Starting phenix.real_space_refine on Tue Feb 3 17:43:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yco_72779/02_2026/9yco_72779.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yco_72779/02_2026/9yco_72779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yco_72779/02_2026/9yco_72779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yco_72779/02_2026/9yco_72779.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yco_72779/02_2026/9yco_72779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yco_72779/02_2026/9yco_72779.map" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 31 5.49 5 Mg 1 5.21 5 S 44 5.16 5 C 3467 2.51 5 N 964 2.21 5 O 1133 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5645 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 971 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "B" Number of atoms: 4009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 4009 Classifications: {'peptide': 505} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 476} Chain breaks: 1 Chain: "C" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 659 Classifications: {'RNA': 31} Modifications used: {'rna3p_pur': 16, 'rna3p_pyr': 15} Link IDs: {'rna3p': 30} Chain breaks: 1 Chain: "A" 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} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 1, ' ZN': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 527 SG CYS A 74 44.009 28.983 45.324 1.00 57.25 S ATOM 553 SG CYS A 77 44.721 27.896 41.687 1.00 55.31 S ATOM 651 SG CYS A 90 45.622 25.533 44.591 1.00 69.04 S ATOM 859 SG CYS A 117 41.687 17.947 62.394 1.00104.49 S ATOM 880 SG CYS A 120 38.712 15.873 61.340 1.00105.91 S ATOM 949 SG CYS A 128 38.106 18.645 63.856 1.00105.07 S ATOM 963 SG CYS A 130 39.978 15.697 64.970 1.00121.87 S ATOM 2576 SG CYS B 207 60.505 55.447 56.110 1.00 63.34 S ATOM 2596 SG CYS B 210 60.805 59.085 57.182 1.00 72.83 S ATOM 2718 SG CYS B 226 61.279 58.201 53.540 1.00 63.78 S ATOM 3017 SG CYS B 261 56.560 71.171 23.419 1.00 60.35 S ATOM 3147 SG CYS B 279 54.887 69.807 26.705 1.00 61.83 S ATOM 4522 SG CYS B 448 75.826 107.004 58.736 1.00185.69 S ATOM 4605 SG CYS B 474 77.922 106.708 55.973 1.00181.96 S ATOM 4647 SG CYS B 481 78.360 103.252 59.223 1.00163.96 S Time building chain proxies: 1.03, per 1000 atoms: 0.18 Number of scatterers: 5645 At special positions: 0 Unit cell: (97.2712, 121.589, 79.5005, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 S 44 16.00 P 31 15.00 Mg 1 11.99 O 1133 8.00 N 964 7.00 C 3467 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: 0.40 Conformation dependent library (CDL) restraints added in 227.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 201 " pdb="ZN ZN A 201 " - pdb=" NE2 HIS A 83 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 77 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 90 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 74 " pdb=" ZN A 202 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 120 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 130 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 117 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 128 " pdb=" ZN B 602 " pdb="ZN ZN B 602 " - pdb=" ND1 HIS B 229 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 210 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 226 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 207 " pdb=" ZN B 603 " pdb="ZN ZN B 603 " - pdb=" NE2 HIS B 257 " pdb="ZN ZN B 603 " - pdb=" ND1 HIS B 264 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 279 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 261 " pdb=" ZN B 604 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 474 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 448 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 481 " Number of angles added : 13 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1188 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 8 sheets defined 31.0% alpha, 17.0% beta 15 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 removed outlier: 3.564A pdb=" N SER A 15 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU A 16 " --> pdb=" O SER A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 33 Processing helix chain 'A' and resid 74 through 80 Processing helix chain 'A' and resid 85 through 89 removed outlier: 3.626A pdb=" N VAL A 89 " --> pdb=" O VAL A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 106 through 114 Processing helix chain 'B' and resid 75 through 82 Processing helix chain 'B' and resid 143 through 155 removed outlier: 3.817A pdb=" N LYS B 147 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N HIS B 148 " --> pdb=" O GLN B 145 " (cutoff:3.500A) Proline residue: B 151 - end of helix Processing helix chain 'B' and resid 158 through 175 Processing helix chain 'B' and resid 187 through 196 removed outlier: 3.728A pdb=" N ALA B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 248 removed outlier: 3.509A pdb=" N GLY B 248 " --> pdb=" O GLN B 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 245 through 248' Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.520A pdb=" N ARG B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TYR B 260 " --> pdb=" O ASN B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 287 Processing helix chain 'B' and resid 301 through 323 removed outlier: 3.535A pdb=" N ARG B 310 " --> pdb=" O ASN B 306 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN B 315 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG B 318 " --> pdb=" O ARG B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 326 No H-bonds generated for 'chain 'B' and resid 324 through 326' Processing helix chain 'B' and resid 428 through 433 removed outlier: 3.518A pdb=" N PHE B 432 " --> pdb=" O VAL B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 477 Processing helix chain 'B' and resid 481 through 502 removed outlier: 3.665A pdb=" N ARG B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY B 502 " --> pdb=" O VAL B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 519 removed outlier: 3.775A pdb=" N ASN B 515 " --> pdb=" O ASP B 512 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TRP B 517 " --> pdb=" O TYR B 514 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER B 518 " --> pdb=" O ASN B 515 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR B 519 " --> pdb=" O LEU B 516 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 55 removed outlier: 4.362A pdb=" N VAL B 124 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 116 through 118 removed outlier: 7.023A pdb=" N ASN B 104 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA B 96 " --> pdb=" O ASN B 104 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ALA B 94 " --> pdb=" O PRO B 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 116 through 118 removed outlier: 7.023A pdb=" N ASN B 104 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA B 96 " --> pdb=" O ASN B 104 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ALA B 94 " --> pdb=" O PRO B 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 199 through 200 Processing sheet with id=AA6, first strand: chain 'B' and resid 361 through 362 removed outlier: 3.533A pdb=" N PHE B 351 " --> pdb=" O ASP B 331 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TRP B 381 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N CYS B 378 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N CYS B 395 " --> pdb=" O CYS B 378 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N PHE B 380 " --> pdb=" O CYS B 395 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N PHE B 397 " --> pdb=" O PHE B 380 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 406 through 408 Processing sheet with id=AA8, first strand: chain 'B' and resid 442 through 443 removed outlier: 6.763A pdb=" N TYR B 442 " --> pdb=" O ILE B 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 169 hydrogen bonds defined for protein. 453 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 35 hydrogen bonds 66 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 0.69 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1654 1.34 - 1.46: 1273 1.46 - 1.57: 2815 1.57 - 1.69: 60 1.69 - 1.81: 53 Bond restraints: 5855 Sorted by residual: bond pdb=" N ILE B 287 " pdb=" CA ILE B 287 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.06e-02 8.90e+03 1.34e+01 bond pdb=" N ASP B 37 " pdb=" CA ASP B 37 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.10e-02 8.26e+03 1.17e+01 bond pdb=" N VAL A 89 " pdb=" CA VAL A 89 " ideal model delta sigma weight residual 1.458 1.492 -0.033 1.12e-02 7.97e+03 8.90e+00 bond pdb=" N ILE A 99 " pdb=" CA ILE A 99 " ideal model delta sigma weight residual 1.462 1.490 -0.029 1.01e-02 9.80e+03 8.10e+00 bond pdb=" N ASP A 22 " pdb=" CA ASP A 22 " ideal model delta sigma weight residual 1.463 1.496 -0.033 1.22e-02 6.72e+03 7.43e+00 ... (remaining 5850 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 7511 1.26 - 2.53: 466 2.53 - 3.79: 103 3.79 - 5.06: 25 5.06 - 6.32: 7 Bond angle restraints: 8112 Sorted by residual: angle pdb=" N ASN B 496 " pdb=" CA ASN B 496 " pdb=" C ASN B 496 " ideal model delta sigma weight residual 111.07 106.96 4.11 1.07e+00 8.73e-01 1.47e+01 angle pdb=" N LEU B 379 " pdb=" CA LEU B 379 " pdb=" CB LEU B 379 " ideal model delta sigma weight residual 110.16 116.48 -6.32 1.65e+00 3.67e-01 1.47e+01 angle pdb=" CA ASP B 293 " pdb=" C ASP B 293 " pdb=" O ASP B 293 " ideal model delta sigma weight residual 122.36 118.04 4.32 1.21e+00 6.83e-01 1.28e+01 angle pdb=" C ASN B 382 " pdb=" CA ASN B 382 " pdb=" CB ASN B 382 " ideal model delta sigma weight residual 111.73 116.76 -5.03 1.42e+00 4.96e-01 1.25e+01 angle pdb=" N MET B 369 " pdb=" CA MET B 369 " pdb=" C MET B 369 " ideal model delta sigma weight residual 112.92 108.66 4.26 1.23e+00 6.61e-01 1.20e+01 ... (remaining 8107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 3153 17.35 - 34.71: 211 34.71 - 52.06: 58 52.06 - 69.42: 41 69.42 - 86.77: 9 Dihedral angle restraints: 3472 sinusoidal: 1616 harmonic: 1856 Sorted by residual: dihedral pdb=" CA ASP A 64 " pdb=" CB ASP A 64 " pdb=" CG ASP A 64 " pdb=" OD1 ASP A 64 " ideal model delta sinusoidal sigma weight residual -30.00 -88.06 58.06 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CB GLU B 487 " pdb=" CG GLU B 487 " pdb=" CD GLU B 487 " pdb=" OE1 GLU B 487 " ideal model delta sinusoidal sigma weight residual 0.00 86.23 -86.23 1 3.00e+01 1.11e-03 9.96e+00 dihedral pdb=" CG ARG B 84 " pdb=" CD ARG B 84 " pdb=" NE ARG B 84 " pdb=" CZ ARG B 84 " ideal model delta sinusoidal sigma weight residual 90.00 133.11 -43.11 2 1.50e+01 4.44e-03 9.96e+00 ... (remaining 3469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 793 0.069 - 0.138: 95 0.138 - 0.208: 14 0.208 - 0.277: 5 0.277 - 0.346: 1 Chirality restraints: 908 Sorted by residual: chirality pdb=" CG LEU B 379 " pdb=" CB LEU B 379 " pdb=" CD1 LEU B 379 " pdb=" CD2 LEU B 379 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA ILE A 99 " pdb=" N ILE A 99 " pdb=" C ILE A 99 " pdb=" CB ILE A 99 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ILE B 294 " pdb=" N ILE B 294 " pdb=" C ILE B 294 " pdb=" CB ILE B 294 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 905 not shown) Planarity restraints: 931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 289 " 0.272 9.50e-02 1.11e+02 1.22e-01 9.10e+00 pdb=" NE ARG B 289 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 289 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG B 289 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 289 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 508 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.89e+00 pdb=" C TYR B 508 " -0.038 2.00e-02 2.50e+03 pdb=" O TYR B 508 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS B 509 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 19 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO B 20 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 20 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 20 " 0.025 5.00e-02 4.00e+02 ... (remaining 928 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 8 2.38 - 3.01: 2841 3.01 - 3.64: 8466 3.64 - 4.27: 13621 4.27 - 4.90: 21608 Nonbonded interactions: 46544 Sorted by model distance: nonbonded pdb=" OD2 ASP B 273 " pdb="MG MG B 601 " model vdw 1.749 2.170 nonbonded pdb=" OE2 GLU B 92 " pdb="MG MG B 601 " model vdw 1.925 2.170 nonbonded pdb=" OD2 ASP B 90 " pdb="MG MG B 601 " model vdw 2.008 2.170 nonbonded pdb=" OP1 G C 39 " pdb="MG MG B 601 " model vdw 2.280 2.170 nonbonded pdb=" OG1 THR B 75 " pdb=" OE2 GLU B 78 " model vdw 2.321 3.040 ... (remaining 46539 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.810 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 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 : 0.008 0.535 5874 Z= 0.376 Angle : 0.739 6.319 8125 Z= 0.471 Chirality : 0.051 0.346 908 Planarity : 0.006 0.122 931 Dihedral : 15.187 86.770 2284 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.31), residues: 630 helix: -0.82 (0.36), residues: 153 sheet: -0.32 (0.55), residues: 81 loop : -0.49 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 105 TYR 0.025 0.001 TYR B 488 PHE 0.008 0.001 PHE B 73 TRP 0.007 0.001 TRP A 123 HIS 0.008 0.001 HIS B 420 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 5855) covalent geometry : angle 0.73260 ( 8112) hydrogen bonds : bond 0.15478 ( 198) hydrogen bonds : angle 6.05605 ( 519) metal coordination : bond 0.12281 ( 19) metal coordination : angle 2.52130 ( 13) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.115 Fit side-chains revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7843 (m-30) cc_final: 0.7447 (m-30) REVERT: A 57 VAL cc_start: 0.8485 (m) cc_final: 0.8191 (t) REVERT: A 104 VAL cc_start: 0.8091 (m) cc_final: 0.7889 (t) REVERT: A 121 GLN cc_start: 0.7740 (mm110) cc_final: 0.7513 (mm110) REVERT: B 71 LYS cc_start: 0.8405 (ttpp) cc_final: 0.8203 (ttpp) REVERT: B 97 SER cc_start: 0.7658 (p) cc_final: 0.7091 (t) REVERT: B 164 ARG cc_start: 0.7974 (mtt180) cc_final: 0.7736 (mtt90) REVERT: B 250 VAL cc_start: 0.8537 (p) cc_final: 0.8291 (m) REVERT: B 295 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7886 (mt-10) REVERT: B 369 MET cc_start: 0.6110 (mmt) cc_final: 0.5902 (mpp) REVERT: B 398 ASP cc_start: 0.8186 (t70) cc_final: 0.7887 (t0) REVERT: B 419 LYS cc_start: 0.8683 (ttpp) cc_final: 0.8054 (ttpp) outliers start: 0 outliers final: 1 residues processed: 120 average time/residue: 0.4011 time to fit residues: 50.4788 Evaluate side-chains 101 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 377 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 0.0970 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 0.3980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN B 272 ASN B 382 ASN B 496 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.151400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.117523 restraints weight = 7474.059| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.86 r_work: 0.3326 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5874 Z= 0.154 Angle : 0.510 6.322 8125 Z= 0.266 Chirality : 0.042 0.165 908 Planarity : 0.004 0.039 931 Dihedral : 12.864 73.740 1167 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.02 % Allowed : 12.50 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.32), residues: 630 helix: 0.11 (0.38), residues: 157 sheet: -0.38 (0.50), residues: 94 loop : -0.19 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 81 TYR 0.020 0.001 TYR B 488 PHE 0.011 0.001 PHE B 380 TRP 0.006 0.001 TRP B 381 HIS 0.006 0.002 HIS B 484 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 5855) covalent geometry : angle 0.50548 ( 8112) hydrogen bonds : bond 0.04312 ( 198) hydrogen bonds : angle 4.34668 ( 519) metal coordination : bond 0.01114 ( 19) metal coordination : angle 1.77766 ( 13) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.116 Fit side-chains revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7880 (m-30) cc_final: 0.7579 (m-30) REVERT: A 121 GLN cc_start: 0.8006 (mm110) cc_final: 0.7770 (mp10) REVERT: B 71 LYS cc_start: 0.8359 (ttpp) cc_final: 0.8142 (ttpp) REVERT: B 76 ARG cc_start: 0.8079 (mmm-85) cc_final: 0.7567 (ttt180) REVERT: B 97 SER cc_start: 0.7630 (p) cc_final: 0.7069 (t) REVERT: B 116 ASN cc_start: 0.8323 (m110) cc_final: 0.8038 (m110) REVERT: B 164 ARG cc_start: 0.8255 (mtt180) cc_final: 0.7973 (mtt90) REVERT: B 295 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7797 (mt-10) REVERT: B 419 LYS cc_start: 0.8789 (ttpp) cc_final: 0.8027 (ttpp) REVERT: B 513 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7898 (pp) outliers start: 11 outliers final: 3 residues processed: 100 average time/residue: 0.3878 time to fit residues: 40.6350 Evaluate side-chains 100 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 513 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 2 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 chunk 51 optimal weight: 0.4980 chunk 57 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 ASN B 120 GLN B 211 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.150425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.117123 restraints weight = 7404.302| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.83 r_work: 0.3325 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5874 Z= 0.222 Angle : 0.546 6.461 8125 Z= 0.282 Chirality : 0.044 0.156 908 Planarity : 0.004 0.042 931 Dihedral : 12.935 73.891 1165 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.84 % Allowed : 13.42 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.33), residues: 630 helix: 0.20 (0.39), residues: 155 sheet: -0.52 (0.50), residues: 96 loop : -0.14 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 81 TYR 0.012 0.002 TYR B 488 PHE 0.015 0.002 PHE B 432 TRP 0.009 0.001 TRP B 292 HIS 0.007 0.002 HIS B 349 Details of bonding type rmsd covalent geometry : bond 0.00528 ( 5855) covalent geometry : angle 0.53701 ( 8112) hydrogen bonds : bond 0.04583 ( 198) hydrogen bonds : angle 4.30494 ( 519) metal coordination : bond 0.01189 ( 19) metal coordination : angle 2.58074 ( 13) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7843 (m-30) cc_final: 0.7470 (m-30) REVERT: B 71 LYS cc_start: 0.8233 (ttpp) cc_final: 0.8010 (ttpp) REVERT: B 76 ARG cc_start: 0.8044 (mmm-85) cc_final: 0.7535 (ttt180) REVERT: B 97 SER cc_start: 0.7614 (p) cc_final: 0.7109 (t) REVERT: B 164 ARG cc_start: 0.8222 (mtt180) cc_final: 0.7957 (mtt90) REVERT: B 269 VAL cc_start: 0.7333 (OUTLIER) cc_final: 0.7049 (t) REVERT: B 513 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7985 (pp) outliers start: 10 outliers final: 4 residues processed: 95 average time/residue: 0.4592 time to fit residues: 45.6097 Evaluate side-chains 95 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 513 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 9 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 7 optimal weight: 0.3980 chunk 16 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 0.0070 overall best weight: 0.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN B 211 ASN B 420 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.151389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.118269 restraints weight = 7459.630| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.83 r_work: 0.3340 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5874 Z= 0.121 Angle : 0.479 6.483 8125 Z= 0.246 Chirality : 0.040 0.148 908 Planarity : 0.004 0.041 931 Dihedral : 12.835 73.753 1165 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.10 % Allowed : 13.97 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.34), residues: 630 helix: 0.64 (0.41), residues: 155 sheet: -0.80 (0.50), residues: 96 loop : -0.04 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 13 TYR 0.011 0.001 TYR B 488 PHE 0.009 0.001 PHE B 380 TRP 0.008 0.001 TRP B 292 HIS 0.005 0.001 HIS B 349 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 5855) covalent geometry : angle 0.47351 ( 8112) hydrogen bonds : bond 0.03656 ( 198) hydrogen bonds : angle 4.05202 ( 519) metal coordination : bond 0.00642 ( 19) metal coordination : angle 1.88043 ( 13) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7926 (m-30) cc_final: 0.7706 (m-30) REVERT: A 124 ILE cc_start: 0.8787 (mt) cc_final: 0.8483 (tp) REVERT: B 50 PRO cc_start: 0.8262 (Cg_endo) cc_final: 0.7992 (Cg_exo) REVERT: B 71 LYS cc_start: 0.8243 (ttpp) cc_final: 0.8002 (ttpp) REVERT: B 76 ARG cc_start: 0.8089 (mmm-85) cc_final: 0.7614 (ttt180) REVERT: B 97 SER cc_start: 0.7610 (p) cc_final: 0.7094 (t) REVERT: B 164 ARG cc_start: 0.8199 (mtt180) cc_final: 0.7926 (mtt90) REVERT: B 269 VAL cc_start: 0.7181 (OUTLIER) cc_final: 0.6898 (t) REVERT: B 332 ILE cc_start: 0.7720 (mt) cc_final: 0.7458 (tp) REVERT: B 513 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7870 (pp) outliers start: 6 outliers final: 3 residues processed: 96 average time/residue: 0.4687 time to fit residues: 47.0477 Evaluate side-chains 97 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 513 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 1 optimal weight: 0.1980 chunk 8 optimal weight: 0.0970 chunk 54 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 0.0050 chunk 37 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 21 optimal weight: 0.4980 chunk 24 optimal weight: 0.3980 overall best weight: 0.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.152388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.119188 restraints weight = 7568.424| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.85 r_work: 0.3343 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5874 Z= 0.103 Angle : 0.473 8.134 8125 Z= 0.242 Chirality : 0.040 0.144 908 Planarity : 0.004 0.039 931 Dihedral : 12.807 73.702 1165 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.47 % Allowed : 14.34 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.34), residues: 630 helix: 0.86 (0.41), residues: 157 sheet: -0.93 (0.51), residues: 87 loop : 0.05 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 13 TYR 0.011 0.001 TYR B 488 PHE 0.009 0.001 PHE B 380 TRP 0.007 0.001 TRP B 292 HIS 0.005 0.001 HIS B 349 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 5855) covalent geometry : angle 0.46907 ( 8112) hydrogen bonds : bond 0.03354 ( 198) hydrogen bonds : angle 3.94240 ( 519) metal coordination : bond 0.00507 ( 19) metal coordination : angle 1.61995 ( 13) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7906 (m-30) cc_final: 0.7690 (m-30) REVERT: A 124 ILE cc_start: 0.8800 (mt) cc_final: 0.8230 (OUTLIER) REVERT: B 50 PRO cc_start: 0.8166 (Cg_endo) cc_final: 0.7917 (Cg_exo) REVERT: B 71 LYS cc_start: 0.8238 (ttpp) cc_final: 0.7984 (ttpp) REVERT: B 76 ARG cc_start: 0.8113 (mmm-85) cc_final: 0.7643 (ttt180) REVERT: B 164 ARG cc_start: 0.8136 (mtt180) cc_final: 0.7920 (mtt90) REVERT: B 263 VAL cc_start: 0.8550 (t) cc_final: 0.8266 (p) REVERT: B 269 VAL cc_start: 0.7063 (OUTLIER) cc_final: 0.6743 (t) REVERT: B 332 ILE cc_start: 0.7719 (mt) cc_final: 0.7469 (tp) REVERT: B 513 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7865 (pp) outliers start: 8 outliers final: 5 residues processed: 99 average time/residue: 0.4526 time to fit residues: 46.8909 Evaluate side-chains 97 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 513 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 0.0770 chunk 20 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 62 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 0.0170 chunk 32 optimal weight: 0.5980 chunk 36 optimal weight: 0.0040 chunk 65 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.152558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.119491 restraints weight = 7445.451| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.83 r_work: 0.3344 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5874 Z= 0.112 Angle : 0.473 7.080 8125 Z= 0.241 Chirality : 0.040 0.143 908 Planarity : 0.004 0.039 931 Dihedral : 12.811 73.732 1165 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.65 % Allowed : 15.62 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.34), residues: 630 helix: 0.94 (0.41), residues: 157 sheet: -1.02 (0.52), residues: 87 loop : 0.09 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 81 TYR 0.011 0.001 TYR B 488 PHE 0.007 0.001 PHE B 397 TRP 0.007 0.001 TRP B 292 HIS 0.005 0.001 HIS B 349 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 5855) covalent geometry : angle 0.46763 ( 8112) hydrogen bonds : bond 0.03310 ( 198) hydrogen bonds : angle 3.92382 ( 519) metal coordination : bond 0.00588 ( 19) metal coordination : angle 1.86761 ( 13) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7912 (m-30) cc_final: 0.7683 (m-30) REVERT: A 121 GLN cc_start: 0.8071 (mp10) cc_final: 0.7660 (mp-120) REVERT: A 124 ILE cc_start: 0.8810 (mt) cc_final: 0.8217 (OUTLIER) REVERT: B 50 PRO cc_start: 0.8170 (Cg_endo) cc_final: 0.7908 (Cg_exo) REVERT: B 71 LYS cc_start: 0.8233 (ttpp) cc_final: 0.7979 (ttpp) REVERT: B 76 ARG cc_start: 0.8079 (mmm-85) cc_final: 0.7490 (ttt180) REVERT: B 164 ARG cc_start: 0.8135 (mtt180) cc_final: 0.7884 (mtt90) REVERT: B 263 VAL cc_start: 0.8557 (t) cc_final: 0.8280 (p) REVERT: B 269 VAL cc_start: 0.6996 (OUTLIER) cc_final: 0.6707 (t) REVERT: B 369 MET cc_start: 0.6561 (mpp) cc_final: 0.6339 (mpm) REVERT: B 513 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7844 (pp) outliers start: 9 outliers final: 6 residues processed: 101 average time/residue: 0.4957 time to fit residues: 52.1653 Evaluate side-chains 100 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 513 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 56 optimal weight: 0.0670 chunk 24 optimal weight: 0.1980 chunk 62 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 1 optimal weight: 0.0980 chunk 52 optimal weight: 0.8980 chunk 41 optimal weight: 0.0970 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.2516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 HIS B 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.152529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.119374 restraints weight = 7603.569| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.88 r_work: 0.3346 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5874 Z= 0.104 Angle : 0.469 6.290 8125 Z= 0.239 Chirality : 0.040 0.140 908 Planarity : 0.004 0.038 931 Dihedral : 12.808 73.711 1165 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.47 % Allowed : 16.18 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.34), residues: 630 helix: 1.01 (0.41), residues: 157 sheet: -1.05 (0.52), residues: 87 loop : 0.15 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 84 TYR 0.010 0.001 TYR B 488 PHE 0.009 0.001 PHE B 380 TRP 0.006 0.001 TRP B 292 HIS 0.005 0.001 HIS B 349 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 5855) covalent geometry : angle 0.46450 ( 8112) hydrogen bonds : bond 0.03184 ( 198) hydrogen bonds : angle 3.87639 ( 519) metal coordination : bond 0.00552 ( 19) metal coordination : angle 1.62933 ( 13) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7912 (m-30) cc_final: 0.7684 (m-30) REVERT: A 121 GLN cc_start: 0.8056 (mp10) cc_final: 0.7605 (mp-120) REVERT: A 124 ILE cc_start: 0.8819 (mt) cc_final: 0.8234 (OUTLIER) REVERT: B 50 PRO cc_start: 0.8139 (Cg_endo) cc_final: 0.7921 (Cg_exo) REVERT: B 71 LYS cc_start: 0.8236 (ttpp) cc_final: 0.7995 (ttpp) REVERT: B 76 ARG cc_start: 0.8076 (mmm-85) cc_final: 0.7466 (ttt180) REVERT: B 128 GLU cc_start: 0.7362 (pm20) cc_final: 0.7144 (pm20) REVERT: B 164 ARG cc_start: 0.8165 (mtt180) cc_final: 0.7932 (mtt90) REVERT: B 259 ARG cc_start: 0.8675 (ttm-80) cc_final: 0.8432 (ttp-170) REVERT: B 263 VAL cc_start: 0.8559 (t) cc_final: 0.8283 (p) REVERT: B 269 VAL cc_start: 0.6926 (OUTLIER) cc_final: 0.6634 (t) REVERT: B 308 CYS cc_start: 0.6932 (m) cc_final: 0.6481 (m) REVERT: B 332 ILE cc_start: 0.7746 (mt) cc_final: 0.7505 (tp) REVERT: B 496 ASN cc_start: 0.8011 (m-40) cc_final: 0.7803 (m-40) REVERT: B 513 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7839 (pp) outliers start: 8 outliers final: 6 residues processed: 99 average time/residue: 0.4179 time to fit residues: 43.3208 Evaluate side-chains 103 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 513 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 27 optimal weight: 0.8980 chunk 47 optimal weight: 0.1980 chunk 22 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 10 optimal weight: 0.0970 chunk 50 optimal weight: 5.9990 chunk 19 optimal weight: 0.0980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.152047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.119062 restraints weight = 7448.863| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.83 r_work: 0.3339 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5874 Z= 0.139 Angle : 0.496 7.879 8125 Z= 0.251 Chirality : 0.041 0.158 908 Planarity : 0.004 0.038 931 Dihedral : 12.838 73.797 1165 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.65 % Allowed : 16.18 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.34), residues: 630 helix: 0.99 (0.41), residues: 157 sheet: -1.01 (0.50), residues: 93 loop : 0.10 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 81 TYR 0.012 0.001 TYR B 488 PHE 0.009 0.001 PHE B 432 TRP 0.009 0.001 TRP B 292 HIS 0.005 0.001 HIS B 349 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 5855) covalent geometry : angle 0.49044 ( 8112) hydrogen bonds : bond 0.03459 ( 198) hydrogen bonds : angle 3.96767 ( 519) metal coordination : bond 0.00735 ( 19) metal coordination : angle 1.89696 ( 13) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.115 Fit side-chains revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7915 (m-30) cc_final: 0.7689 (m-30) REVERT: A 124 ILE cc_start: 0.8800 (mt) cc_final: 0.8219 (OUTLIER) REVERT: B 50 PRO cc_start: 0.8160 (Cg_endo) cc_final: 0.7956 (Cg_exo) REVERT: B 71 LYS cc_start: 0.8239 (ttpp) cc_final: 0.7991 (ttpp) REVERT: B 76 ARG cc_start: 0.8074 (mmm-85) cc_final: 0.7498 (ttt180) REVERT: B 128 GLU cc_start: 0.7388 (pm20) cc_final: 0.7144 (pm20) REVERT: B 164 ARG cc_start: 0.8133 (mtt180) cc_final: 0.7917 (mtt90) REVERT: B 259 ARG cc_start: 0.8661 (ttm-80) cc_final: 0.8405 (ttp-170) REVERT: B 269 VAL cc_start: 0.7046 (OUTLIER) cc_final: 0.6754 (t) REVERT: B 308 CYS cc_start: 0.6935 (m) cc_final: 0.6474 (m) REVERT: B 332 ILE cc_start: 0.7722 (mt) cc_final: 0.7451 (tp) REVERT: B 369 MET cc_start: 0.6534 (mpp) cc_final: 0.6290 (mpm) REVERT: B 513 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7857 (pp) outliers start: 9 outliers final: 7 residues processed: 103 average time/residue: 0.4243 time to fit residues: 45.7516 Evaluate side-chains 104 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 513 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 29 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 45 optimal weight: 0.0970 chunk 16 optimal weight: 0.3980 chunk 39 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 19 optimal weight: 0.0870 chunk 1 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN B 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.152095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.118942 restraints weight = 7512.091| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.86 r_work: 0.3339 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5874 Z= 0.132 Angle : 0.489 7.357 8125 Z= 0.248 Chirality : 0.040 0.152 908 Planarity : 0.004 0.039 931 Dihedral : 12.830 73.768 1165 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.65 % Allowed : 15.99 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.34), residues: 630 helix: 0.99 (0.41), residues: 157 sheet: -1.14 (0.52), residues: 87 loop : 0.10 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 84 TYR 0.012 0.001 TYR B 488 PHE 0.008 0.001 PHE B 432 TRP 0.007 0.001 TRP B 292 HIS 0.006 0.001 HIS B 349 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 5855) covalent geometry : angle 0.48345 ( 8112) hydrogen bonds : bond 0.03371 ( 198) hydrogen bonds : angle 3.96807 ( 519) metal coordination : bond 0.00725 ( 19) metal coordination : angle 1.86782 ( 13) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7926 (m-30) cc_final: 0.7702 (m-30) REVERT: A 124 ILE cc_start: 0.8793 (mt) cc_final: 0.8230 (OUTLIER) REVERT: B 71 LYS cc_start: 0.8231 (ttpp) cc_final: 0.7994 (ttpp) REVERT: B 76 ARG cc_start: 0.8096 (mmm-85) cc_final: 0.7523 (ttt180) REVERT: B 128 GLU cc_start: 0.7373 (pm20) cc_final: 0.7125 (pm20) REVERT: B 259 ARG cc_start: 0.8671 (ttm-80) cc_final: 0.8424 (ttp-170) REVERT: B 269 VAL cc_start: 0.6983 (OUTLIER) cc_final: 0.6714 (t) REVERT: B 332 ILE cc_start: 0.7758 (mt) cc_final: 0.7481 (tp) REVERT: B 513 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7848 (pp) outliers start: 9 outliers final: 7 residues processed: 99 average time/residue: 0.4579 time to fit residues: 47.4853 Evaluate side-chains 101 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 513 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 34 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 41 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.150754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.117676 restraints weight = 7579.583| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.86 r_work: 0.3322 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5874 Z= 0.200 Angle : 0.542 7.605 8125 Z= 0.276 Chirality : 0.043 0.171 908 Planarity : 0.005 0.054 931 Dihedral : 12.889 73.902 1165 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.29 % Allowed : 16.73 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.34), residues: 630 helix: 0.87 (0.41), residues: 155 sheet: -1.03 (0.51), residues: 93 loop : 0.07 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 164 TYR 0.014 0.002 TYR B 488 PHE 0.011 0.002 PHE B 432 TRP 0.008 0.001 TRP B 292 HIS 0.007 0.001 HIS B 349 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 5855) covalent geometry : angle 0.53441 ( 8112) hydrogen bonds : bond 0.03896 ( 198) hydrogen bonds : angle 4.10655 ( 519) metal coordination : bond 0.01031 ( 19) metal coordination : angle 2.35254 ( 13) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7921 (m-30) cc_final: 0.7619 (m-30) REVERT: A 124 ILE cc_start: 0.8792 (mt) cc_final: 0.8214 (OUTLIER) REVERT: B 76 ARG cc_start: 0.8101 (mmm-85) cc_final: 0.7636 (ttt180) REVERT: B 128 GLU cc_start: 0.7386 (pm20) cc_final: 0.7157 (pm20) REVERT: B 259 ARG cc_start: 0.8665 (ttm-80) cc_final: 0.8410 (ttp-170) REVERT: B 269 VAL cc_start: 0.7127 (OUTLIER) cc_final: 0.6711 (t) REVERT: B 332 ILE cc_start: 0.7773 (mt) cc_final: 0.7477 (tp) outliers start: 7 outliers final: 8 residues processed: 96 average time/residue: 0.4395 time to fit residues: 44.2031 Evaluate side-chains 99 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 513 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 61 optimal weight: 0.1980 chunk 3 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 chunk 16 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.151498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.118520 restraints weight = 7452.580| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.84 r_work: 0.3333 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5874 Z= 0.149 Angle : 0.518 7.670 8125 Z= 0.263 Chirality : 0.041 0.152 908 Planarity : 0.005 0.048 931 Dihedral : 12.866 73.785 1165 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.29 % Allowed : 16.91 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.34), residues: 630 helix: 0.90 (0.41), residues: 157 sheet: -1.20 (0.52), residues: 87 loop : 0.04 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 164 TYR 0.013 0.001 TYR B 488 PHE 0.009 0.001 PHE B 432 TRP 0.008 0.001 TRP B 292 HIS 0.006 0.001 HIS B 349 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 5855) covalent geometry : angle 0.51260 ( 8112) hydrogen bonds : bond 0.03551 ( 198) hydrogen bonds : angle 4.06599 ( 519) metal coordination : bond 0.00799 ( 19) metal coordination : angle 1.96465 ( 13) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1977.10 seconds wall clock time: 34 minutes 23.89 seconds (2063.89 seconds total)