Starting phenix.real_space_refine on Tue Aug 4 17:30:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w4s_65643/08_2026/9w4s_65643.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w4s_65643/08_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_65643/08_2026/9w4s_65643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w4s_65643/08_2026/9w4s_65643.map" model { file = "/net/cci-nas-00/data/ceres_data/9w4s_65643/08_2026/9w4s_65643.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w4s_65643/08_2026/9w4s_65643.cif" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.016 sd= 0.477 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 57 5.49 5 S 31 5.16 5 C 3276 2.51 5 N 966 2.21 5 O 1145 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: 1.05, per 1000 atoms: 0.19 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: 0.42 Conformation dependent library (CDL) restraints added in 175.1 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: 0.44 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: 1.00 Time building geometry restraints manager: 0.57 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: 7125 1.51 - 3.01: 735 3.01 - 4.52: 90 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: 582 0.042 - 0.084: 201 0.084 - 0.126: 96 0.126 - 0.168: 44 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: 0.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.030 Find NCS groups from input model: 0.020 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: 0.010 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.340 ------------------------------------------------------------------------------- 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 : 0.005 0.043 5726 Z= 0.298 Angle : 0.995 8.500 7990 Z= 0.738 Chirality : 0.058 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 0.00448 / 0.30 ( 5714) covalent geometry : angle 0.98787 / 0.74 ( 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 : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.1005 time to fit residues: 14.2118 Evaluate side-chains 86 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.107 ------------------------------------------------------------------------------- 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: 0.8980 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: 8.9990 overall best weight: 1.4992 ------------------------------------------------------------------------------- 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 = 0.4399 r_free = 0.4399 target = 0.123715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.094647 restraints weight = 29720.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.097342 restraints weight = 21783.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.099186 restraints weight = 17517.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.100401 restraints weight = 14916.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.100840 restraints weight = 13316.697| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 5726 Z= 0.174 Angle : 0.748 8.346 7990 Z= 0.408 Chirality : 0.046 0.218 930 Planarity : 0.006 0.053 804 Dihedral : 20.389 109.763 1464 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 4.25 % Allowed : 19.32 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.34), residues: 523 helix: -0.56 (0.33), residues: 194 sheet: -1.68 (0.56), residues: 71 loop : -1.50 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 459 TYR 0.038 0.003 TYR A 695 PHE 0.034 0.003 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 0.00374 / 0.17 ( 5714) covalent geometry : angle 0.73858 / 0.41 ( 7983) hydrogen bonds : bond 0.06841 / 4.51 ( 193) hydrogen bonds : angle 6.83252 / 4.86 ( 500) metal coordination : bond 0.00752 / 0.48 ( 12) metal coordination : angle 4.01352 / 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 96 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ARG cc_start: 0.9249 (tpt90) cc_final: 0.8960 (tpm170) REVERT: A 285 GLU cc_start: 0.9181 (tt0) cc_final: 0.8743 (tp30) REVERT: A 287 ASP cc_start: 0.9252 (m-30) cc_final: 0.8730 (m-30) REVERT: A 327 ARG cc_start: 0.9141 (ttt90) cc_final: 0.8771 (tpm170) REVERT: A 496 LEU cc_start: 0.6860 (OUTLIER) cc_final: 0.6348 (mt) REVERT: A 631 GLN cc_start: 0.8712 (tt0) cc_final: 0.8169 (tp40) REVERT: A 646 LEU cc_start: 0.8244 (mt) cc_final: 0.7926 (mp) REVERT: A 648 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8777 (mp0) REVERT: A 673 ILE cc_start: 0.8940 (mt) cc_final: 0.8539 (tp) REVERT: A 675 ASP cc_start: 0.8494 (t70) cc_final: 0.8207 (t0) REVERT: B 51 MET cc_start: 0.2816 (ptt) cc_final: 0.2233 (ptt) REVERT: B 167 ILE cc_start: 0.9640 (OUTLIER) cc_final: 0.9329 (tt) outliers start: 20 outliers final: 8 residues processed: 90 average time/residue: 0.0830 time to fit residues: 9.0796 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 : 0.166 ------------------------------------------------------------------------------- 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 457 VAL Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 498 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: 20.0000 chunk 22 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.4378 r_free = 0.4378 target = 0.123411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.095649 restraints weight = 36556.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.097900 restraints weight = 27734.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.098474 restraints weight = 22798.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.100290 restraints weight = 20554.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.100718 restraints weight = 18390.693| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 5726 Z= 0.185 Angle : 0.739 9.432 7990 Z= 0.398 Chirality : 0.044 0.202 930 Planarity : 0.006 0.055 804 Dihedral : 20.308 110.223 1452 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 24.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 5.52 % Allowed : 19.32 % Favored : 75.16 % 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: -1.68 (0.35), residues: 523 helix: -0.29 (0.34), residues: 197 sheet: -1.97 (0.56), residues: 71 loop : -1.45 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 661 TYR 0.058 0.003 TYR A 695 PHE 0.048 0.003 PHE A 529 TRP 0.011 0.002 TRP A 503 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 ( 5714) covalent geometry : angle 0.72874 / 0.40 ( 7983) hydrogen bonds : bond 0.06578 / 4.32 ( 193) hydrogen bonds : angle 6.69002 / 4.74 ( 500) metal coordination : bond 0.01502 / 0.74 ( 12) metal coordination : angle 4.25278 / 2.43 ( 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 97 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.129 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: 0.9200 (tt0) cc_final: 0.8681 (tp30) REVERT: A 287 ASP cc_start: 0.9293 (m-30) cc_final: 0.8431 (m-30) REVERT: A 324 LYS cc_start: 0.8694 (ttmm) cc_final: 0.8450 (ttmt) REVERT: A 327 ARG cc_start: 0.9233 (ttt90) cc_final: 0.8909 (tpp80) REVERT: A 377 GLN cc_start: 0.9441 (tp-100) cc_final: 0.9190 (tp40) REVERT: A 381 GLU cc_start: 0.9229 (mt-10) cc_final: 0.8842 (mt-10) REVERT: A 522 PHE cc_start: 0.8540 (t80) cc_final: 0.8034 (t80) REVERT: A 524 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9119 (mp) REVERT: A 631 GLN cc_start: 0.8664 (tt0) cc_final: 0.8130 (tp40) REVERT: A 646 LEU cc_start: 0.8472 (mt) cc_final: 0.8262 (mt) REVERT: A 648 GLU cc_start: 0.9254 (mm-30) cc_final: 0.8964 (mp0) REVERT: A 656 GLN cc_start: 0.8475 (tm-30) cc_final: 0.8136 (tm-30) REVERT: A 673 ILE cc_start: 0.9017 (mt) cc_final: 0.8615 (tt) REVERT: B 58 MET cc_start: 0.3085 (ptm) cc_final: 0.2608 (ttt) REVERT: B 167 ILE cc_start: 0.9649 (OUTLIER) cc_final: 0.9375 (tt) outliers start: 26 outliers final: 16 residues processed: 91 average time/residue: 0.0771 time to fit residues: 8.7064 Evaluate side-chains 81 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.102 ------------------------------------------------------------------------------- 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 497 VAL 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 660 THR 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: 8.9990 chunk 41 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 45 optimal weight: 30.0000 chunk 2 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 31 optimal weight: 0.0980 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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 = 0.4328 r_free = 0.4328 target = 0.119361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.090719 restraints weight = 31455.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.093336 restraints weight = 23524.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.094275 restraints weight = 19130.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.095982 restraints weight = 16968.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.096473 restraints weight = 15075.321| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 5726 Z= 0.191 Angle : 0.879 42.378 7990 Z= 0.414 Chirality : 0.043 0.159 930 Planarity : 0.006 0.060 804 Dihedral : 20.279 110.529 1450 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 26.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 5.10 % Allowed : 19.96 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.35), residues: 523 helix: -0.29 (0.35), residues: 204 sheet: -2.07 (0.58), residues: 63 loop : -1.54 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 283 TYR 0.015 0.002 TYR A 520 PHE 0.032 0.003 PHE A 529 TRP 0.045 0.003 TRP A 503 HIS 0.007 0.002 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.19 ( 5714) covalent geometry : angle 0.73735 / 0.40 ( 7983) hydrogen bonds : bond 0.06345 / 4.19 ( 193) hydrogen bonds : angle 6.73116 / 4.73 ( 500) metal coordination : bond 0.01715 / 1.16 ( 12) metal coordination : angle 16.15559 / 11.49 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 GLU cc_start: 0.9257 (tt0) cc_final: 0.8754 (tp30) REVERT: A 327 ARG cc_start: 0.9292 (ttt90) cc_final: 0.8923 (tpp80) REVERT: A 370 ASP cc_start: 0.9651 (p0) cc_final: 0.9195 (p0) REVERT: A 374 ARG cc_start: 0.9683 (OUTLIER) cc_final: 0.9473 (ptp-170) REVERT: A 377 GLN cc_start: 0.9390 (tp-100) cc_final: 0.9157 (tp-100) REVERT: A 522 PHE cc_start: 0.8635 (t80) cc_final: 0.8171 (t80) REVERT: A 524 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9068 (mp) REVERT: A 631 GLN cc_start: 0.8745 (tt0) cc_final: 0.8262 (tp40) REVERT: A 646 LEU cc_start: 0.8524 (mt) cc_final: 0.8312 (mt) REVERT: A 648 GLU cc_start: 0.9287 (mm-30) cc_final: 0.8892 (mp0) REVERT: A 656 GLN cc_start: 0.8527 (tm-30) cc_final: 0.8167 (tm-30) REVERT: A 673 ILE cc_start: 0.9157 (mt) cc_final: 0.8761 (tt) REVERT: B 58 MET cc_start: 0.1147 (ptm) cc_final: 0.0225 (ttt) REVERT: B 167 ILE cc_start: 0.9669 (OUTLIER) cc_final: 0.9422 (tt) outliers start: 24 outliers final: 14 residues processed: 82 average time/residue: 0.0821 time to fit residues: 8.2261 Evaluate side-chains 81 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 502 TYR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 20.0000 chunk 51 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 GLN A 351 HIS ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.124518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.096758 restraints weight = 37258.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.099205 restraints weight = 27798.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.100804 restraints weight = 22848.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.101248 restraints weight = 19736.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.102554 restraints weight = 18234.365| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 5726 Z= 0.151 Angle : 0.807 34.017 7990 Z= 0.389 Chirality : 0.043 0.186 930 Planarity : 0.005 0.041 804 Dihedral : 20.188 108.401 1450 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 22.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 5.52 % Allowed : 20.17 % 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: -1.64 (0.36), residues: 523 helix: -0.28 (0.34), residues: 205 sheet: -2.21 (0.55), residues: 68 loop : -1.37 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 661 TYR 0.015 0.002 TYR A 640 PHE 0.039 0.003 PHE A 529 TRP 0.022 0.002 TRP A 503 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 5714) covalent geometry : angle 0.70840 / 0.38 ( 7983) hydrogen bonds : bond 0.05442 / 3.60 ( 193) hydrogen bonds : angle 6.49939 / 4.56 ( 500) metal coordination : bond 0.01966 / 1.47 ( 12) metal coordination : angle 13.04431 / 9.26 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.106 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: 0.9280 (tt0) cc_final: 0.8608 (tp30) REVERT: A 327 ARG cc_start: 0.9248 (ttt90) cc_final: 0.8902 (tpp80) REVERT: A 383 MET cc_start: 0.9328 (mmm) cc_final: 0.9020 (mpp) REVERT: A 459 ARG cc_start: 0.8537 (tpp80) cc_final: 0.8247 (tpp80) REVERT: A 522 PHE cc_start: 0.8626 (t80) cc_final: 0.8273 (t80) REVERT: A 524 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.8949 (mp) REVERT: A 631 GLN cc_start: 0.8698 (tt0) cc_final: 0.8206 (tp40) REVERT: A 648 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8896 (mp0) REVERT: A 656 GLN cc_start: 0.8486 (tm-30) cc_final: 0.8278 (tm-30) REVERT: A 673 ILE cc_start: 0.9064 (mt) cc_final: 0.8659 (tt) REVERT: B 58 MET cc_start: 0.3411 (ptm) cc_final: 0.2801 (ttt) outliers start: 26 outliers final: 14 residues processed: 83 average time/residue: 0.0883 time to fit residues: 8.9080 Evaluate side-chains 76 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 502 TYR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 670 ARG Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 81 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 20 optimal weight: 7.9990 chunk 1 optimal weight: 0.5980 chunk 27 optimal weight: 0.3980 chunk 24 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 GLN ** A 532 GLN ** 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 = 0.4348 r_free = 0.4348 target = 0.121433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.090627 restraints weight = 29370.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.093355 restraints weight = 22118.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.095124 restraints weight = 17975.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.096352 restraints weight = 15496.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.097169 restraints weight = 13922.522| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.4145 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= 0.165 Angle : 0.780 28.739 7990 Z= 0.388 Chirality : 0.046 0.469 930 Planarity : 0.005 0.037 804 Dihedral : 20.176 108.516 1448 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 23.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.82 % Allowed : 22.08 % 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: -1.56 (0.36), residues: 523 helix: -0.16 (0.35), residues: 205 sheet: -2.23 (0.55), residues: 68 loop : -1.34 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 661 TYR 0.016 0.002 TYR A 640 PHE 0.039 0.003 PHE A 529 TRP 0.049 0.003 TRP A 503 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 5714) covalent geometry : angle 0.70560 / 0.38 ( 7983) hydrogen bonds : bond 0.05555 / 3.71 ( 193) hydrogen bonds : angle 6.54037 / 4.54 ( 500) metal coordination : bond 0.01313 / 0.92 ( 12) metal coordination : angle 11.25741 / 7.92 ( 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 85 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.124 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: 0.9285 (tt0) cc_final: 0.8632 (tp30) REVERT: A 327 ARG cc_start: 0.9326 (ttt90) cc_final: 0.8952 (tpp80) REVERT: A 381 GLU cc_start: 0.9317 (mt-10) cc_final: 0.9093 (mt-10) REVERT: A 383 MET cc_start: 0.9404 (mmm) cc_final: 0.9074 (mpp) REVERT: A 500 PHE cc_start: 0.2801 (OUTLIER) cc_final: 0.0399 (t80) REVERT: A 524 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9057 (mp) REVERT: A 631 GLN cc_start: 0.8829 (tt0) cc_final: 0.8313 (tp40) REVERT: A 637 LEU cc_start: 0.7120 (mt) cc_final: 0.6680 (mt) REVERT: A 646 LEU cc_start: 0.7694 (mt) cc_final: 0.7448 (tp) REVERT: A 648 GLU cc_start: 0.9264 (mm-30) cc_final: 0.8916 (mp0) REVERT: A 656 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8435 (tm-30) REVERT: A 673 ILE cc_start: 0.9172 (mt) cc_final: 0.8741 (tt) REVERT: B 58 MET cc_start: 0.1203 (ptm) cc_final: 0.0352 (ttt) outliers start: 18 outliers final: 13 residues processed: 79 average time/residue: 0.0887 time to fit residues: 8.4909 Evaluate side-chains 78 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 500 PHE Chi-restraints excluded: chain A residue 502 TYR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 670 ARG Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 81 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 53 optimal weight: 30.0000 chunk 41 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 27 optimal weight: 0.0980 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 532 GLN ** 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 = 0.4348 r_free = 0.4348 target = 0.121415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.091329 restraints weight = 30198.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.094066 restraints weight = 22402.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.095859 restraints weight = 18085.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.097129 restraints weight = 15517.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.097990 restraints weight = 13853.261| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5726 Z= 0.151 Angle : 0.752 24.155 7990 Z= 0.383 Chirality : 0.044 0.365 930 Planarity : 0.005 0.037 804 Dihedral : 20.158 107.962 1448 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 23.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 4.46 % Allowed : 22.29 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.36), residues: 523 helix: -0.17 (0.35), residues: 205 sheet: -2.23 (0.56), residues: 68 loop : -1.36 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 661 TYR 0.016 0.002 TYR A 640 PHE 0.044 0.003 PHE A 529 TRP 0.046 0.003 TRP A 503 HIS 0.007 0.001 HIS B 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 5714) covalent geometry : angle 0.69998 / 0.38 ( 7983) hydrogen bonds : bond 0.05432 / 3.61 ( 193) hydrogen bonds : angle 6.47056 / 4.51 ( 500) metal coordination : bond 0.01206 / 0.86 ( 12) metal coordination : angle 9.29159 / 6.59 ( 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 85 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.126 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: 0.9268 (tt0) cc_final: 0.8587 (tp30) REVERT: A 327 ARG cc_start: 0.9343 (ttt90) cc_final: 0.8969 (tpp80) REVERT: A 383 MET cc_start: 0.9401 (mmm) cc_final: 0.9093 (mpp) REVERT: A 433 LEU cc_start: 0.6903 (tp) cc_final: 0.6684 (mt) REVERT: A 500 PHE cc_start: 0.2705 (OUTLIER) cc_final: 0.0311 (t80) REVERT: A 524 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9062 (mp) REVERT: A 631 GLN cc_start: 0.8816 (tt0) cc_final: 0.8325 (tp40) REVERT: A 637 LEU cc_start: 0.7336 (mt) cc_final: 0.7030 (mt) REVERT: A 646 LEU cc_start: 0.7724 (mt) cc_final: 0.7475 (tp) REVERT: A 648 GLU cc_start: 0.9265 (mm-30) cc_final: 0.8911 (mp0) REVERT: A 656 GLN cc_start: 0.8688 (tm-30) cc_final: 0.8357 (tm-30) REVERT: A 673 ILE cc_start: 0.9183 (mt) cc_final: 0.8765 (tt) REVERT: A 705 ARG cc_start: 0.7446 (mtt90) cc_final: 0.7180 (ttm110) REVERT: B 58 MET cc_start: 0.1208 (ptm) cc_final: 0.0282 (ttt) outliers start: 21 outliers final: 14 residues processed: 78 average time/residue: 0.0867 time to fit residues: 8.2628 Evaluate side-chains 77 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.114 ------------------------------------------------------------------------------- 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 423 MET 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 524 LEU 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 A residue 670 ARG 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: 7.9990 chunk 53 optimal weight: 30.0000 chunk 2 optimal weight: 2.9990 chunk 56 optimal weight: 30.0000 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 46 optimal weight: 0.3980 chunk 4 optimal weight: 20.0000 chunk 7 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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 = 0.4353 r_free = 0.4353 target = 0.121833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.092675 restraints weight = 31409.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.095243 restraints weight = 23406.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.096961 restraints weight = 19044.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.098173 restraints weight = 16407.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.099029 restraints weight = 14694.663| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5726 Z= 0.155 Angle : 0.759 21.777 7990 Z= 0.389 Chirality : 0.046 0.509 930 Planarity : 0.005 0.037 804 Dihedral : 20.145 107.724 1448 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 24.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.67 % Allowed : 21.66 % Favored : 73.67 % 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: -1.62 (0.36), residues: 523 helix: -0.24 (0.35), residues: 205 sheet: -2.29 (0.55), residues: 68 loop : -1.35 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 661 TYR 0.016 0.002 TYR A 640 PHE 0.048 0.003 PHE A 529 TRP 0.047 0.003 TRP A 503 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 5714) covalent geometry : angle 0.71249 / 0.38 ( 7983) hydrogen bonds : bond 0.05350 / 3.58 ( 193) hydrogen bonds : angle 6.40791 / 4.45 ( 500) metal coordination : bond 0.01029 / 0.67 ( 12) metal coordination : angle 8.88671 / 6.20 ( 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 88 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.163 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 285 GLU cc_start: 0.9282 (tt0) cc_final: 0.8572 (tp30) REVERT: A 327 ARG cc_start: 0.9319 (ttt90) cc_final: 0.8947 (tpp80) REVERT: A 500 PHE cc_start: 0.3005 (OUTLIER) cc_final: 0.0472 (t80) REVERT: A 524 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9019 (mp) REVERT: A 631 GLN cc_start: 0.8801 (tt0) cc_final: 0.8323 (tp-100) REVERT: A 637 LEU cc_start: 0.7193 (mt) cc_final: 0.6862 (mt) REVERT: A 646 LEU cc_start: 0.7769 (mt) cc_final: 0.7545 (tp) REVERT: A 648 GLU cc_start: 0.9247 (mm-30) cc_final: 0.8945 (mp0) REVERT: A 656 GLN cc_start: 0.8692 (tm-30) cc_final: 0.8362 (tm-30) REVERT: A 673 ILE cc_start: 0.9211 (mt) cc_final: 0.8812 (tt) REVERT: A 705 ARG cc_start: 0.7376 (mtt90) cc_final: 0.6826 (ttm110) REVERT: B 58 MET cc_start: 0.2045 (ptm) cc_final: 0.1161 (ttt) outliers start: 22 outliers final: 15 residues processed: 81 average time/residue: 0.0907 time to fit residues: 8.9753 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 : 0.129 ------------------------------------------------------------------------------- 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 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 655 ILE Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 670 ARG 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: 30.0000 chunk 25 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 39 optimal weight: 0.1980 chunk 29 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 55 optimal weight: 40.0000 chunk 8 optimal weight: 8.9990 overall best weight: 4.6388 ------------------------------------------------------------------------------- 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 = 0.4288 r_free = 0.4288 target = 0.117587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.088438 restraints weight = 31744.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.090843 restraints weight = 24195.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.092342 restraints weight = 20054.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.093401 restraints weight = 17539.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.094276 restraints weight = 15883.305| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 5726 Z= 0.232 Angle : 0.852 21.870 7990 Z= 0.438 Chirality : 0.048 0.472 930 Planarity : 0.005 0.038 804 Dihedral : 20.323 110.889 1448 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 32.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 4.25 % Allowed : 22.08 % Favored : 73.67 % 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: -1.61 (0.36), residues: 523 helix: -0.27 (0.36), residues: 199 sheet: -2.27 (0.58), residues: 63 loop : -1.32 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 699 TYR 0.016 0.002 TYR A 640 PHE 0.040 0.003 PHE A 529 TRP 0.058 0.004 TRP A 503 HIS 0.004 0.001 HIS A 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.23 ( 5714) covalent geometry : angle 0.80759 / 0.43 ( 7983) hydrogen bonds : bond 0.06432 / 4.30 ( 193) hydrogen bonds : angle 6.84044 / 4.83 ( 500) metal coordination : bond 0.01593 / 1.01 ( 12) metal coordination : angle 9.18406 / 6.34 ( 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 88 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 GLU cc_start: 0.9323 (tt0) cc_final: 0.8619 (tp30) REVERT: A 327 ARG cc_start: 0.9384 (ttt90) cc_final: 0.9085 (tpp80) REVERT: A 382 GLU cc_start: 0.9786 (tp30) cc_final: 0.9474 (tp30) REVERT: A 433 LEU cc_start: 0.6849 (tp) cc_final: 0.6644 (mt) REVERT: A 500 PHE cc_start: 0.3205 (OUTLIER) cc_final: 0.0583 (t80) REVERT: A 524 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8969 (mp) REVERT: A 631 GLN cc_start: 0.8879 (tt0) cc_final: 0.8576 (tp-100) REVERT: A 637 LEU cc_start: 0.7370 (mt) cc_final: 0.7090 (mt) REVERT: A 646 LEU cc_start: 0.8124 (mt) cc_final: 0.7909 (tp) REVERT: A 648 GLU cc_start: 0.9272 (mm-30) cc_final: 0.9013 (mp0) REVERT: A 656 GLN cc_start: 0.8624 (tm-30) cc_final: 0.8245 (tm-30) REVERT: A 673 ILE cc_start: 0.9261 (mt) cc_final: 0.8874 (tt) REVERT: B 58 MET cc_start: 0.1820 (ptm) cc_final: 0.0758 (ttt) outliers start: 20 outliers final: 18 residues processed: 81 average time/residue: 0.0903 time to fit residues: 9.0147 Evaluate side-chains 84 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 423 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 12 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 55 optimal weight: 30.0000 chunk 5 optimal weight: 7.9990 chunk 34 optimal weight: 0.3980 chunk 57 optimal weight: 30.0000 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 52 optimal weight: 8.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.4351 r_free = 0.4351 target = 0.121637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.093480 restraints weight = 31269.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.096123 restraints weight = 23023.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.097846 restraints weight = 18465.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.098999 restraints weight = 15736.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.099916 restraints weight = 14085.228| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.4996 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= 0.165 Angle : 0.828 18.680 7990 Z= 0.429 Chirality : 0.048 0.516 930 Planarity : 0.005 0.037 804 Dihedral : 20.301 109.180 1448 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 25.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.40 % Allowed : 23.35 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.36), residues: 523 helix: -0.39 (0.35), residues: 198 sheet: -2.40 (0.55), residues: 68 loop : -1.18 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 661 TYR 0.034 0.003 TYR A 695 PHE 0.051 0.003 PHE A 529 TRP 0.056 0.003 TRP A 503 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 5714) covalent geometry : angle 0.79541 / 0.43 ( 7983) hydrogen bonds : bond 0.05529 / 3.68 ( 193) hydrogen bonds : angle 6.66704 / 4.67 ( 500) metal coordination : bond 0.01427 / 0.77 ( 12) metal coordination : angle 7.78161 / 5.32 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.180 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: 0.9275 (tt0) cc_final: 0.8570 (tp30) REVERT: A 327 ARG cc_start: 0.9271 (ttt90) cc_final: 0.8919 (tpp80) REVERT: A 382 GLU cc_start: 0.9807 (tp30) cc_final: 0.9484 (tp30) REVERT: A 433 LEU cc_start: 0.6671 (tp) cc_final: 0.6464 (mt) REVERT: A 500 PHE cc_start: 0.2839 (OUTLIER) cc_final: 0.0201 (t80) REVERT: A 524 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9066 (mm) REVERT: A 631 GLN cc_start: 0.8834 (tt0) cc_final: 0.8382 (tp-100) REVERT: A 648 GLU cc_start: 0.9216 (mm-30) cc_final: 0.8940 (mp0) REVERT: A 656 GLN cc_start: 0.8650 (tm-30) cc_final: 0.8332 (tm-30) REVERT: A 673 ILE cc_start: 0.8958 (mt) cc_final: 0.8526 (tt) REVERT: A 675 ASP cc_start: 0.8790 (t0) cc_final: 0.8123 (t0) REVERT: B 58 MET cc_start: 0.1860 (ptm) cc_final: 0.0884 (ttt) outliers start: 16 outliers final: 13 residues processed: 77 average time/residue: 0.0927 time to fit residues: 8.9092 Evaluate side-chains 76 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 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 670 ARG 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: 20.0000 chunk 32 optimal weight: 0.3980 chunk 9 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 7 optimal weight: 0.0970 chunk 48 optimal weight: 0.9980 chunk 50 optimal weight: 40.0000 chunk 38 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.123717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.095404 restraints weight = 31421.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.098077 restraints weight = 23309.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.099800 restraints weight = 18747.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.100938 restraints weight = 16038.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.101752 restraints weight = 14290.389| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.5242 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= 0.163 Angle : 0.839 15.436 7990 Z= 0.438 Chirality : 0.048 0.512 930 Planarity : 0.006 0.063 804 Dihedral : 20.192 107.992 1448 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 23.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.61 % Allowed : 23.99 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.36), residues: 523 helix: -0.41 (0.35), residues: 197 sheet: -2.49 (0.54), residues: 68 loop : -1.16 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 705 TYR 0.028 0.002 TYR A 695 PHE 0.029 0.003 PHE B 47 TRP 0.053 0.004 TRP A 503 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 5714) covalent geometry : angle 0.81749 / 0.44 ( 7983) hydrogen bonds : bond 0.05358 / 3.56 ( 193) hydrogen bonds : angle 6.51301 / 4.55 ( 500) metal coordination : bond 0.01439 / 0.69 ( 12) metal coordination : angle 6.36723 / 4.37 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1297.85 seconds wall clock time: 22 minutes 50.65 seconds (1370.65 seconds total)