues processed: 83 average time/residue: 0.0826 time to fit residues: 8.4841 Evaluate side-chains 77 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 500 PHE Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 81 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 51 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 0.0020 chunk 4 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.122095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.093234 restraints weight = 31329.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.095895 restraints weight = 22895.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.097617 restraints weight = 18349.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.098840 restraints weight = 15684.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.099712 restraints weight = 13970.984| |-----------------------------------------------------------------------------| r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5726 Z= 0.138 Angle : 0.720 7.557 7990 Z= 0.375 Chirality : 0.042 0.162 930 Planarity : 0.005 0.042 804 Dihedral : 20.302 111.066 1448 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 23.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.82 % Allowed : 22.72 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -1.47 (0.37), residues: 523 helix: -0.17 (0.35), residues: 204 sheet: -1.92 (0.63), residues: 63 loop : -1.33 (0.42), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 283 TYR 0.048 0.003 TYR A 695 PHE 0.042 0.003 PHE A 529 TRP 0.032 0.002 TRP A 503 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 5714) covalent geometry : angle 0.71531 ( 7983) hydrogen bonds : bond 0.05042 ( 193) hydrogen bonds : angle 6.33894 ( 500) metal coordination : bond 0.01000 ( 12) metal coordination : angle 2.98003 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8710 (mt-10) REVERT: A 500 PHE cc_start: 0.3111 (OUTLIER) cc_final: 0.0744 (t80) REVERT: A 524 LEU cc_start: 0.9357 (mm) cc_final: 0.9058 (mp) REVERT: A 631 GLN cc_start: 0.8700 (tt0) cc_final: 0.8284 (tp-100) REVERT: A 646 LEU cc_start: 0.8281 (mt) cc_final: 0.7960 (mm) REVERT: A 648 GLU cc_start: 0.9160 (mm-30) cc_final: 0.8922 (mp0) REVERT: A 673 ILE cc_start: 0.9081 (mt) cc_final: 0.8668 (tt) REVERT: B 58 MET cc_start: 0.2101 (ptm) cc_final: 0.0701 (ttt) outliers start: 18 outliers final: 14 residues processed: 82 average time/residue: 0.1079 time to fit residues: 10.8235 Evaluate side-chains 78 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 500 PHE Chi-restraints excluded: chain A residue 502 TYR Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 154 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 20 optimal weight: 40.0000 chunk 53 optimal weight: 9.9990 chunk 2 optimal weight: 0.4980 chunk 56 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 GLN ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.119542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.090963 restraints weight = 30946.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.093379 restraints weight = 23138.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.094936 restraints weight = 18933.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.096121 restraints weight = 16403.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.096919 restraints weight = 14744.854| |-----------------------------------------------------------------------------| r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5726 Z= 0.171 Angle : 0.756 10.718 7990 Z= 0.390 Chirality : 0.046 0.493 930 Planarity : 0.006 0.071 804 Dihedral : 20.260 110.112 1448 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 27.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 4.46 % Allowed : 22.51 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -1.47 (0.37), residues: 523 helix: -0.15 (0.36), residues: 198 sheet: -1.97 (0.62), residues: 63 loop : -1.31 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 283 TYR 0.043 0.003 TYR A 695 PHE 0.028 0.003 PHE A 493 TRP 0.053 0.003 TRP A 503 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 5714) covalent geometry : angle 0.74429 ( 7983) hydrogen bonds : bond 0.05517 ( 193) hydrogen bonds : angle 6.52879 ( 500) metal coordination : bond 0.01067 ( 12) metal coordination : angle 4.45111 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8819 (mt-10) REVERT: A 500 PHE cc_start: 0.3454 (OUTLIER) cc_final: 0.0857 (t80) REVERT: A 524 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9000 (mp) REVERT: A 631 GLN cc_start: 0.8809 (tt0) cc_final: 0.8369 (tp-100) REVERT: A 646 LEU cc_start: 0.8386 (mt) cc_final: 0.8043 (mm) REVERT: A 648 GLU cc_start: 0.9162 (mm-30) cc_final: 0.8950 (mp0) REVERT: A 673 ILE cc_start: 0.9169 (mt) cc_final: 0.8728 (tt) REVERT: B 58 MET cc_start: 0.1843 (ptm) cc_final: 0.0823 (ttt) outliers start: 21 outliers final: 15 residues processed: 80 average time/residue: 0.1145 time to fit residues: 11.2271 Evaluate side-chains 78 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 500 PHE Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 154 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 57 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 20 optimal weight: 30.0000 chunk 35 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 49 optimal weight: 0.0020 chunk 10 optimal weight: 6.9990 chunk 55 optimal weight: 20.0000 chunk 8 optimal weight: 3.9990 overall best weight: 3.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.117233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.087545 restraints weight = 29841.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.089761 restraints weight = 23027.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.091444 restraints weight = 19266.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.092599 restraints weight = 16734.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.093422 restraints weight = 15133.059| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.5538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5726 Z= 0.190 Angle : 0.773 9.891 7990 Z= 0.400 Chirality : 0.046 0.398 930 Planarity : 0.006 0.053 804 Dihedral : 20.303 111.092 1448 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 31.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.61 % Allowed : 23.14 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -1.57 (0.36), residues: 523 helix: -0.21 (0.36), residues: 196 sheet: -2.22 (0.60), residues: 63 loop : -1.33 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 654 TYR 0.045 0.003 TYR A 695 PHE 0.056 0.003 PHE A 529 TRP 0.053 0.003 TRP A 503 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 5714) covalent geometry : angle 0.76496 ( 7983) hydrogen bonds : bond 0.05808 ( 193) hydrogen bonds : angle 6.73149 ( 500) metal coordination : bond 0.01492 ( 12) metal coordination : angle 3.92179 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 LEU cc_start: 0.6883 (tp) cc_final: 0.6550 (mt) REVERT: A 500 PHE cc_start: 0.3422 (OUTLIER) cc_final: 0.0858 (t80) REVERT: A 524 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9032 (mp) REVERT: A 631 GLN cc_start: 0.8815 (tt0) cc_final: 0.8415 (tp-100) REVERT: A 646 LEU cc_start: 0.8405 (mt) cc_final: 0.8023 (mm) REVERT: A 648 GLU cc_start: 0.9222 (mm-30) cc_final: 0.8981 (mp0) REVERT: A 673 ILE cc_start: 0.9193 (mt) cc_final: 0.8726 (tt) REVERT: A 675 ASP cc_start: 0.8809 (t0) cc_final: 0.8281 (t0) REVERT: B 58 MET cc_start: 0.1609 (ptm) cc_final: 0.0016 (ttt) outliers start: 17 outliers final: 14 residues processed: 79 average time/residue: 0.1004 time to fit residues: 9.5875 Evaluate side-chains 78 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 500 PHE Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 154 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 12 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 656 GLN ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.118287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.089009 restraints weight = 31102.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.091380 restraints weight = 23606.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.092995 restraints weight = 19558.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.094132 restraints weight = 17009.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.094903 restraints weight = 15364.280| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.5724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5726 Z= 0.182 Angle : 0.778 10.196 7990 Z= 0.404 Chirality : 0.044 0.234 930 Planarity : 0.006 0.064 804 Dihedral : 20.288 111.916 1448 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 29.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.82 % Allowed : 23.14 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -1.66 (0.36), residues: 523 helix: -0.27 (0.36), residues: 198 sheet: -2.22 (0.60), residues: 63 loop : -1.40 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 283 TYR 0.049 0.003 TYR A 695 PHE 0.034 0.003 PHE A 529 TRP 0.056 0.003 TRP A 503 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 5714) covalent geometry : angle 0.77109 ( 7983) hydrogen bonds : bond 0.05619 ( 193) hydrogen bonds : angle 6.74609 ( 500) metal coordination : bond 0.01495 ( 12) metal coordination : angle 3.50763 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 500 PHE cc_start: 0.2973 (OUTLIER) cc_final: 0.0357 (t80) REVERT: A 524 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9022 (mp) REVERT: A 631 GLN cc_start: 0.8774 (tt0) cc_final: 0.8347 (tp-100) REVERT: A 637 LEU cc_start: 0.7373 (mt) cc_final: 0.6632 (tp) REVERT: A 646 LEU cc_start: 0.8456 (mt) cc_final: 0.8168 (mm) REVERT: A 648 GLU cc_start: 0.9231 (mm-30) cc_final: 0.8979 (mp0) REVERT: A 673 ILE cc_start: 0.9310 (mt) cc_final: 0.8917 (tt) REVERT: B 58 MET cc_start: 0.2658 (ptm) cc_final: 0.1146 (ttt) outliers start: 18 outliers final: 15 residues processed: 77 average time/residue: 0.0987 time to fit residues: 9.2925 Evaluate side-chains 80 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 500 PHE Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 154 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 5 optimal weight: 7.9990 chunk 32 optimal weight: 0.0770 chunk 9 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 50 optimal weight: 30.0000 chunk 38 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.118748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.089363 restraints weight = 30974.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.091768 restraints weight = 23657.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.093262 restraints weight = 19610.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.094453 restraints weight = 17175.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.095270 restraints weight = 15511.760| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.5832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5726 Z= 0.176 Angle : 0.784 12.321 7990 Z= 0.407 Chirality : 0.044 0.248 930 Planarity : 0.006 0.049 804 Dihedral : 20.270 110.972 1448 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 29.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.82 % Allowed : 23.14 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -1.60 (0.37), residues: 523 helix: -0.26 (0.36), residues: 197 sheet: -2.25 (0.59), residues: 63 loop : -1.32 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 654 TYR 0.049 0.003 TYR A 695 PHE 0.062 0.003 PHE B 47 TRP 0.057 0.004 TRP A 503 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 5714) covalent geometry : angle 0.77733 ( 7983) hydrogen bonds : bond 0.05528 ( 193) hydrogen bonds : angle 6.73718 ( 500) metal coordination : bond 0.01127 ( 12) metal coordination : angle 3.40966 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1474.62 seconds wall clock time: 25 minutes 55.86 seconds (1555.86 seconds total)