Starting phenix.real_space_refine on Thu Jul 2 01:45:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w4s_65643/07_2026/9w4s_65643.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w4s_65643/07_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_65643/07_2026/9w4s_65643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w4s_65643/07_2026/9w4s_65643.map" model { file = "/net/cci-nas-00/data/ceres_data/9w4s_65643/07_2026/9w4s_65643.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w4s_65643/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.27, per 1000 atoms: 0.23 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: 0.33 Conformation dependent library (CDL) restraints added in 96.3 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: 0.57 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: 0.92 Time building geometry restraints manager: 0.44 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=" N9 A C 49 " pdb=" C4 A C 49 " ideal model delta sigma weight residual 1.374 1.396 -0.022 6.00e-03 2.78e+04 1.29e+01 bond pdb=" N9 A C 54 " pdb=" C4 A C 54 " ideal model delta sigma weight residual 1.374 1.392 -0.018 6.00e-03 2.78e+04 8.99e+00 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=" C5 C C 63 " pdb=" C6 C C 63 " ideal model delta sigma weight residual 1.339 1.321 0.018 8.00e-03 1.56e+04 4.89e+00 bond pdb=" N9 A C 64 " pdb=" C4 A C 64 " ideal model delta sigma weight residual 1.374 1.362 0.012 6.00e-03 2.78e+04 4.00e+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=" N1 C C 63 " pdb=" C6 C C 63 " pdb=" C5 C C 63 " ideal model delta sigma weight residual 121.00 123.49 -2.49 5.00e-01 4.00e+00 2.48e+01 angle pdb=" C2 A C 54 " pdb=" N3 A C 54 " pdb=" C4 A C 54 " ideal model delta sigma weight residual 110.60 112.95 -2.35 5.00e-01 4.00e+00 2.21e+01 angle pdb=" C2 A C 49 " pdb=" N3 A C 49 " pdb=" C4 A C 49 " ideal model delta sigma weight residual 110.60 112.93 -2.33 5.00e-01 4.00e+00 2.17e+01 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=" C2 C C 39 " pdb=" N1 C C 39 " pdb=" C6 C C 39 " ideal model delta sigma weight residual 120.30 118.46 1.84 4.00e-01 6.25e+00 2.13e+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: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.450 Find NCS groups from input model: 0.030 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: 9.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 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= 0.287 Angle : 0.947 8.500 7990 Z= 0.679 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/Z covalent geometry : bond 0.00444 / 0.29 ( 5714) covalent geometry : angle 0.93943 / 0.68 ( 7983) hydrogen bonds : bond 0.19463 / 12.92 ( 193) hydrogen bonds : angle 8.37503 / 6.10 ( 500) metal coordination : bond 0.01333 / 0.84 ( 12) metal coordination : angle 4.21956 / 2.30 ( 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 : 0.175 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: 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: 0.1198 time to fit residues: 16.8832 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 : 0.108 ------------------------------------------------------------------------------- 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: 20.0000 chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 0.5980 chunk 56 optimal weight: 30.0000 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: 1.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4402 r_free = 0.4402 target = 0.124033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.095266 restraints weight = 30060.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.097865 restraints weight = 22134.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.098854 restraints weight = 17850.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.100640 restraints weight = 15751.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.101121 restraints weight = 13912.392| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 5726 Z= 0.178 Angle : 0.754 8.388 7990 Z= 0.412 Chirality : 0.045 0.219 930 Planarity : 0.006 0.059 804 Dihedral : 20.504 112.250 1464 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 20.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 4.25 % Allowed : 18.90 % Favored : 76.86 % 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: -1.82 (0.34), residues: 523 helix: -0.57 (0.33), residues: 197 sheet: -1.67 (0.57), residues: 71 loop : -1.51 (0.38), residues: 255 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 0.036 0.004 PHE A 529 TRP 0.011 0.002 TRP A 503 HIS 0.006 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 ( 5714) covalent geometry : angle 0.74445 / 0.41 ( 7983) hydrogen bonds : bond 0.06753 / 4.50 ( 193) hydrogen bonds : angle 6.79676 / 4.82 ( 500) metal coordination : bond 0.00653 / 0.40 ( 12) metal coordination : angle 4.00823 / 2.16 ( 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 98 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.171 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 283 ARG cc_start: 0.9217 (tpt90) cc_final: 0.8951 (tpm170) REVERT: A 285 GLU cc_start: 0.9177 (tt0) cc_final: 0.8730 (tp30) REVERT: A 287 ASP cc_start: 0.9219 (m-30) cc_final: 0.8712 (m-30) REVERT: A 327 ARG cc_start: 0.9102 (ttt90) cc_final: 0.8733 (tpm170) REVERT: A 383 MET cc_start: 0.9440 (mmm) cc_final: 0.9231 (mpp) REVERT: A 496 LEU cc_start: 0.6707 (OUTLIER) cc_final: 0.6312 (mt) REVERT: A 524 LEU cc_start: 0.9429 (mm) cc_final: 0.9220 (mp) REVERT: A 631 GLN cc_start: 0.8701 (tt0) cc_final: 0.8160 (tp40) REVERT: A 646 LEU cc_start: 0.8213 (mt) cc_final: 0.7907 (mp) REVERT: A 648 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8769 (mp0) REVERT: A 656 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8129 (tm-30) REVERT: A 673 ILE cc_start: 0.8925 (mt) cc_final: 0.8479 (tp) REVERT: B 51 MET cc_start: 0.2521 (ptt) cc_final: 0.1849 (ptt) REVERT: B 167 ILE cc_start: 0.9637 (OUTLIER) cc_final: 0.9323 (tt) outliers start: 20 outliers final: 8 residues processed: 93 average time/residue: 0.0998 time to fit residues: 11.2685 Evaluate side-chains 75 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.158 ------------------------------------------------------------------------------- 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 406 PHE Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 496 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 167 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 40 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4398 r_free = 0.4398 target = 0.124735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.097199 restraints weight = 36624.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.098373 restraints weight = 27370.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.100721 restraints weight = 23157.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.101287 restraints weight = 19825.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.102536 restraints weight = 18175.393| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 5726 Z= 0.171 Angle : 0.736 10.333 7990 Z= 0.399 Chirality : 0.044 0.163 930 Planarity : 0.006 0.046 804 Dihedral : 20.276 111.907 1450 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 22.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 4.67 % Allowed : 19.53 % Favored : 75.80 % 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: -1.58 (0.35), residues: 523 helix: -0.18 (0.34), residues: 195 sheet: -1.94 (0.58), residues: 68 loop : -1.43 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 661 TYR 0.054 0.003 TYR A 695 PHE 0.051 0.003 PHE A 529 TRP 0.011 0.002 TRP A 503 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 ( 5714) covalent geometry : angle 0.72813 / 0.40 ( 7983) hydrogen bonds : bond 0.06319 / 4.15 ( 193) hydrogen bonds : angle 6.58189 / 4.65 ( 500) metal coordination : bond 0.01208 / 0.66 ( 12) metal coordination : angle 3.76652 / 2.11 ( 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 94 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.171 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 285 GLU cc_start: 0.9185 (tt0) cc_final: 0.8658 (tp30) REVERT: A 287 ASP cc_start: 0.9264 (m-30) cc_final: 0.8405 (m-30) REVERT: A 327 ARG cc_start: 0.9186 (ttt90) cc_final: 0.8864 (tpp80) REVERT: A 342 ARG cc_start: 0.9093 (tpp-160) cc_final: 0.8825 (mtp85) REVERT: A 377 GLN cc_start: 0.9388 (tp-100) cc_final: 0.9182 (tp40) REVERT: A 500 PHE cc_start: 0.3419 (OUTLIER) cc_final: 0.0806 (t80) REVERT: A 524 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9095 (mp) REVERT: A 631 GLN cc_start: 0.8648 (tt0) cc_final: 0.8114 (tp40) REVERT: A 648 GLU cc_start: 0.9235 (mm-30) cc_final: 0.8942 (mp0) REVERT: A 656 GLN cc_start: 0.8469 (tm-30) cc_final: 0.8252 (tm-30) REVERT: A 673 ILE cc_start: 0.9012 (mt) cc_final: 0.8605 (tt) REVERT: A 675 ASP cc_start: 0.8519 (t0) cc_final: 0.7982 (t0) REVERT: B 58 MET cc_start: 0.3107 (ptm) cc_final: 0.2635 (ttt) REVERT: B 167 ILE cc_start: 0.9634 (OUTLIER) cc_final: 0.9347 (tt) outliers start: 22 outliers final: 14 residues processed: 89 average time/residue: 0.1048 time to fit residues: 11.3647 Evaluate side-chains 79 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 406 PHE 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 500 PHE Chi-restraints excluded: chain A residue 502 TYR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain B residue 74 VAL 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: 6.9990 chunk 41 optimal weight: 8.9990 chunk 37 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 0.0970 chunk 26 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.120791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.091687 restraints weight = 30692.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.094100 restraints weight = 23024.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.095899 restraints weight = 18895.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.097141 restraints weight = 16201.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.098011 restraints weight = 14460.962| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 5726 Z= 0.190 Angle : 0.898 42.930 7990 Z= 0.420 Chirality : 0.044 0.146 930 Planarity : 0.006 0.057 804 Dihedral : 20.345 111.926 1450 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 25.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.67 % Allowed : 21.23 % 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: -1.81 (0.35), residues: 523 helix: -0.47 (0.34), residues: 202 sheet: -2.02 (0.56), residues: 68 loop : -1.51 (0.40), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 283 TYR 0.016 0.002 TYR A 640 PHE 0.060 0.003 PHE A 529 TRP 0.041 0.003 TRP A 503 HIS 0.006 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 ( 5714) covalent geometry : angle 0.75228 / 0.40 ( 7983) hydrogen bonds : bond 0.06184 / 4.08 ( 193) hydrogen bonds : angle 6.61304 / 4.67 ( 500) metal coordination : bond 0.01899 / 1.37 ( 12) metal coordination : angle 16.59734 / 11.75 ( 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 86 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.132 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: A 285 GLU cc_start: 0.9270 (tt0) cc_final: 0.8736 (tp30) REVERT: A 327 ARG cc_start: 0.9213 (ttt90) cc_final: 0.8880 (tpp80) REVERT: A 377 GLN cc_start: 0.9393 (tp-100) cc_final: 0.9179 (tp-100) REVERT: A 383 MET cc_start: 0.9433 (mmm) cc_final: 0.9127 (mpp) REVERT: A 522 PHE cc_start: 0.8603 (t80) cc_final: 0.8079 (t80) REVERT: A 631 GLN cc_start: 0.8703 (tt0) cc_final: 0.8182 (tp40) REVERT: A 646 LEU cc_start: 0.8255 (mt) cc_final: 0.7908 (mm) REVERT: A 648 GLU cc_start: 0.9250 (mm-30) cc_final: 0.8863 (mp0) REVERT: A 656 GLN cc_start: 0.8669 (tm-30) cc_final: 0.8408 (tm-30) REVERT: A 673 ILE cc_start: 0.9123 (mt) cc_final: 0.8755 (tt) REVERT: B 58 MET cc_start: 0.0837 (ptm) cc_final: -0.0001 (ttt) REVERT: B 167 ILE cc_start: 0.9664 (OUTLIER) cc_final: 0.9403 (tt) outliers start: 22 outliers final: 11 residues processed: 80 average time/residue: 0.1035 time to fit residues: 10.1483 Evaluate side-chains 70 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.180 ------------------------------------------------------------------------------- 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 482 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 502 TYR 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 167 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 16 optimal weight: 0.4980 chunk 12 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 532 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.123396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.094015 restraints weight = 31197.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.096693 restraints weight = 23240.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.097724 restraints weight = 18764.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.099547 restraints weight = 16541.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.100126 restraints weight = 14580.034| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 5726 Z= 0.154 Angle : 0.822 33.616 7990 Z= 0.396 Chirality : 0.044 0.166 930 Planarity : 0.006 0.103 804 Dihedral : 20.300 110.300 1450 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 22.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.46 % Allowed : 21.23 % Favored : 74.31 % 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: -1.71 (0.36), residues: 523 helix: -0.47 (0.33), residues: 201 sheet: -2.02 (0.57), residues: 68 loop : -1.34 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 670 TYR 0.015 0.002 TYR A 640 PHE 0.061 0.003 PHE A 529 TRP 0.043 0.003 TRP A 503 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 5714) covalent geometry : angle 0.72577 / 0.38 ( 7983) hydrogen bonds : bond 0.05614 / 3.70 ( 193) hydrogen bonds : angle 6.49915 / 4.55 ( 500) metal coordination : bond 0.01371 / 0.93 ( 12) metal coordination : angle 13.05652 / 9.22 ( 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 84 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.112 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: A 285 GLU cc_start: 0.9280 (tt0) cc_final: 0.8678 (tp30) REVERT: A 327 ARG cc_start: 0.9236 (ttt90) cc_final: 0.9019 (tpp80) REVERT: A 342 ARG cc_start: 0.9111 (tpp-160) cc_final: 0.8831 (mtp85) REVERT: A 377 GLN cc_start: 0.9397 (tp-100) cc_final: 0.9166 (tp-100) REVERT: A 383 MET cc_start: 0.9448 (mmm) cc_final: 0.9165 (mpp) REVERT: A 522 PHE cc_start: 0.8660 (t80) cc_final: 0.8175 (t80) REVERT: A 631 GLN cc_start: 0.8727 (tt0) cc_final: 0.8205 (tp40) REVERT: A 646 LEU cc_start: 0.8404 (mt) cc_final: 0.8060 (mm) REVERT: A 648 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8896 (mp0) REVERT: A 656 GLN cc_start: 0.8703 (tm-30) cc_final: 0.8358 (tm-30) REVERT: A 673 ILE cc_start: 0.9048 (mt) cc_final: 0.8664 (tt) REVERT: A 675 ASP cc_start: 0.8606 (t0) cc_final: 0.8328 (t0) REVERT: B 58 MET cc_start: 0.1495 (ptm) cc_final: 0.0603 (ttt) REVERT: B 167 ILE cc_start: 0.9657 (OUTLIER) cc_final: 0.9429 (tt) outliers start: 21 outliers final: 10 residues processed: 78 average time/residue: 0.0834 time to fit residues: 8.1388 Evaluate side-chains 68 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 HIS 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 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 Chi-restraints excluded: chain B residue 167 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 20 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 51 optimal weight: 40.0000 chunk 45 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.123357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.096002 restraints weight = 37519.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.097970 restraints weight = 28703.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.099702 restraints weight = 24037.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.100259 restraints weight = 20692.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.101443 restraints weight = 18688.622| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5726 Z= 0.177 Angle : 0.795 27.652 7990 Z= 0.397 Chirality : 0.043 0.155 930 Planarity : 0.006 0.054 804 Dihedral : 20.324 111.793 1450 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 25.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.61 % Allowed : 22.93 % 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: -1.64 (0.35), residues: 523 helix: -0.24 (0.34), residues: 204 sheet: -2.00 (0.60), residues: 63 loop : -1.49 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 670 TYR 0.014 0.002 TYR A 640 PHE 0.064 0.003 PHE A 529 TRP 0.035 0.003 TRP A 503 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 ( 5714) covalent geometry : angle 0.72344 / 0.39 ( 7983) hydrogen bonds : bond 0.05839 / 3.88 ( 193) hydrogen bonds : angle 6.49388 / 4.53 ( 500) metal coordination : bond 0.01567 / 1.05 ( 12) metal coordination : angle 11.17805 / 7.80 ( 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 79 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 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: A 285 GLU cc_start: 0.9268 (tt0) cc_final: 0.8565 (tp30) REVERT: A 342 ARG cc_start: 0.8996 (tpp-160) cc_final: 0.8761 (mtp85) REVERT: A 377 GLN cc_start: 0.9303 (tp-100) cc_final: 0.9063 (tp-100) REVERT: A 383 MET cc_start: 0.9387 (mmm) cc_final: 0.9138 (mpp) REVERT: A 500 PHE cc_start: 0.3449 (OUTLIER) cc_final: 0.0457 (t80) REVERT: A 631 GLN cc_start: 0.8758 (tt0) cc_final: 0.8305 (tp40) REVERT: A 646 LEU cc_start: 0.8354 (mt) cc_final: 0.8063 (mm) REVERT: A 648 GLU cc_start: 0.9230 (mm-30) cc_final: 0.8938 (mp0) REVERT: A 656 GLN cc_start: 0.8668 (tm-30) cc_final: 0.8381 (tm-30) REVERT: A 673 ILE cc_start: 0.9102 (mt) cc_final: 0.8752 (tt) REVERT: B 58 MET cc_start: 0.3839 (ptm) cc_final: 0.3228 (ttt) outliers start: 17 outliers final: 10 residues processed: 74 average time/residue: 0.0954 time to fit residues: 8.7819 Evaluate side-chains 68 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 HIS 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 500 PHE Chi-restraints excluded: chain A residue 502 TYR 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 81 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 ASN ** 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 = 0.4341 r_free = 0.4341 target = 0.122129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.094138 restraints weight = 37688.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.096529 restraints weight = 29219.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.097067 restraints weight = 24207.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.098717 restraints weight = 21938.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.099223 restraints weight = 19764.884| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5726 Z= 0.192 Angle : 0.816 25.095 7990 Z= 0.407 Chirality : 0.044 0.162 930 Planarity : 0.005 0.042 804 Dihedral : 20.414 109.406 1448 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 28.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.03 % Allowed : 21.44 % Favored : 74.52 % 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: -1.70 (0.35), residues: 523 helix: -0.26 (0.34), residues: 204 sheet: -2.07 (0.59), residues: 63 loop : -1.55 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 699 TYR 0.015 0.002 TYR A 640 PHE 0.048 0.003 PHE A 529 TRP 0.025 0.002 TRP A 503 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 ( 5714) covalent geometry : angle 0.76108 / 0.40 ( 7983) hydrogen bonds : bond 0.05974 / 3.98 ( 193) hydrogen bonds : angle 6.49560 / 4.54 ( 500) metal coordination : bond 0.01665 / 1.08 ( 12) metal coordination : angle 9.97814 / 6.98 ( 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 77 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.122 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: A 285 GLU cc_start: 0.9285 (tt0) cc_final: 0.8589 (tp30) REVERT: A 342 ARG cc_start: 0.9104 (tpp-160) cc_final: 0.8844 (mtp85) REVERT: A 383 MET cc_start: 0.9491 (mmm) cc_final: 0.9206 (mpp) REVERT: A 500 PHE cc_start: 0.2952 (OUTLIER) cc_final: 0.0481 (t80) REVERT: A 524 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9016 (mp) REVERT: A 631 GLN cc_start: 0.8852 (tt0) cc_final: 0.8406 (tp-100) REVERT: A 646 LEU cc_start: 0.8464 (mt) cc_final: 0.8168 (mm) REVERT: A 648 GLU cc_start: 0.9282 (mm-30) cc_final: 0.8931 (mp0) REVERT: A 656 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8362 (tm-30) REVERT: A 673 ILE cc_start: 0.9124 (mt) cc_final: 0.8717 (tt) REVERT: B 58 MET cc_start: 0.4002 (ptm) cc_final: 0.3362 (ttt) outliers start: 19 outliers final: 11 residues processed: 72 average time/residue: 0.0678 time to fit residues: 6.2520 Evaluate side-chains 70 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 HIS 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 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 81 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 20 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 56 optimal weight: 20.0000 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 46 optimal weight: 7.9990 chunk 4 optimal weight: 0.4980 chunk 7 optimal weight: 0.0270 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 overall best weight: 1.8442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.123650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.095601 restraints weight = 37268.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.096662 restraints weight = 28441.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.099120 restraints weight = 24336.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.099658 restraints weight = 21023.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.100873 restraints weight = 19366.353| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 5726 Z= 0.159 Angle : 0.820 21.076 7990 Z= 0.410 Chirality : 0.045 0.237 930 Planarity : 0.005 0.038 804 Dihedral : 20.373 109.674 1448 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 24.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.61 % Allowed : 20.81 % Favored : 75.58 % 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: -1.65 (0.36), residues: 523 helix: -0.38 (0.34), residues: 211 sheet: -2.18 (0.56), residues: 68 loop : -1.32 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 661 TYR 0.014 0.002 TYR A 640 PHE 0.054 0.003 PHE A 529 TRP 0.038 0.002 TRP A 503 HIS 0.004 0.001 HIS A 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 ( 5714) covalent geometry : angle 0.77879 / 0.40 ( 7983) hydrogen bonds : bond 0.05568 / 3.74 ( 193) hydrogen bonds : angle 6.54112 / 4.56 ( 500) metal coordination : bond 0.01096 / 0.77 ( 12) metal coordination : angle 8.68437 / 6.00 ( 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 78 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 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: A 285 GLU cc_start: 0.9254 (tt0) cc_final: 0.8530 (tp30) REVERT: A 500 PHE cc_start: 0.2715 (OUTLIER) cc_final: 0.0211 (t80) REVERT: A 501 ARG cc_start: 0.8613 (tpp80) cc_final: 0.8410 (mtm-85) REVERT: A 524 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8958 (mp) REVERT: A 631 GLN cc_start: 0.8851 (tt0) cc_final: 0.8455 (tp-100) REVERT: A 646 LEU cc_start: 0.8367 (mt) cc_final: 0.8075 (mm) REVERT: A 648 GLU cc_start: 0.9226 (mm-30) cc_final: 0.8969 (mp0) REVERT: A 656 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8289 (tm-30) REVERT: A 673 ILE cc_start: 0.9078 (mt) cc_final: 0.8660 (tt) REVERT: B 58 MET cc_start: 0.3692 (ptm) cc_final: 0.3123 (ttt) outliers start: 17 outliers final: 14 residues processed: 73 average time/residue: 0.0960 time to fit residues: 8.5846 Evaluate side-chains 76 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.179 ------------------------------------------------------------------------------- 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 498 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 524 LEU 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 81 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 57 optimal weight: 20.0000 chunk 25 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 10 optimal weight: 6.9990 chunk 55 optimal weight: 30.0000 chunk 8 optimal weight: 2.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.124340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.096860 restraints weight = 37221.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.099216 restraints weight = 28127.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.100859 restraints weight = 23038.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.101835 restraints weight = 19797.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.102232 restraints weight = 17899.432| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.4818 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= 0.160 Angle : 0.830 18.018 7990 Z= 0.422 Chirality : 0.050 0.597 930 Planarity : 0.005 0.038 804 Dihedral : 20.271 108.336 1448 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 24.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.61 % Allowed : 21.87 % Favored : 74.52 % 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: -1.70 (0.36), residues: 523 helix: -0.40 (0.34), residues: 199 sheet: -2.16 (0.57), residues: 68 loop : -1.34 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 405 TYR 0.013 0.002 TYR A 640 PHE 0.057 0.003 PHE A 529 TRP 0.048 0.003 TRP A 503 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 ( 5714) covalent geometry : angle 0.80037 / 0.42 ( 7983) hydrogen bonds : bond 0.05562 / 3.71 ( 193) hydrogen bonds : angle 6.65074 / 4.67 ( 500) metal coordination : bond 0.01128 / 0.72 ( 12) metal coordination : angle 7.48923 / 5.17 ( 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 80 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.178 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: A 285 GLU cc_start: 0.9244 (tt0) cc_final: 0.8495 (tp30) REVERT: A 500 PHE cc_start: 0.3234 (OUTLIER) cc_final: 0.0454 (t80) REVERT: A 524 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8863 (mp) REVERT: A 631 GLN cc_start: 0.8732 (tt0) cc_final: 0.8401 (tp-100) REVERT: A 646 LEU cc_start: 0.8261 (mt) cc_final: 0.8002 (mm) REVERT: A 656 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8265 (tm-30) REVERT: A 673 ILE cc_start: 0.9037 (mt) cc_final: 0.8656 (tt) REVERT: A 675 ASP cc_start: 0.8672 (t0) cc_final: 0.8057 (t0) REVERT: B 58 MET cc_start: 0.3632 (ptm) cc_final: 0.2992 (ttt) outliers start: 17 outliers final: 12 residues processed: 75 average time/residue: 0.0896 time to fit residues: 8.4263 Evaluate side-chains 74 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.175 ------------------------------------------------------------------------------- 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 493 PHE Chi-restraints excluded: chain A residue 498 LEU 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 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 81 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 12 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 55 optimal weight: 30.0000 chunk 5 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 57 optimal weight: 20.0000 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 52 optimal weight: 0.0770 overall best weight: 2.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.122575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.095447 restraints weight = 37165.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.097651 restraints weight = 28318.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.099048 restraints weight = 23634.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.100094 restraints weight = 20701.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.100808 restraints weight = 18756.691| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.5072 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 : 0.868 17.123 7990 Z= 0.442 Chirality : 0.049 0.542 930 Planarity : 0.006 0.040 804 Dihedral : 20.288 108.812 1448 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 29.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.40 % Allowed : 22.51 % 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: -1.79 (0.36), residues: 523 helix: -0.42 (0.35), residues: 199 sheet: -2.19 (0.59), residues: 63 loop : -1.48 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 705 TYR 0.015 0.002 TYR A 640 PHE 0.059 0.003 PHE A 529 TRP 0.043 0.004 TRP A 503 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 ( 5714) covalent geometry : angle 0.84106 / 0.44 ( 7983) hydrogen bonds : bond 0.05971 / 3.96 ( 193) hydrogen bonds : angle 6.79096 / 4.75 ( 500) metal coordination : bond 0.01073 / 0.74 ( 12) metal coordination : angle 7.23786 / 4.97 ( 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 84 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.158 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 282 GLU cc_start: 0.9232 (tm-30) cc_final: 0.9011 (tm-30) REVERT: A 285 GLU cc_start: 0.9274 (tt0) cc_final: 0.8561 (tp30) REVERT: A 370 ASP cc_start: 0.9606 (p0) cc_final: 0.9243 (p0) REVERT: A 500 PHE cc_start: 0.3287 (OUTLIER) cc_final: 0.0704 (t80) REVERT: A 524 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8976 (mp) REVERT: A 631 GLN cc_start: 0.8876 (tt0) cc_final: 0.8491 (tp-100) REVERT: A 656 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8344 (tm-30) REVERT: A 673 ILE cc_start: 0.9166 (mt) cc_final: 0.8908 (tt) REVERT: B 58 MET cc_start: 0.4035 (ptm) cc_final: 0.3325 (ttt) outliers start: 16 outliers final: 12 residues processed: 79 average time/residue: 0.0974 time to fit residues: 9.6290 Evaluate side-chains 72 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 493 PHE Chi-restraints excluded: chain A residue 498 LEU 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 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 81 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 5 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 52 optimal weight: 0.0040 chunk 29 optimal weight: 0.9980 chunk 7 optimal weight: 0.0030 chunk 48 optimal weight: 20.0000 chunk 50 optimal weight: 40.0000 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 overall best weight: 0.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 351 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.125041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.097893 restraints weight = 37187.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.100160 restraints weight = 27818.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.101913 restraints weight = 22721.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.102993 restraints weight = 19558.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.103584 restraints weight = 17648.829| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.5265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5726 Z= 0.169 Angle : 0.892 15.961 7990 Z= 0.457 Chirality : 0.050 0.524 930 Planarity : 0.006 0.090 804 Dihedral : 20.201 106.951 1448 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 26.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.97 % Allowed : 24.20 % Favored : 72.82 % 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: -1.82 (0.36), residues: 523 helix: -0.47 (0.35), residues: 199 sheet: -2.41 (0.54), residues: 68 loop : -1.38 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 374 TYR 0.013 0.002 TYR A 640 PHE 0.063 0.003 PHE A 529 TRP 0.063 0.003 TRP A 503 HIS 0.003 0.001 HIS A 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 ( 5714) covalent geometry : angle 0.87377 / 0.45 ( 7983) hydrogen bonds : bond 0.05443 / 3.60 ( 193) hydrogen bonds : angle 6.67118 / 4.63 ( 500) metal coordination : bond 0.01122 / 0.63 ( 12) metal coordination : angle 6.13252 / 4.18 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1556.46 seconds wall clock time: 27 minutes 23.00 seconds (1643.00 seconds total)