Starting phenix.real_space_refine on Tue Aug 4 18:07:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ycn_72778/08_2026/9ycn_72778.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ycn_72778/08_2026/9ycn_72778.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/9ycn_72778/08_2026/9ycn_72778.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ycn_72778/08_2026/9ycn_72778.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ycn_72778/08_2026/9ycn_72778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ycn_72778/08_2026/9ycn_72778.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= 0.013 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 1132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 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: 5644 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: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 658 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 44.007 28.944 45.309 1.00 51.85 S ATOM 553 SG CYS A 77 44.708 27.791 41.704 1.00 54.34 S ATOM 651 SG CYS A 90 45.513 25.477 44.644 1.00 62.19 S ATOM 859 SG CYS A 117 41.831 17.775 62.435 1.00100.84 S ATOM 880 SG CYS A 120 38.868 15.687 61.375 1.00100.16 S ATOM 949 SG CYS A 128 38.300 18.653 63.703 1.00109.46 S ATOM 963 SG CYS A 130 40.102 15.563 64.982 1.00115.71 S ATOM 2576 SG CYS B 207 60.627 55.273 56.066 1.00 49.65 S ATOM 2596 SG CYS B 210 61.252 58.847 57.233 1.00 60.09 S ATOM 2718 SG CYS B 226 61.231 58.071 53.514 1.00 51.66 S ATOM 3017 SG CYS B 261 56.620 70.926 23.452 1.00 49.63 S ATOM 3147 SG CYS B 279 54.728 69.570 26.632 1.00 55.12 S ATOM 4522 SG CYS B 448 76.256 106.730 57.987 1.00191.50 S ATOM 4605 SG CYS B 474 79.215 105.765 55.824 1.00189.42 S ATOM 4647 SG CYS B 481 77.690 103.160 58.187 1.00188.54 S Time building chain proxies: 1.16, per 1000 atoms: 0.21 Number of scatterers: 5644 At special positions: 0 Unit cell: (96.3359, 120.654, 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 1132 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: 0.47 Conformation dependent library (CDL) restraints added in 109.3 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 90 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 74 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 77 " pdb=" ZN A 202 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 120 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 117 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 130 " 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=" ND1 HIS B 484 " 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 : 16 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 30.5% alpha, 17.3% beta 15 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 removed outlier: 3.550A pdb=" N SER A 15 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 3.679A 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: 3.739A 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 30 through 34 Processing helix chain 'B' and resid 75 through 82 Processing helix chain 'B' and resid 146 through 155 Proline residue: B 151 - end of helix Processing helix chain 'B' and resid 158 through 175 removed outlier: 3.726A pdb=" N ARG B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 removed outlier: 3.877A pdb=" N ALA B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 248 removed outlier: 3.539A 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 259 removed outlier: 3.518A pdb=" N ASN B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 287 Processing helix chain 'B' and resid 301 through 323 Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 472 through 477 Processing helix chain 'B' and resid 481 through 502 Processing helix chain 'B' and resid 512 through 519 removed outlier: 3.930A 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: 4.275A pdb=" N VAL B 124 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 115 through 118 removed outlier: 3.630A pdb=" N VAL B 115 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ASN B 104 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA B 96 " --> pdb=" O ASN B 104 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ALA B 94 " --> pdb=" O PRO B 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 115 through 118 removed outlier: 3.630A pdb=" N VAL B 115 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ASN B 104 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA B 96 " --> pdb=" O ASN B 104 " (cutoff:3.500A) removed outlier: 5.242A 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: 6.599A pdb=" N LYS B 328 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU B 379 " --> pdb=" O LYS B 328 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TYR B 330 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N TRP B 381 " --> pdb=" O TYR B 330 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE B 332 " --> pdb=" O TRP B 381 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS B 395 " --> 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: 5.998A pdb=" N TYR B 442 " --> pdb=" O ILE B 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 178 hydrogen bonds defined for protein. 468 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 35 hydrogen bonds 66 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 1.26 Time building geometry restraints manager: 0.60 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: 1641 1.34 - 1.46: 1289 1.46 - 1.57: 2811 1.57 - 1.69: 60 1.69 - 1.81: 53 Bond restraints: 5854 Sorted by residual: bond pdb=" N ASP B 37 " pdb=" CA ASP B 37 " ideal model delta sigma weight residual 1.458 1.501 -0.043 1.12e-02 7.97e+03 1.48e+01 bond pdb=" N VAL B 480 " pdb=" CA VAL B 480 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 9.83e+00 bond pdb=" N VAL B 417 " pdb=" CA VAL B 417 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.27e-02 6.20e+03 8.08e+00 bond pdb=" N HIS B 420 " pdb=" CA HIS B 420 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.18e-02 7.18e+03 7.91e+00 bond pdb=" N ASP A 64 " pdb=" CA ASP A 64 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.16e-02 7.43e+03 7.26e+00 ... (remaining 5849 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 7382 1.21 - 2.42: 523 2.42 - 3.62: 164 3.62 - 4.83: 26 4.83 - 6.04: 15 Bond angle restraints: 8110 Sorted by residual: angle pdb=" N VAL B 263 " pdb=" CA VAL B 263 " pdb=" C VAL B 263 " ideal model delta sigma weight residual 112.96 108.96 4.00 1.00e+00 1.00e+00 1.60e+01 angle pdb=" C GLU B 302 " pdb=" CA GLU B 302 " pdb=" CB GLU B 302 " ideal model delta sigma weight residual 110.88 116.65 -5.77 1.57e+00 4.06e-01 1.35e+01 angle pdb=" C ARG B 139 " pdb=" N PRO B 140 " pdb=" CA PRO B 140 " ideal model delta sigma weight residual 119.66 122.15 -2.49 7.30e-01 1.88e+00 1.17e+01 angle pdb=" O5' U C 13 " pdb=" C5' U C 13 " pdb=" C4' U C 13 " ideal model delta sigma weight residual 109.40 112.12 -2.72 8.00e-01 1.56e+00 1.15e+01 angle pdb=" N ILE B 340 " pdb=" CA ILE B 340 " pdb=" C ILE B 340 " ideal model delta sigma weight residual 111.45 108.35 3.10 9.30e-01 1.16e+00 1.11e+01 ... (remaining 8105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.32: 3091 15.32 - 30.63: 249 30.63 - 45.94: 72 45.94 - 61.26: 32 61.26 - 76.57: 22 Dihedral angle restraints: 3466 sinusoidal: 1610 harmonic: 1856 Sorted by residual: dihedral pdb=" CA ASP B 343 " pdb=" C ASP B 343 " pdb=" N PRO B 344 " pdb=" CA PRO B 344 " ideal model delta harmonic sigma weight residual 180.00 161.65 18.35 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA ALA B 187 " pdb=" C ALA B 187 " pdb=" N HIS B 188 " pdb=" CA HIS B 188 " ideal model delta harmonic sigma weight residual 180.00 -163.46 -16.54 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CG ARG B 163 " pdb=" CD ARG B 163 " pdb=" NE ARG B 163 " pdb=" CZ ARG B 163 " ideal model delta sinusoidal sigma weight residual 90.00 134.44 -44.44 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 3463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 804 0.095 - 0.189: 99 0.189 - 0.284: 0 0.284 - 0.379: 0 0.379 - 0.473: 5 Chirality restraints: 908 Sorted by residual: chirality pdb=" P A C 10 " pdb=" OP1 A C 10 " pdb=" OP2 A C 10 " pdb=" O5' A C 10 " both_signs ideal model delta sigma weight residual True 2.41 -2.88 -0.47 2.00e-01 2.50e+01 5.60e+00 chirality pdb=" P G C 8 " pdb=" OP1 G C 8 " pdb=" OP2 G C 8 " pdb=" O5' G C 8 " both_signs ideal model delta sigma weight residual True 2.41 -2.88 -0.47 2.00e-01 2.50e+01 5.55e+00 chirality pdb=" P G C 9 " pdb=" OP1 G C 9 " pdb=" OP2 G C 9 " pdb=" O5' G C 9 " both_signs ideal model delta sigma weight residual True 2.41 -2.87 -0.46 2.00e-01 2.50e+01 5.29e+00 ... (remaining 905 not shown) Planarity restraints: 931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP B 292 " 0.011 2.00e-02 2.50e+03 2.32e-02 5.39e+00 pdb=" C TRP B 292 " -0.040 2.00e-02 2.50e+03 pdb=" O TRP B 292 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP B 293 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 82 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.59e+00 pdb=" CD GLN B 82 " -0.037 2.00e-02 2.50e+03 pdb=" OE1 GLN B 82 " 0.014 2.00e-02 2.50e+03 pdb=" NE2 GLN B 82 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 440 " 0.008 2.00e-02 2.50e+03 1.44e-02 3.63e+00 pdb=" CG PHE B 440 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE B 440 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE B 440 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE B 440 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 440 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 440 " -0.002 2.00e-02 2.50e+03 ... (remaining 928 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 25 2.53 - 3.12: 4015 3.12 - 3.72: 8921 3.72 - 4.31: 13071 4.31 - 4.90: 20676 Nonbonded interactions: 46708 Sorted by model distance: nonbonded pdb=" OE2 GLU B 92 " pdb="MG MG B 601 " model vdw 1.940 2.170 nonbonded pdb=" OD2 ASP B 90 " pdb="MG MG B 601 " model vdw 2.049 2.170 nonbonded pdb=" O LYS B 203 " pdb=" OH TYR B 237 " model vdw 2.266 3.040 nonbonded pdb=" OD2 ASP B 273 " pdb="MG MG B 601 " model vdw 2.281 2.170 nonbonded pdb=" ND2 ASN A 4 " pdb=" OP1 U C 30 " model vdw 2.324 3.120 ... (remaining 46703 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: 2.990 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.940 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: 0.000 Load rotamer database and sin/cos tables:8.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 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 5874 Z= 0.313 Angle : 0.790 6.038 8126 Z= 0.521 Chirality : 0.062 0.473 908 Planarity : 0.005 0.036 931 Dihedral : 14.526 76.572 2278 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % 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: -0.53 (0.33), residues: 630 helix: -0.37 (0.39), residues: 161 sheet: -0.05 (0.52), residues: 93 loop : -0.34 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 105 TYR 0.025 0.001 TYR B 491 PHE 0.032 0.002 PHE B 440 TRP 0.011 0.001 TRP B 381 HIS 0.004 0.001 HIS B 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.31 ( 5854) covalent geometry : angle 0.78960 / 0.52 ( 8110) hydrogen bonds : bond 0.14822 / 8.77 ( 206) hydrogen bonds : angle 5.77412 / 3.81 ( 534) metal coordination : bond 0.00429 / 0.26 ( 20) metal coordination : angle 1.04888 / 0.61 ( 16) *********************** 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 113 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.197 Fit side-chains REVERT: A 60 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7287 (mm-30) REVERT: A 89 VAL cc_start: 0.8062 (t) cc_final: 0.7802 (m) REVERT: A 128 CYS cc_start: 0.7051 (t) cc_final: 0.6818 (t) REVERT: A 129 ASN cc_start: 0.7702 (m110) cc_final: 0.7476 (m110) REVERT: B 128 GLU cc_start: 0.7719 (pm20) cc_final: 0.7441 (pm20) REVERT: B 168 GLN cc_start: 0.8477 (tp-100) cc_final: 0.8114 (tp40) REVERT: B 176 LYS cc_start: 0.7901 (mmpt) cc_final: 0.7647 (mmpt) REVERT: B 262 SER cc_start: 0.8295 (m) cc_final: 0.7883 (p) REVERT: B 379 LEU cc_start: 0.7109 (mm) cc_final: 0.6866 (mp) REVERT: B 420 HIS cc_start: 0.7992 (m-70) cc_final: 0.7632 (m90) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.5670 time to fit residues: 66.9124 Evaluate side-chains 101 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 0.2980 chunk 53 optimal weight: 0.0170 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 0.0670 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 GLN B 44 ASN B 82 GLN B 116 ASN B 145 GLN B 222 GLN B 246 GLN B 272 ASN B 496 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.151915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.119201 restraints weight = 7438.918| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.66 r_work: 0.3367 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5874 Z= 0.137 Angle : 0.494 6.011 8126 Z= 0.261 Chirality : 0.041 0.158 908 Planarity : 0.004 0.028 931 Dihedral : 12.433 73.552 1159 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.02 % Allowed : 10.11 % Favored : 87.87 % 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: -0.06 (0.33), residues: 630 helix: 0.67 (0.40), residues: 161 sheet: -0.18 (0.54), residues: 86 loop : -0.25 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 139 TYR 0.010 0.001 TYR B 491 PHE 0.018 0.002 PHE B 373 TRP 0.009 0.001 TRP B 381 HIS 0.004 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 5854) covalent geometry : angle 0.49132 / 0.26 ( 8110) hydrogen bonds : bond 0.04165 / 2.62 ( 206) hydrogen bonds : angle 4.45885 / 2.93 ( 534) metal coordination : bond 0.00491 / 0.30 ( 20) metal coordination : angle 1.33243 / 0.75 ( 16) *********************** 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 109 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.225 Fit side-chains REVERT: A 60 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7391 (mm-30) REVERT: A 128 CYS cc_start: 0.7500 (t) cc_final: 0.7265 (t) REVERT: B 77 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7224 (tp30) REVERT: B 128 GLU cc_start: 0.7716 (pm20) cc_final: 0.7428 (pm20) REVERT: B 262 SER cc_start: 0.8317 (m) cc_final: 0.7896 (p) REVERT: B 373 PHE cc_start: 0.7537 (m-80) cc_final: 0.7310 (m-80) REVERT: B 420 HIS cc_start: 0.8033 (m-70) cc_final: 0.7791 (m90) outliers start: 11 outliers final: 4 residues processed: 103 average time/residue: 0.5598 time to fit residues: 60.2926 Evaluate side-chains 101 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 294 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 2 optimal weight: 0.0370 chunk 63 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 HIS A 121 GLN B 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.151018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.118478 restraints weight = 7406.979| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.66 r_work: 0.3357 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5874 Z= 0.178 Angle : 0.504 5.896 8126 Z= 0.267 Chirality : 0.041 0.158 908 Planarity : 0.004 0.032 931 Dihedral : 12.446 73.679 1159 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.65 % Allowed : 12.13 % Favored : 86.21 % 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: -0.01 (0.33), residues: 630 helix: 0.84 (0.39), residues: 161 sheet: -0.30 (0.55), residues: 86 loop : -0.24 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 13 TYR 0.012 0.001 TYR B 491 PHE 0.012 0.002 PHE B 432 TRP 0.010 0.001 TRP B 381 HIS 0.005 0.001 HIS B 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 ( 5854) covalent geometry : angle 0.50215 / 0.27 ( 8110) hydrogen bonds : bond 0.04292 / 2.69 ( 206) hydrogen bonds : angle 4.35953 / 2.89 ( 534) metal coordination : bond 0.00626 / 0.37 ( 20) metal coordination : angle 1.20329 / 0.72 ( 16) *********************** 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 106 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.195 Fit side-chains REVERT: A 60 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7378 (mm-30) REVERT: A 128 CYS cc_start: 0.7551 (t) cc_final: 0.7307 (t) REVERT: B 77 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7234 (tp30) REVERT: B 128 GLU cc_start: 0.7605 (pm20) cc_final: 0.7330 (pm20) REVERT: B 168 GLN cc_start: 0.8273 (tp40) cc_final: 0.7957 (tp40) REVERT: B 262 SER cc_start: 0.8354 (m) cc_final: 0.7941 (p) REVERT: B 309 CYS cc_start: 0.7730 (m) cc_final: 0.7408 (m) REVERT: B 369 MET cc_start: 0.6925 (mpt) cc_final: 0.5720 (mpt) REVERT: B 373 PHE cc_start: 0.7598 (m-80) cc_final: 0.7280 (m-80) outliers start: 9 outliers final: 7 residues processed: 101 average time/residue: 0.5940 time to fit residues: 62.5593 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 : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 507 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 56 optimal weight: 0.4980 chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 0.3980 chunk 9 optimal weight: 0.8980 chunk 17 optimal weight: 0.2980 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 0.0270 chunk 31 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 GLN B 116 ASN B 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.151804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.119168 restraints weight = 7363.950| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.65 r_work: 0.3371 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5874 Z= 0.125 Angle : 0.455 5.795 8126 Z= 0.241 Chirality : 0.040 0.148 908 Planarity : 0.003 0.028 931 Dihedral : 12.425 73.625 1159 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.57 % Allowed : 12.50 % 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: 0.06 (0.33), residues: 630 helix: 0.99 (0.39), residues: 166 sheet: -0.59 (0.58), residues: 76 loop : -0.19 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 13 TYR 0.009 0.001 TYR B 491 PHE 0.018 0.001 PHE B 441 TRP 0.008 0.001 TRP B 381 HIS 0.004 0.001 HIS B 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 ( 5854) covalent geometry : angle 0.45193 / 0.24 ( 8110) hydrogen bonds : bond 0.03733 / 2.38 ( 206) hydrogen bonds : angle 4.17462 / 2.76 ( 534) metal coordination : bond 0.00470 / 0.26 ( 20) metal coordination : angle 1.22171 / 0.71 ( 16) *********************** 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 112 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.195 Fit side-chains REVERT: A 60 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7315 (mm-30) REVERT: A 128 CYS cc_start: 0.7483 (t) cc_final: 0.7241 (t) REVERT: B 77 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7110 (tp30) REVERT: B 128 GLU cc_start: 0.7577 (pm20) cc_final: 0.7298 (pm20) REVERT: B 168 GLN cc_start: 0.8258 (tp40) cc_final: 0.7917 (tp40) REVERT: B 262 SER cc_start: 0.8349 (m) cc_final: 0.7942 (p) REVERT: B 305 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.6951 (tp) REVERT: B 309 CYS cc_start: 0.7731 (m) cc_final: 0.7312 (m) REVERT: B 369 MET cc_start: 0.6924 (mpt) cc_final: 0.5729 (mpt) REVERT: B 373 PHE cc_start: 0.7625 (m-80) cc_final: 0.7311 (m-80) outliers start: 14 outliers final: 8 residues processed: 106 average time/residue: 0.5449 time to fit residues: 60.4245 Evaluate side-chains 107 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 507 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 18 optimal weight: 0.0970 chunk 7 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 58 optimal weight: 0.0770 chunk 53 optimal weight: 0.5980 chunk 37 optimal weight: 0.4980 chunk 50 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 GLN B 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.150256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.116992 restraints weight = 7426.346| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.72 r_work: 0.3360 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5874 Z= 0.138 Angle : 0.459 5.835 8126 Z= 0.243 Chirality : 0.040 0.151 908 Planarity : 0.004 0.028 931 Dihedral : 12.411 73.689 1159 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.02 % Allowed : 13.79 % 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: 0.09 (0.33), residues: 630 helix: 1.10 (0.39), residues: 166 sheet: -0.64 (0.57), residues: 76 loop : -0.20 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 164 TYR 0.009 0.001 TYR B 416 PHE 0.013 0.001 PHE B 441 TRP 0.008 0.001 TRP B 381 HIS 0.004 0.001 HIS B 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 5854) covalent geometry : angle 0.45662 / 0.24 ( 8110) hydrogen bonds : bond 0.03742 / 2.37 ( 206) hydrogen bonds : angle 4.11391 / 2.72 ( 534) metal coordination : bond 0.00479 / 0.27 ( 20) metal coordination : angle 1.12031 / 0.65 ( 16) *********************** 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 110 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.192 Fit side-chains REVERT: A 60 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7313 (mm-30) REVERT: A 128 CYS cc_start: 0.7494 (t) cc_final: 0.7255 (t) REVERT: B 77 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7113 (tp30) REVERT: B 128 GLU cc_start: 0.7560 (pm20) cc_final: 0.7273 (pm20) REVERT: B 168 GLN cc_start: 0.8254 (tp40) cc_final: 0.7897 (tp40) REVERT: B 262 SER cc_start: 0.8332 (m) cc_final: 0.7968 (t) REVERT: B 309 CYS cc_start: 0.7704 (m) cc_final: 0.7282 (m) REVERT: B 369 MET cc_start: 0.6921 (mpt) cc_final: 0.5763 (mpt) REVERT: B 373 PHE cc_start: 0.7621 (m-80) cc_final: 0.7302 (m-80) outliers start: 11 outliers final: 7 residues processed: 104 average time/residue: 0.5813 time to fit residues: 63.0030 Evaluate side-chains 106 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 507 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 51 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 0.0170 chunk 20 optimal weight: 0.4980 chunk 50 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 36 optimal weight: 0.1980 chunk 65 optimal weight: 4.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 GLN B 205 GLN B 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.150303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.117179 restraints weight = 7476.945| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.73 r_work: 0.3359 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5874 Z= 0.132 Angle : 0.451 5.807 8126 Z= 0.238 Chirality : 0.040 0.147 908 Planarity : 0.004 0.035 931 Dihedral : 12.398 73.662 1159 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.21 % Allowed : 14.71 % Favored : 83.09 % 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 (0.33), residues: 630 helix: 1.17 (0.39), residues: 166 sheet: -0.61 (0.55), residues: 82 loop : -0.18 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 164 TYR 0.008 0.001 TYR B 416 PHE 0.020 0.001 PHE B 441 TRP 0.010 0.001 TRP B 506 HIS 0.004 0.001 HIS B 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 5854) covalent geometry : angle 0.44861 / 0.24 ( 8110) hydrogen bonds : bond 0.03677 / 2.33 ( 206) hydrogen bonds : angle 4.06949 / 2.69 ( 534) metal coordination : bond 0.00507 / 0.28 ( 20) metal coordination : angle 1.14717 / 0.65 ( 16) *********************** 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 112 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.122 Fit side-chains REVERT: A 60 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7303 (mm-30) REVERT: A 128 CYS cc_start: 0.7501 (t) cc_final: 0.7273 (t) REVERT: B 77 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7156 (tp30) REVERT: B 115 VAL cc_start: 0.8480 (t) cc_final: 0.8235 (t) REVERT: B 128 GLU cc_start: 0.7572 (pm20) cc_final: 0.7287 (pm20) REVERT: B 168 GLN cc_start: 0.8281 (tp40) cc_final: 0.7931 (tp40) REVERT: B 262 SER cc_start: 0.8327 (m) cc_final: 0.7984 (t) REVERT: B 305 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.6962 (tp) REVERT: B 309 CYS cc_start: 0.7725 (m) cc_final: 0.7305 (m) REVERT: B 369 MET cc_start: 0.6973 (mpt) cc_final: 0.5925 (mpt) REVERT: B 373 PHE cc_start: 0.7601 (m-80) cc_final: 0.7292 (m-80) outliers start: 12 outliers final: 8 residues processed: 106 average time/residue: 0.5381 time to fit residues: 59.5604 Evaluate side-chains 107 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 507 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 24 optimal weight: 0.2980 chunk 62 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 42 optimal weight: 0.0270 chunk 1 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 GLN B 205 GLN B 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.150044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.116809 restraints weight = 7505.463| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.77 r_work: 0.3352 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5874 Z= 0.148 Angle : 0.462 5.840 8126 Z= 0.244 Chirality : 0.040 0.148 908 Planarity : 0.004 0.032 931 Dihedral : 12.400 73.714 1159 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.39 % Allowed : 15.07 % Favored : 82.54 % 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 (0.33), residues: 630 helix: 0.92 (0.39), residues: 173 sheet: -0.65 (0.57), residues: 69 loop : -0.15 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 164 TYR 0.008 0.001 TYR B 491 PHE 0.022 0.002 PHE B 441 TRP 0.011 0.001 TRP B 506 HIS 0.005 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 5854) covalent geometry : angle 0.46016 / 0.24 ( 8110) hydrogen bonds : bond 0.03777 / 2.38 ( 206) hydrogen bonds : angle 4.07667 / 2.71 ( 534) metal coordination : bond 0.00520 / 0.29 ( 20) metal coordination : angle 1.10312 / 0.63 ( 16) *********************** 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 112 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.123 Fit side-chains REVERT: A 128 CYS cc_start: 0.7495 (t) cc_final: 0.7275 (t) REVERT: B 32 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8082 (ptpp) REVERT: B 77 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7151 (tp30) REVERT: B 115 VAL cc_start: 0.8493 (t) cc_final: 0.8245 (t) REVERT: B 128 GLU cc_start: 0.7576 (pm20) cc_final: 0.7292 (pm20) REVERT: B 168 GLN cc_start: 0.8272 (tp40) cc_final: 0.7923 (tp40) REVERT: B 262 SER cc_start: 0.8338 (m) cc_final: 0.7992 (t) REVERT: B 305 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.6975 (tp) REVERT: B 309 CYS cc_start: 0.7737 (m) cc_final: 0.7313 (m) REVERT: B 369 MET cc_start: 0.6966 (mpt) cc_final: 0.5883 (mpt) REVERT: B 373 PHE cc_start: 0.7624 (m-80) cc_final: 0.7280 (m-80) outliers start: 13 outliers final: 8 residues processed: 105 average time/residue: 0.5322 time to fit residues: 58.0805 Evaluate side-chains 110 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 507 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 14 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.1980 chunk 47 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 40 optimal weight: 0.2980 chunk 10 optimal weight: 0.0470 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 GLN B 205 GLN B 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.150552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.117538 restraints weight = 7406.618| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.74 r_work: 0.3363 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5874 Z= 0.125 Angle : 0.450 5.838 8126 Z= 0.238 Chirality : 0.039 0.143 908 Planarity : 0.003 0.029 931 Dihedral : 12.387 73.691 1159 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.21 % Allowed : 15.26 % Favored : 82.54 % 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: 0.09 (0.33), residues: 630 helix: 1.06 (0.39), residues: 172 sheet: -0.66 (0.55), residues: 75 loop : -0.18 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 164 TYR 0.008 0.001 TYR B 491 PHE 0.017 0.001 PHE B 441 TRP 0.010 0.001 TRP B 506 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 5854) covalent geometry : angle 0.44736 / 0.24 ( 8110) hydrogen bonds : bond 0.03589 / 2.27 ( 206) hydrogen bonds : angle 4.01518 / 2.66 ( 534) metal coordination : bond 0.00495 / 0.26 ( 20) metal coordination : angle 1.10967 / 0.62 ( 16) *********************** 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 112 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.187 Fit side-chains REVERT: A 128 CYS cc_start: 0.7468 (t) cc_final: 0.7257 (t) REVERT: B 77 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7125 (tp30) REVERT: B 128 GLU cc_start: 0.7569 (pm20) cc_final: 0.7278 (pm20) REVERT: B 168 GLN cc_start: 0.8264 (tp40) cc_final: 0.7913 (tp40) REVERT: B 262 SER cc_start: 0.8330 (m) cc_final: 0.7989 (t) REVERT: B 305 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.6965 (tp) REVERT: B 309 CYS cc_start: 0.7732 (m) cc_final: 0.7300 (m) REVERT: B 369 MET cc_start: 0.6955 (mpt) cc_final: 0.5897 (mpt) REVERT: B 373 PHE cc_start: 0.7637 (m-80) cc_final: 0.7353 (m-80) outliers start: 12 outliers final: 8 residues processed: 106 average time/residue: 0.5113 time to fit residues: 56.5970 Evaluate side-chains 107 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 507 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 18 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 37 optimal weight: 0.1980 chunk 29 optimal weight: 0.1980 chunk 7 optimal weight: 0.0670 chunk 45 optimal weight: 3.9990 chunk 16 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 overall best weight: 0.2918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 HIS B 82 GLN B 116 ASN B 205 GLN B 246 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.151015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.118076 restraints weight = 7341.558| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.70 r_work: 0.3378 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5874 Z= 0.110 Angle : 0.444 5.807 8126 Z= 0.236 Chirality : 0.039 0.143 908 Planarity : 0.003 0.030 931 Dihedral : 12.378 73.666 1159 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % 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: 0.20 (0.33), residues: 630 helix: 1.36 (0.40), residues: 166 sheet: -0.69 (0.54), residues: 82 loop : -0.17 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 164 TYR 0.008 0.001 TYR B 416 PHE 0.023 0.001 PHE B 441 TRP 0.010 0.001 TRP B 506 HIS 0.003 0.001 HIS B 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 5854) covalent geometry : angle 0.43968 / 0.24 ( 8110) hydrogen bonds : bond 0.03421 / 2.18 ( 206) hydrogen bonds : angle 3.97794 / 2.64 ( 534) metal coordination : bond 0.00445 / 0.26 ( 20) metal coordination : angle 1.46350 / 0.78 ( 16) *********************** 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: 8 poor density : 94 time to evaluate : 0.117 Fit side-chains REVERT: A 128 CYS cc_start: 0.7428 (t) cc_final: 0.7221 (t) REVERT: B 32 LYS cc_start: 0.8359 (ptpp) cc_final: 0.8153 (pttp) REVERT: B 77 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7112 (tp30) REVERT: B 128 GLU cc_start: 0.7546 (pm20) cc_final: 0.7223 (pm20) REVERT: B 168 GLN cc_start: 0.8261 (tp40) cc_final: 0.7911 (tp40) REVERT: B 262 SER cc_start: 0.8310 (m) cc_final: 0.7978 (t) REVERT: B 305 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.6962 (tp) REVERT: B 309 CYS cc_start: 0.7683 (m) cc_final: 0.7255 (m) REVERT: B 369 MET cc_start: 0.6975 (mpt) cc_final: 0.5820 (mpt) REVERT: B 373 PHE cc_start: 0.7647 (m-80) cc_final: 0.7369 (m-80) outliers start: 8 outliers final: 7 residues processed: 99 average time/residue: 0.5126 time to fit residues: 52.8893 Evaluate side-chains 103 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 507 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 0.0170 chunk 3 optimal weight: 0.4980 chunk 47 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 56 optimal weight: 0.0470 chunk 35 optimal weight: 0.2980 chunk 33 optimal weight: 0.0980 chunk 45 optimal weight: 0.9990 overall best weight: 0.1916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 GLN B 205 GLN B 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.151974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.118882 restraints weight = 7417.885| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.72 r_work: 0.3389 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5874 Z= 0.089 Angle : 0.424 5.753 8126 Z= 0.225 Chirality : 0.038 0.140 908 Planarity : 0.003 0.030 931 Dihedral : 12.338 73.645 1159 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.10 % Allowed : 16.73 % 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: 0.32 (0.33), residues: 630 helix: 1.52 (0.40), residues: 167 sheet: -0.84 (0.55), residues: 76 loop : -0.09 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 164 TYR 0.008 0.001 TYR B 488 PHE 0.019 0.001 PHE B 441 TRP 0.006 0.001 TRP B 506 HIS 0.004 0.001 HIS B 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 ( 5854) covalent geometry : angle 0.42142 / 0.23 ( 8110) hydrogen bonds : bond 0.03188 / 2.04 ( 206) hydrogen bonds : angle 3.87851 / 2.57 ( 534) metal coordination : bond 0.00532 / 0.27 ( 20) metal coordination : angle 1.06168 / 0.60 ( 16) ********************** 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 100 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.165 Fit side-chains REVERT: A 128 CYS cc_start: 0.7430 (t) cc_final: 0.7216 (t) REVERT: B 32 LYS cc_start: 0.8337 (ptpp) cc_final: 0.8135 (pttp) REVERT: B 77 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7058 (tp30) REVERT: B 128 GLU cc_start: 0.7554 (pm20) cc_final: 0.7242 (pm20) REVERT: B 168 GLN cc_start: 0.8274 (tp40) cc_final: 0.7923 (tp40) REVERT: B 262 SER cc_start: 0.8296 (m) cc_final: 0.7981 (t) REVERT: B 305 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.6975 (tp) REVERT: B 309 CYS cc_start: 0.7717 (m) cc_final: 0.7310 (m) REVERT: B 369 MET cc_start: 0.6980 (mpt) cc_final: 0.5956 (mpt) outliers start: 6 outliers final: 5 residues processed: 97 average time/residue: 0.4861 time to fit residues: 49.2575 Evaluate side-chains 99 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 507 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 18 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 16 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 54 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 205 GLN B 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.150573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.117611 restraints weight = 7248.096| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.69 r_work: 0.3371 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2213 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= 0.178 Angle : 0.482 5.893 8126 Z= 0.256 Chirality : 0.041 0.150 908 Planarity : 0.004 0.041 931 Dihedral : 12.381 73.827 1159 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.10 % Allowed : 16.73 % 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: -0.01 (0.33), residues: 630 helix: 0.90 (0.39), residues: 173 sheet: -0.77 (0.56), residues: 69 loop : -0.21 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 164 TYR 0.011 0.001 TYR B 416 PHE 0.026 0.002 PHE B 441 TRP 0.009 0.001 TRP B 506 HIS 0.004 0.001 HIS B 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 ( 5854) covalent geometry : angle 0.47976 / 0.26 ( 8110) hydrogen bonds : bond 0.03858 / 2.41 ( 206) hydrogen bonds : angle 4.07788 / 2.71 ( 534) metal coordination : bond 0.00554 / 0.33 ( 20) metal coordination : angle 1.14266 / 0.69 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2302.64 seconds wall clock time: 39 minutes 48.06 seconds (2388.06 seconds total)