Starting phenix.real_space_refine on Tue Feb 3 23:10:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qec_53054/02_2026/9qec_53054.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qec_53054/02_2026/9qec_53054.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qec_53054/02_2026/9qec_53054.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qec_53054/02_2026/9qec_53054.map" model { file = "/net/cci-nas-00/data/ceres_data/9qec_53054/02_2026/9qec_53054.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qec_53054/02_2026/9qec_53054.cif" } resolution = 2.9 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= 0.005 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: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 4929 2.51 5 N 1316 2.21 5 O 1409 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s 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: 7688 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 753, 6060 Classifications: {'peptide': 753} Link IDs: {'PTRANS': 35, 'TRANS': 717} Chain breaks: 4 Chain: "B" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1582 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 11, 'TRANS': 187} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 46 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Time building chain proxies: 1.24, per 1000 atoms: 0.16 Number of scatterers: 7688 At special positions: 0 Unit cell: (79.56, 98.94, 126.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1409 8.00 N 1316 7.00 C 4929 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: 0.50 Conformation dependent library (CDL) restraints added in 176.4 milliseconds 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1834 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 6 sheets defined 60.7% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 16 through 28 Processing helix chain 'A' and resid 40 through 52 Processing helix chain 'A' and resid 65 through 80 Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.574A pdb=" N TYR A 98 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU A 99 " --> pdb=" O ASN A 95 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY A 104 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 121 Processing helix chain 'A' and resid 136 through 141 removed outlier: 3.558A pdb=" N ILE A 139 " --> pdb=" O ALA A 136 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 140 " --> pdb=" O HIS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 156 Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 177 through 185 removed outlier: 3.559A pdb=" N VAL A 181 " --> pdb=" O HIS A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 219 through 244 Processing helix chain 'A' and resid 245 through 248 removed outlier: 3.804A pdb=" N GLU A 248 " --> pdb=" O PRO A 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 245 through 248' Processing helix chain 'A' and resid 253 through 259 removed outlier: 3.609A pdb=" N ILE A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 271 Processing helix chain 'A' and resid 272 through 277 removed outlier: 5.875A pdb=" N HIS A 275 " --> pdb=" O PRO A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 301 removed outlier: 3.622A pdb=" N LYS A 282 " --> pdb=" O GLY A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 320 Processing helix chain 'A' and resid 329 through 343 removed outlier: 3.590A pdb=" N SER A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET A 335 " --> pdb=" O SER A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 398 removed outlier: 4.252A pdb=" N GLU A 382 " --> pdb=" O ASN A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 440 removed outlier: 6.913A pdb=" N ALA A 428 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 9.223A pdb=" N GLU A 429 " --> pdb=" O THR A 425 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 456 removed outlier: 3.509A pdb=" N GLU A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET A 451 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS A 452 " --> pdb=" O GLU A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 574 Processing helix chain 'A' and resid 584 through 597 Processing helix chain 'A' and resid 613 through 641 removed outlier: 3.642A pdb=" N ALA A 638 " --> pdb=" O ILE A 634 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A 639 " --> pdb=" O ARG A 635 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 641 " --> pdb=" O LYS A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 692 removed outlier: 3.931A pdb=" N ARG A 692 " --> pdb=" O ARG A 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 689 through 692' Processing helix chain 'A' and resid 694 through 703 removed outlier: 3.845A pdb=" N GLY A 703 " --> pdb=" O ILE A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 739 Processing helix chain 'A' and resid 739 through 752 removed outlier: 3.799A pdb=" N SER A 743 " --> pdb=" O GLY A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 777 Processing helix chain 'A' and resid 783 through 795 Processing helix chain 'A' and resid 805 through 817 removed outlier: 3.602A pdb=" N GLU A 811 " --> pdb=" O HIS A 807 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS A 817 " --> pdb=" O PHE A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 855 removed outlier: 3.902A pdb=" N ASP A 850 " --> pdb=" O PRO A 846 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE A 851 " --> pdb=" O GLY A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 870 removed outlier: 4.259A pdb=" N ARG A 864 " --> pdb=" O ALA A 860 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N SER A 865 " --> pdb=" O LYS A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 879 Processing helix chain 'A' and resid 880 through 889 Processing helix chain 'A' and resid 890 through 902 Processing helix chain 'A' and resid 904 through 910 removed outlier: 3.815A pdb=" N VAL A 908 " --> pdb=" O SER A 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 108 Processing helix chain 'B' and resid 112 through 116 removed outlier: 3.977A pdb=" N VAL B 116 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 149 Processing helix chain 'B' and resid 151 through 161 removed outlier: 3.544A pdb=" N GLY B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 193 Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 230 through 241 removed outlier: 3.616A pdb=" N THR B 241 " --> pdb=" O GLU B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 257 Processing helix chain 'B' and resid 259 through 266 Processing helix chain 'B' and resid 267 through 273 Processing helix chain 'B' and resid 278 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 88 removed outlier: 3.647A pdb=" N ALA A 109 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU A 58 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N LEU A 132 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU A 60 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N TYR A 134 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU A 32 " --> pdb=" O TYR A 191 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N TRP A 193 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL A 34 " --> pdb=" O TRP A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 216 removed outlier: 6.652A pdb=" N VAL A 578 " --> pdb=" O TYR A 606 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N LEU A 608 " --> pdb=" O VAL A 578 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU A 580 " --> pdb=" O LEU A 608 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N TYR A 610 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU A 408 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 344 through 345 removed outlier: 3.785A pdb=" N GLU A 372 " --> pdb=" O HIS A 345 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 705 through 709 removed outlier: 6.730A pdb=" N ILE A 684 " --> pdb=" O GLU A 707 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL A 709 " --> pdb=" O ILE A 684 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N VAL A 686 " --> pdb=" O VAL A 709 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 723 through 728 removed outlier: 5.787A pdb=" N CYS A 723 " --> pdb=" O VAL A 756 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU A 758 " --> pdb=" O CYS A 723 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N GLU A 725 " --> pdb=" O LEU A 758 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N GLU A 760 " --> pdb=" O GLU A 725 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LYS A 727 " --> pdb=" O GLU A 760 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 121 through 123 removed outlier: 5.715A pdb=" N ILE B 101 " --> pdb=" O GLU B 122 " (cutoff:3.500A) 406 hydrogen bonds defined for protein. 1173 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.97 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2511 1.35 - 1.46: 1719 1.46 - 1.58: 3564 1.58 - 1.70: 1 1.70 - 1.82: 48 Bond restraints: 7843 Sorted by residual: bond pdb=" CA GLU A 721 " pdb=" CB GLU A 721 " ideal model delta sigma weight residual 1.539 1.602 -0.062 4.88e-02 4.20e+02 1.63e+00 bond pdb=" CG ARG A 180 " pdb=" CD ARG A 180 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.14e+00 bond pdb=" C GLU A 549 " pdb=" N PRO A 550 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.03e+00 bond pdb=" CB GLU B 225 " pdb=" CG GLU B 225 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.63e-01 bond pdb=" CB ASN A 167 " pdb=" CG ASN A 167 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.50e-02 1.60e+03 8.38e-01 ... (remaining 7838 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 10515 2.11 - 4.22: 88 4.22 - 6.33: 14 6.33 - 8.44: 1 8.44 - 10.55: 1 Bond angle restraints: 10619 Sorted by residual: angle pdb=" CB MET A 688 " pdb=" CG MET A 688 " pdb=" SD MET A 688 " ideal model delta sigma weight residual 112.70 123.25 -10.55 3.00e+00 1.11e-01 1.24e+01 angle pdb=" CG ARG A 180 " pdb=" CD ARG A 180 " pdb=" NE ARG A 180 " ideal model delta sigma weight residual 112.00 117.51 -5.51 2.20e+00 2.07e-01 6.27e+00 angle pdb=" CA LEU B 148 " pdb=" CB LEU B 148 " pdb=" CG LEU B 148 " ideal model delta sigma weight residual 116.30 124.69 -8.39 3.50e+00 8.16e-02 5.75e+00 angle pdb=" CA ASN A 167 " pdb=" CB ASN A 167 " pdb=" CG ASN A 167 " ideal model delta sigma weight residual 112.60 114.88 -2.28 1.00e+00 1.00e+00 5.18e+00 angle pdb=" CB ARG A 180 " pdb=" CG ARG A 180 " pdb=" CD ARG A 180 " ideal model delta sigma weight residual 111.30 116.46 -5.16 2.30e+00 1.89e-01 5.04e+00 ... (remaining 10614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 3967 17.72 - 35.44: 563 35.44 - 53.16: 205 53.16 - 70.87: 37 70.87 - 88.59: 14 Dihedral angle restraints: 4786 sinusoidal: 1968 harmonic: 2818 Sorted by residual: dihedral pdb=" CA GLU A 549 " pdb=" C GLU A 549 " pdb=" N PRO A 550 " pdb=" CA PRO A 550 " ideal model delta harmonic sigma weight residual 180.00 160.31 19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ASN B 147 " pdb=" C ASN B 147 " pdb=" N LEU B 148 " pdb=" CA LEU B 148 " ideal model delta harmonic sigma weight residual 180.00 162.57 17.43 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASP B 151 " pdb=" CB ASP B 151 " pdb=" CG ASP B 151 " pdb=" OD1 ASP B 151 " ideal model delta sinusoidal sigma weight residual -30.00 -87.06 57.06 1 2.00e+01 2.50e-03 1.09e+01 ... (remaining 4783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 912 0.038 - 0.075: 216 0.075 - 0.113: 86 0.113 - 0.151: 5 0.151 - 0.188: 1 Chirality restraints: 1220 Sorted by residual: chirality pdb=" CB VAL A 249 " pdb=" CA VAL A 249 " pdb=" CG1 VAL A 249 " pdb=" CG2 VAL A 249 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.85e-01 chirality pdb=" CA ILE A 546 " pdb=" N ILE A 546 " pdb=" C ILE A 546 " pdb=" CB ILE A 546 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA ILE B 197 " pdb=" N ILE B 197 " pdb=" C ILE B 197 " pdb=" CB ILE B 197 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.66e-01 ... (remaining 1217 not shown) Planarity restraints: 1353 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 167 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" C ASN A 167 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN A 167 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA A 168 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 719 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO A 720 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 720 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 720 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 180 " -0.135 9.50e-02 1.11e+02 6.10e-02 2.93e+00 pdb=" NE ARG A 180 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 180 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 180 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 180 " -0.000 2.00e-02 2.50e+03 ... (remaining 1350 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1252 2.76 - 3.30: 7108 3.30 - 3.83: 12946 3.83 - 4.37: 14718 4.37 - 4.90: 25658 Nonbonded interactions: 61682 Sorted by model distance: nonbonded pdb=" OG SER A 880 " pdb=" OD1 ASP A 882 " model vdw 2.228 3.040 nonbonded pdb=" O SER A 398 " pdb=" OG SER A 398 " model vdw 2.245 3.040 nonbonded pdb=" OH TYR A 46 " pdb=" OE1 GLU A 79 " model vdw 2.259 3.040 nonbonded pdb=" O ARG B 207 " pdb=" OG1 THR B 211 " model vdw 2.308 3.040 nonbonded pdb=" O GLY A 259 " pdb=" NH1 ARG A 292 " model vdw 2.311 3.120 ... (remaining 61677 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.100 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 : 0.002 0.062 7843 Z= 0.098 Angle : 0.485 10.553 10619 Z= 0.241 Chirality : 0.038 0.188 1220 Planarity : 0.004 0.061 1353 Dihedral : 19.120 88.594 2952 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.39 % Favored : 96.30 % Rotamer: Outliers : 3.99 % Allowed : 30.75 % Favored : 65.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.91 (0.29), residues: 945 helix: 1.53 (0.24), residues: 529 sheet: 0.16 (0.49), residues: 134 loop : -0.91 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 180 TYR 0.007 0.001 TYR A 751 PHE 0.012 0.001 PHE A 431 TRP 0.004 0.001 TRP A 802 HIS 0.007 0.001 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 7843) covalent geometry : angle 0.48546 (10619) hydrogen bonds : bond 0.20086 ( 406) hydrogen bonds : angle 5.80955 ( 1173) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 0.201 Fit side-chains outliers start: 34 outliers final: 33 residues processed: 141 average time/residue: 0.4528 time to fit residues: 67.4134 Evaluate side-chains 137 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 419 GLN Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 705 ASP Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 859 ASN Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain C residue 76 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN A 75 GLN A 83 HIS A 137 HIS A 154 GLN A 201 ASN A 215 HIS A 256 ASN A 300 GLN A 308 ASN A 555 HIS A 590 GLN A 794 HIS A 868 HIS A 902 HIS B 110 ASN B 154 HIS ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.149165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.116108 restraints weight = 9416.288| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.17 r_work: 0.3154 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 7843 Z= 0.192 Angle : 0.592 7.693 10619 Z= 0.303 Chirality : 0.043 0.195 1220 Planarity : 0.005 0.048 1353 Dihedral : 8.391 86.368 1098 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.13 % Favored : 95.56 % Rotamer: Outliers : 6.46 % Allowed : 25.59 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.72 (0.29), residues: 945 helix: 1.38 (0.23), residues: 541 sheet: 0.17 (0.47), residues: 141 loop : -1.18 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 180 TYR 0.009 0.001 TYR A 751 PHE 0.018 0.002 PHE A 160 TRP 0.009 0.001 TRP A 450 HIS 0.006 0.001 HIS A 794 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 7843) covalent geometry : angle 0.59225 (10619) hydrogen bonds : bond 0.05437 ( 406) hydrogen bonds : angle 4.31301 ( 1173) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 125 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 269 TYR cc_start: 0.8269 (OUTLIER) cc_final: 0.7731 (m-10) REVERT: A 346 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7757 (mt) REVERT: A 451 MET cc_start: 0.6784 (ptt) cc_final: 0.6489 (ptt) REVERT: A 595 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8692 (tmt170) REVERT: B 187 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8120 (ttmt) REVERT: C 77 LEU cc_start: 0.3348 (OUTLIER) cc_final: 0.3080 (pt) outliers start: 55 outliers final: 28 residues processed: 165 average time/residue: 0.4921 time to fit residues: 85.3122 Evaluate side-chains 149 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 595 ARG Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 782 ASN Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 859 ASN Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 77 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 87 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 GLN A 902 HIS B 118 ASN ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.151040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.118737 restraints weight = 9392.904| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.04 r_work: 0.3137 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 7843 Z= 0.208 Angle : 0.603 7.977 10619 Z= 0.307 Chirality : 0.044 0.195 1220 Planarity : 0.005 0.049 1353 Dihedral : 7.624 57.120 1078 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.13 % Favored : 95.56 % Rotamer: Outliers : 6.10 % Allowed : 25.59 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.49 (0.28), residues: 945 helix: 1.27 (0.23), residues: 542 sheet: -0.04 (0.46), residues: 141 loop : -1.38 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 180 TYR 0.008 0.001 TYR A 606 PHE 0.016 0.002 PHE A 160 TRP 0.009 0.001 TRP A 802 HIS 0.006 0.001 HIS B 290 Details of bonding type rmsd covalent geometry : bond 0.00509 ( 7843) covalent geometry : angle 0.60261 (10619) hydrogen bonds : bond 0.05322 ( 406) hydrogen bonds : angle 4.22943 ( 1173) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 124 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 260 LYS cc_start: 0.8031 (mtmm) cc_final: 0.7767 (mtpp) REVERT: A 269 TYR cc_start: 0.8169 (OUTLIER) cc_final: 0.7593 (m-10) REVERT: A 287 ASP cc_start: 0.7865 (m-30) cc_final: 0.7526 (m-30) REVERT: A 346 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7759 (mt) REVERT: A 451 MET cc_start: 0.6732 (ptt) cc_final: 0.6423 (ptt) REVERT: A 595 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8481 (tpt170) REVERT: B 147 ASN cc_start: 0.7204 (p0) cc_final: 0.6868 (p0) REVERT: B 187 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8026 (ttmt) REVERT: C 77 LEU cc_start: 0.3398 (OUTLIER) cc_final: 0.3146 (pt) outliers start: 52 outliers final: 30 residues processed: 162 average time/residue: 0.4827 time to fit residues: 82.4314 Evaluate side-chains 148 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 595 ARG Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 782 ASN Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 859 ASN Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 77 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 chunk 70 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 HIS A 300 GLN A 902 HIS ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.154237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.122166 restraints weight = 9472.623| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.04 r_work: 0.3181 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 7843 Z= 0.114 Angle : 0.511 7.446 10619 Z= 0.260 Chirality : 0.040 0.188 1220 Planarity : 0.004 0.044 1353 Dihedral : 6.991 55.239 1076 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.70 % Favored : 95.98 % Rotamer: Outliers : 5.05 % Allowed : 26.64 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.74 (0.29), residues: 945 helix: 1.50 (0.23), residues: 544 sheet: -0.21 (0.45), residues: 146 loop : -1.22 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 689 TYR 0.008 0.001 TYR B 152 PHE 0.014 0.001 PHE A 431 TRP 0.009 0.001 TRP A 450 HIS 0.007 0.001 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 7843) covalent geometry : angle 0.51107 (10619) hydrogen bonds : bond 0.03852 ( 406) hydrogen bonds : angle 3.97110 ( 1173) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 123 time to evaluate : 0.212 Fit side-chains REVERT: A 260 LYS cc_start: 0.8117 (mtmm) cc_final: 0.7899 (mtpt) REVERT: A 269 TYR cc_start: 0.8236 (OUTLIER) cc_final: 0.7644 (m-10) REVERT: A 346 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7764 (mt) REVERT: A 451 MET cc_start: 0.6536 (ptt) cc_final: 0.6208 (ptt) REVERT: A 595 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8516 (tpt170) REVERT: A 778 GLU cc_start: 0.4679 (OUTLIER) cc_final: 0.3985 (tp30) REVERT: A 793 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8664 (mt) REVERT: B 147 ASN cc_start: 0.7094 (p0) cc_final: 0.6740 (p0) REVERT: B 160 LEU cc_start: 0.8182 (tp) cc_final: 0.7982 (tp) REVERT: C 77 LEU cc_start: 0.3280 (OUTLIER) cc_final: 0.3016 (pt) outliers start: 43 outliers final: 24 residues processed: 155 average time/residue: 0.5511 time to fit residues: 89.5086 Evaluate side-chains 143 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 296 GLN Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 419 GLN Chi-restraints excluded: chain A residue 595 ARG Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 859 ASN Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain C residue 77 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 38 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 89 optimal weight: 0.0570 chunk 2 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 GLN A 902 HIS B 172 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.152578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.120424 restraints weight = 9432.750| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.02 r_work: 0.3197 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 7843 Z= 0.120 Angle : 0.518 8.264 10619 Z= 0.262 Chirality : 0.040 0.188 1220 Planarity : 0.004 0.045 1353 Dihedral : 6.359 55.845 1070 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.81 % Favored : 95.87 % Rotamer: Outliers : 4.81 % Allowed : 26.64 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.79 (0.29), residues: 945 helix: 1.55 (0.23), residues: 542 sheet: -0.21 (0.44), residues: 146 loop : -1.18 (0.40), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 180 TYR 0.010 0.001 TYR B 152 PHE 0.013 0.001 PHE A 431 TRP 0.007 0.001 TRP A 450 HIS 0.007 0.001 HIS A 902 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 7843) covalent geometry : angle 0.51760 (10619) hydrogen bonds : bond 0.03880 ( 406) hydrogen bonds : angle 3.91820 ( 1173) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 119 time to evaluate : 0.309 Fit side-chains REVERT: A 260 LYS cc_start: 0.8083 (mttm) cc_final: 0.7860 (mtpp) REVERT: A 269 TYR cc_start: 0.8223 (OUTLIER) cc_final: 0.7636 (m-10) REVERT: A 346 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7787 (mt) REVERT: A 451 MET cc_start: 0.6271 (ptt) cc_final: 0.6011 (ptt) REVERT: A 595 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8508 (tpt170) REVERT: A 778 GLU cc_start: 0.4656 (OUTLIER) cc_final: 0.4033 (tp30) REVERT: A 793 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8681 (mt) REVERT: B 147 ASN cc_start: 0.7114 (p0) cc_final: 0.6815 (p0) REVERT: C 77 LEU cc_start: 0.3353 (OUTLIER) cc_final: 0.3091 (pt) outliers start: 41 outliers final: 20 residues processed: 150 average time/residue: 0.5725 time to fit residues: 90.1208 Evaluate side-chains 138 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 296 GLN Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 419 GLN Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 595 ARG Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 782 ASN Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain C residue 77 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 77 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 4 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 0.2980 chunk 36 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 902 HIS B 251 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.152836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.120415 restraints weight = 9375.566| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.03 r_work: 0.3195 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 7843 Z= 0.100 Angle : 0.491 9.034 10619 Z= 0.248 Chirality : 0.039 0.192 1220 Planarity : 0.004 0.049 1353 Dihedral : 5.183 49.237 1056 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.70 % Favored : 95.98 % Rotamer: Outliers : 4.46 % Allowed : 27.46 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.93 (0.29), residues: 945 helix: 1.65 (0.23), residues: 544 sheet: -0.21 (0.44), residues: 146 loop : -1.06 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 180 TYR 0.009 0.001 TYR B 152 PHE 0.013 0.001 PHE A 431 TRP 0.008 0.001 TRP A 450 HIS 0.008 0.001 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 7843) covalent geometry : angle 0.49114 (10619) hydrogen bonds : bond 0.03337 ( 406) hydrogen bonds : angle 3.80661 ( 1173) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 0.286 Fit side-chains REVERT: A 269 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.7607 (m-10) REVERT: A 346 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7757 (mt) REVERT: A 451 MET cc_start: 0.6086 (ptt) cc_final: 0.5842 (ptt) REVERT: A 595 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8620 (tpt170) REVERT: A 817 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.7233 (ptmm) REVERT: B 125 ASP cc_start: 0.6885 (OUTLIER) cc_final: 0.6360 (m-30) REVERT: B 148 LEU cc_start: 0.8042 (mp) cc_final: 0.7791 (mp) REVERT: B 187 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8066 (ttmt) REVERT: B 283 ARG cc_start: 0.6525 (ttp-110) cc_final: 0.6059 (ttm110) REVERT: C 77 LEU cc_start: 0.3225 (OUTLIER) cc_final: 0.2978 (pt) outliers start: 38 outliers final: 19 residues processed: 153 average time/residue: 0.5719 time to fit residues: 91.8270 Evaluate side-chains 142 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 419 GLN Chi-restraints excluded: chain A residue 595 ARG Chi-restraints excluded: chain A residue 782 ASN Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 817 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 859 ASN Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 77 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 69 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.152664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.120056 restraints weight = 9400.808| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.07 r_work: 0.3173 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 7843 Z= 0.106 Angle : 0.505 9.187 10619 Z= 0.255 Chirality : 0.040 0.186 1220 Planarity : 0.004 0.050 1353 Dihedral : 4.485 48.983 1050 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.60 % Favored : 96.08 % Rotamer: Outliers : 4.11 % Allowed : 28.40 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.29), residues: 945 helix: 1.72 (0.23), residues: 544 sheet: -0.21 (0.44), residues: 146 loop : -1.04 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 180 TYR 0.010 0.001 TYR B 152 PHE 0.012 0.001 PHE A 431 TRP 0.007 0.001 TRP A 450 HIS 0.008 0.001 HIS A 902 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 7843) covalent geometry : angle 0.50491 (10619) hydrogen bonds : bond 0.03371 ( 406) hydrogen bonds : angle 3.75148 ( 1173) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 0.289 Fit side-chains REVERT: A 269 TYR cc_start: 0.8111 (OUTLIER) cc_final: 0.7504 (m-10) REVERT: A 346 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7738 (mt) REVERT: A 451 MET cc_start: 0.6067 (ptt) cc_final: 0.5843 (ptt) REVERT: A 595 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8590 (tpt170) REVERT: A 784 ILE cc_start: 0.7764 (mm) cc_final: 0.7359 (mm) REVERT: A 817 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.7201 (ptmm) REVERT: B 125 ASP cc_start: 0.6631 (OUTLIER) cc_final: 0.6127 (m-30) REVERT: B 187 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8020 (ttmt) REVERT: B 226 LYS cc_start: 0.6181 (mppt) cc_final: 0.5899 (mmtt) REVERT: C 77 LEU cc_start: 0.3344 (OUTLIER) cc_final: 0.3105 (pt) outliers start: 35 outliers final: 20 residues processed: 146 average time/residue: 0.5356 time to fit residues: 82.1341 Evaluate side-chains 145 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 419 GLN Chi-restraints excluded: chain A residue 595 ARG Chi-restraints excluded: chain A residue 782 ASN Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 817 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 859 ASN Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 77 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 5 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 GLN A 902 HIS B 251 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.150306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.117802 restraints weight = 9484.763| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.06 r_work: 0.3165 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7843 Z= 0.144 Angle : 0.552 9.386 10619 Z= 0.278 Chirality : 0.041 0.189 1220 Planarity : 0.004 0.050 1353 Dihedral : 4.661 50.067 1050 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.49 % Favored : 96.19 % Rotamer: Outliers : 4.34 % Allowed : 27.58 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.98 (0.29), residues: 945 helix: 1.67 (0.23), residues: 544 sheet: -0.10 (0.46), residues: 141 loop : -1.07 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 180 TYR 0.010 0.001 TYR B 152 PHE 0.013 0.001 PHE A 160 TRP 0.006 0.001 TRP A 802 HIS 0.008 0.001 HIS A 902 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 7843) covalent geometry : angle 0.55180 (10619) hydrogen bonds : bond 0.04005 ( 406) hydrogen bonds : angle 3.82177 ( 1173) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 121 time to evaluate : 0.182 Fit side-chains REVERT: A 141 GLU cc_start: 0.6634 (OUTLIER) cc_final: 0.5569 (mm-30) REVERT: A 269 TYR cc_start: 0.8036 (OUTLIER) cc_final: 0.7448 (m-10) REVERT: A 346 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7760 (mt) REVERT: A 595 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8447 (tpt170) REVERT: A 817 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.7261 (ptmm) REVERT: B 147 ASN cc_start: 0.7288 (p0) cc_final: 0.6989 (p0) REVERT: B 148 LEU cc_start: 0.8029 (mp) cc_final: 0.7790 (mp) REVERT: B 160 LEU cc_start: 0.8038 (tp) cc_final: 0.7816 (tp) REVERT: B 187 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8056 (ttmt) REVERT: C 77 LEU cc_start: 0.3384 (OUTLIER) cc_final: 0.3126 (pt) outliers start: 37 outliers final: 22 residues processed: 148 average time/residue: 0.5213 time to fit residues: 81.1523 Evaluate side-chains 147 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 419 GLN Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 595 ARG Chi-restraints excluded: chain A residue 782 ASN Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 817 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 859 ASN Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 77 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 92 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 902 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.150917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.118302 restraints weight = 9390.645| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.06 r_work: 0.3186 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7843 Z= 0.128 Angle : 0.542 10.312 10619 Z= 0.274 Chirality : 0.041 0.190 1220 Planarity : 0.004 0.060 1353 Dihedral : 4.652 50.645 1050 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.70 % Favored : 95.98 % Rotamer: Outliers : 3.52 % Allowed : 28.76 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.96 (0.29), residues: 945 helix: 1.67 (0.23), residues: 544 sheet: -0.20 (0.44), residues: 146 loop : -1.06 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 180 TYR 0.011 0.001 TYR A 436 PHE 0.012 0.001 PHE A 431 TRP 0.006 0.001 TRP A 802 HIS 0.008 0.001 HIS A 902 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 7843) covalent geometry : angle 0.54222 (10619) hydrogen bonds : bond 0.03788 ( 406) hydrogen bonds : angle 3.82011 ( 1173) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.184 Fit side-chains REVERT: A 269 TYR cc_start: 0.8019 (OUTLIER) cc_final: 0.7425 (m-10) REVERT: A 346 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7755 (mt) REVERT: A 447 GLU cc_start: 0.6866 (pp20) cc_final: 0.6615 (pp20) REVERT: A 451 MET cc_start: 0.6294 (ptt) cc_final: 0.6087 (ptt) REVERT: A 595 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8443 (tpt170) REVERT: A 817 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.7240 (ptmm) REVERT: B 147 ASN cc_start: 0.7276 (p0) cc_final: 0.6968 (p0) REVERT: B 148 LEU cc_start: 0.8031 (mp) cc_final: 0.7760 (mp) REVERT: B 160 LEU cc_start: 0.8083 (tp) cc_final: 0.7842 (tp) REVERT: B 187 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8038 (ttmt) REVERT: B 247 LYS cc_start: 0.7955 (tptp) cc_final: 0.7727 (tptp) REVERT: C 77 LEU cc_start: 0.3372 (OUTLIER) cc_final: 0.3125 (pt) outliers start: 30 outliers final: 23 residues processed: 141 average time/residue: 0.5106 time to fit residues: 75.8122 Evaluate side-chains 144 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 419 GLN Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 595 ARG Chi-restraints excluded: chain A residue 782 ASN Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 817 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 859 ASN Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 77 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 29 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 902 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.152702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.120468 restraints weight = 9508.605| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.08 r_work: 0.3195 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 7843 Z= 0.107 Angle : 0.517 10.678 10619 Z= 0.261 Chirality : 0.040 0.185 1220 Planarity : 0.004 0.063 1353 Dihedral : 4.528 52.742 1050 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.81 % Favored : 95.87 % Rotamer: Outliers : 3.64 % Allowed : 28.76 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.29), residues: 945 helix: 1.74 (0.23), residues: 544 sheet: -0.19 (0.44), residues: 146 loop : -1.01 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 180 TYR 0.013 0.001 TYR A 436 PHE 0.013 0.001 PHE A 431 TRP 0.005 0.001 TRP A 450 HIS 0.009 0.001 HIS A 902 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 7843) covalent geometry : angle 0.51685 (10619) hydrogen bonds : bond 0.03282 ( 406) hydrogen bonds : angle 3.74387 ( 1173) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 0.272 Fit side-chains REVERT: A 269 TYR cc_start: 0.8094 (OUTLIER) cc_final: 0.7519 (m-10) REVERT: A 447 GLU cc_start: 0.6729 (pp20) cc_final: 0.6424 (pp20) REVERT: A 451 MET cc_start: 0.6284 (ptt) cc_final: 0.6063 (ptt) REVERT: A 595 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8597 (tpt170) REVERT: A 682 GLN cc_start: 0.8013 (mt0) cc_final: 0.7802 (mt0) REVERT: A 817 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.7229 (ptmm) REVERT: B 160 LEU cc_start: 0.8039 (tp) cc_final: 0.7836 (tp) REVERT: B 187 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8050 (ttmt) REVERT: B 226 LYS cc_start: 0.6170 (mppt) cc_final: 0.5895 (mmtt) REVERT: B 247 LYS cc_start: 0.7999 (tptp) cc_final: 0.7780 (tptp) REVERT: B 283 ARG cc_start: 0.6543 (ttp-110) cc_final: 0.6118 (ttm110) REVERT: C 77 LEU cc_start: 0.3395 (OUTLIER) cc_final: 0.3142 (pt) outliers start: 31 outliers final: 20 residues processed: 147 average time/residue: 0.5324 time to fit residues: 82.2183 Evaluate side-chains 139 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 419 GLN Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 595 ARG Chi-restraints excluded: chain A residue 782 ASN Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 817 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 859 ASN Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 77 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 43 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 36 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 902 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.154260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.122150 restraints weight = 9527.264| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.07 r_work: 0.3193 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 7843 Z= 0.105 Angle : 0.519 12.202 10619 Z= 0.261 Chirality : 0.040 0.184 1220 Planarity : 0.004 0.062 1353 Dihedral : 4.496 54.487 1050 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.81 % Favored : 95.87 % Rotamer: Outliers : 2.82 % Allowed : 29.46 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.29), residues: 945 helix: 1.72 (0.23), residues: 548 sheet: -0.18 (0.44), residues: 146 loop : -1.10 (0.42), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 180 TYR 0.014 0.001 TYR A 436 PHE 0.012 0.001 PHE A 431 TRP 0.006 0.001 TRP A 450 HIS 0.009 0.001 HIS A 902 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 7843) covalent geometry : angle 0.51911 (10619) hydrogen bonds : bond 0.03227 ( 406) hydrogen bonds : angle 3.70585 ( 1173) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2306.42 seconds wall clock time: 39 minutes 57.89 seconds (2397.89 seconds total)