Starting phenix.real_space_refine on Wed Aug 5 00:59:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ien_35387/08_2026/8ien_35387_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ien_35387/08_2026/8ien_35387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ien_35387/08_2026/8ien_35387_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ien_35387/08_2026/8ien_35387_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ien_35387/08_2026/8ien_35387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ien_35387/08_2026/8ien_35387.map" } resolution = 3.25 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= 0.003 sd= 0.075 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 Al 1 5.89 5 Mg 1 5.21 5 S 53 5.16 5 C 4959 2.51 5 N 1320 2.21 5 O 1340 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s 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: 7678 Number of models: 1 Model: "" Number of chains: 2 Chain: "P" Number of atoms: 7644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 7644 Classifications: {'peptide': 991} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 65, 'TRANS': 922} Chain breaks: 6 Chain: "P" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, 'ALF': 1, 'SPM': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 1.74, per 1000 atoms: 0.23 Number of scatterers: 7678 At special positions: 0 Unit cell: (86.505, 112.785, 124.83, 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) S 53 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1340 8.00 N 1320 7.00 C 4959 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 331.8 milliseconds 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1846 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 5 sheets defined 48.2% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'P' and resid 50 through 59 Processing helix chain 'P' and resid 61 through 66 Processing helix chain 'P' and resid 69 through 77 removed outlier: 3.828A pdb=" N ARG P 76 " --> pdb=" O GLY P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 195 through 201 Processing helix chain 'P' and resid 208 through 217 removed outlier: 3.652A pdb=" N ARG P 212 " --> pdb=" O ASP P 208 " (cutoff:3.500A) Processing helix chain 'P' and resid 227 through 236 Processing helix chain 'P' and resid 238 through 254 Processing helix chain 'P' and resid 256 through 290 Processing helix chain 'P' and resid 310 through 312 No H-bonds generated for 'chain 'P' and resid 310 through 312' Processing helix chain 'P' and resid 403 through 413 removed outlier: 4.003A pdb=" N VAL P 408 " --> pdb=" O LYS P 404 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N HIS P 413 " --> pdb=" O SER P 409 " (cutoff:3.500A) Processing helix chain 'P' and resid 427 through 451 removed outlier: 3.719A pdb=" N ILE P 444 " --> pdb=" O THR P 440 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG P 449 " --> pdb=" O PHE P 445 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG P 451 " --> pdb=" O LEU P 447 " (cutoff:3.500A) Processing helix chain 'P' and resid 456 through 469 removed outlier: 3.582A pdb=" N ARG P 460 " --> pdb=" O GLU P 456 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU P 462 " --> pdb=" O VAL P 458 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL P 469 " --> pdb=" O VAL P 465 " (cutoff:3.500A) Processing helix chain 'P' and resid 472 through 492 removed outlier: 4.347A pdb=" N CYS P 480 " --> pdb=" O ALA P 476 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR P 481 " --> pdb=" O MET P 477 " (cutoff:3.500A) Processing helix chain 'P' and resid 498 through 504 removed outlier: 4.416A pdb=" N ASN P 502 " --> pdb=" O PRO P 498 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU P 503 " --> pdb=" O LEU P 499 " (cutoff:3.500A) Processing helix chain 'P' and resid 549 through 558 Processing helix chain 'P' and resid 571 through 581 Processing helix chain 'P' and resid 656 through 664 removed outlier: 3.583A pdb=" N VAL P 660 " --> pdb=" O SER P 656 " (cutoff:3.500A) Processing helix chain 'P' and resid 673 through 683 removed outlier: 3.614A pdb=" N LEU P 677 " --> pdb=" O PHE P 673 " (cutoff:3.500A) Processing helix chain 'P' and resid 731 through 742 removed outlier: 3.754A pdb=" N VAL P 735 " --> pdb=" O GLN P 731 " (cutoff:3.500A) Processing helix chain 'P' and resid 753 through 765 removed outlier: 3.520A pdb=" N ALA P 757 " --> pdb=" O ASN P 753 " (cutoff:3.500A) Processing helix chain 'P' and resid 826 through 835 Processing helix chain 'P' and resid 840 through 847 Processing helix chain 'P' and resid 855 through 868 Processing helix chain 'P' and resid 882 through 889 Processing helix chain 'P' and resid 914 through 955 removed outlier: 4.249A pdb=" N MET P 918 " --> pdb=" O GLU P 914 " (cutoff:3.500A) Processing helix chain 'P' and resid 959 through 970 Processing helix chain 'P' and resid 970 through 978 Processing helix chain 'P' and resid 998 through 1026 removed outlier: 3.750A pdb=" N LEU P1017 " --> pdb=" O THR P1013 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY P1018 " --> pdb=" O GLY P1014 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY P1019 " --> pdb=" O VAL P1015 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N TYR P1020 " --> pdb=" O GLN P1016 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA P1025 " --> pdb=" O PHE P1021 " (cutoff:3.500A) Processing helix chain 'P' and resid 1037 through 1041 removed outlier: 3.651A pdb=" N ASN P1041 " --> pdb=" O ALA P1038 " (cutoff:3.500A) Processing helix chain 'P' and resid 1044 through 1065 removed outlier: 3.776A pdb=" N THR P1048 " --> pdb=" O ASN P1044 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU P1059 " --> pdb=" O SER P1055 " (cutoff:3.500A) Processing helix chain 'P' and resid 1078 through 1098 Processing helix chain 'P' and resid 1113 through 1139 Processing helix chain 'P' and resid 1141 through 1146 Processing helix chain 'P' and resid 1156 through 1169 Processing sheet with id=AA1, first strand: chain 'P' and resid 40 through 41 removed outlier: 4.136A pdb=" N CYS P 41 " --> pdb=" O ILE P 90 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE P 90 " --> pdb=" O CYS P 41 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N PHE P 103 " --> pdb=" O LEU P 167 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU P 167 " --> pdb=" O PHE P 103 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR P 166 " --> pdb=" O TYR P 173 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE P 174 " --> pdb=" O TYR P 183 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR P 183 " --> pdb=" O ILE P 174 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE P 176 " --> pdb=" O ALA P 181 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA P 181 " --> pdb=" O ILE P 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 303 through 308 removed outlier: 3.843A pdb=" N GLU P 303 " --> pdb=" O ARG P 299 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N CYS P 296 " --> pdb=" O VAL P 319 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N CYS P 317 " --> pdb=" O CYS P 298 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU P 392 " --> pdb=" O VAL P 334 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR P 396 " --> pdb=" O ASP P 330 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ASP P 330 " --> pdb=" O THR P 396 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA P 331 " --> pdb=" O LEU P 374 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU P 374 " --> pdb=" O ALA P 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 351 through 354 removed outlier: 3.770A pdb=" N VAL P 340 " --> pdb=" O VAL P 352 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS P 354 " --> pdb=" O CYS P 338 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASN P 341 " --> pdb=" O ILE P 380 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ILE P 380 " --> pdb=" O ASN P 341 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 493 through 495 removed outlier: 5.895A pdb=" N GLY P 892 " --> pdb=" O PHE P 906 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N SER P 908 " --> pdb=" O GLY P 892 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER P 894 " --> pdb=" O SER P 908 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N VAL P 873 " --> pdb=" O VAL P 891 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N ILE P 893 " --> pdb=" O VAL P 873 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N MET P 875 " --> pdb=" O ILE P 893 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU P 509 " --> pdb=" O GLY P 874 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N CYS P 876 " --> pdb=" O LEU P 509 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N CYS P 511 " --> pdb=" O CYS P 876 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR P 849 " --> pdb=" O ALA P 746 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LEU P 823 " --> pdb=" O GLY P 848 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N HIS P 772 " --> pdb=" O ALA P 824 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER P 788 " --> pdb=" O LEU P 773 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 624 through 627 removed outlier: 4.350A pdb=" N HIS P 626 " --> pdb=" O VAL P 640 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL P 640 " --> pdb=" O HIS P 626 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL P 641 " --> pdb=" O GLU P 650 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLU P 650 " --> pdb=" O VAL P 641 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY P 655 " --> pdb=" O ALA P 689 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA P 689 " --> pdb=" O GLY P 655 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY P 720 " --> pdb=" O LEU P 690 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N SER P 692 " --> pdb=" O LEU P 718 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LEU P 718 " --> pdb=" O SER P 692 " (cutoff:3.500A) 362 hydrogen bonds defined for protein. 1071 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: 1.39 Time building geometry restraints manager: 0.68 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: 2449 1.35 - 1.46: 1687 1.46 - 1.58: 3623 1.58 - 1.70: 0 1.70 - 1.82: 83 Bond restraints: 7842 Sorted by residual: bond pdb=" C11 SPM P1204 " pdb=" C12 SPM P1204 " ideal model delta sigma weight residual 1.527 1.395 0.132 2.00e-02 2.50e+03 4.35e+01 bond pdb=" C12 SPM P1204 " pdb=" C13 SPM P1204 " ideal model delta sigma weight residual 1.527 1.407 0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" F1 ALF P1202 " pdb="AL ALF P1202 " ideal model delta sigma weight residual 1.684 1.785 -0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" F3 ALF P1202 " pdb="AL ALF P1202 " ideal model delta sigma weight residual 1.685 1.785 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" F2 ALF P1202 " pdb="AL ALF P1202 " ideal model delta sigma weight residual 1.685 1.784 -0.099 2.00e-02 2.50e+03 2.47e+01 ... (remaining 7837 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.26: 10663 14.26 - 28.52: 4 28.52 - 42.78: 0 42.78 - 57.04: 0 57.04 - 71.30: 2 Bond angle restraints: 10669 Sorted by residual: angle pdb=" F1 ALF P1202 " pdb="AL ALF P1202 " pdb=" F2 ALF P1202 " ideal model delta sigma weight residual 108.68 179.98 -71.30 3.00e+00 1.11e-01 5.65e+02 angle pdb=" F3 ALF P1202 " pdb="AL ALF P1202 " pdb=" F4 ALF P1202 " ideal model delta sigma weight residual 109.63 180.00 -70.37 3.00e+00 1.11e-01 5.50e+02 angle pdb=" F2 ALF P1202 " pdb="AL ALF P1202 " pdb=" F4 ALF P1202 " ideal model delta sigma weight residual 110.21 89.99 20.22 3.00e+00 1.11e-01 4.54e+01 angle pdb=" F1 ALF P1202 " pdb="AL ALF P1202 " pdb=" F3 ALF P1202 " ideal model delta sigma weight residual 109.69 90.01 19.68 3.00e+00 1.11e-01 4.30e+01 angle pdb=" F2 ALF P1202 " pdb="AL ALF P1202 " pdb=" F3 ALF P1202 " ideal model delta sigma weight residual 109.59 90.01 19.58 3.00e+00 1.11e-01 4.26e+01 ... (remaining 10664 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 4247 17.68 - 35.35: 401 35.35 - 53.03: 71 53.03 - 70.70: 16 70.70 - 88.38: 5 Dihedral angle restraints: 4740 sinusoidal: 1880 harmonic: 2860 Sorted by residual: dihedral pdb=" CA ASP P 189 " pdb=" CB ASP P 189 " pdb=" CG ASP P 189 " pdb=" OD1 ASP P 189 " ideal model delta sinusoidal sigma weight residual -30.00 -86.84 56.84 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CB GLU P 650 " pdb=" CG GLU P 650 " pdb=" CD GLU P 650 " pdb=" OE1 GLU P 650 " ideal model delta sinusoidal sigma weight residual 0.00 88.38 -88.38 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CA LEU P 968 " pdb=" C LEU P 968 " pdb=" N VAL P 969 " pdb=" CA VAL P 969 " ideal model delta harmonic sigma weight residual 180.00 -164.60 -15.40 0 5.00e+00 4.00e-02 9.49e+00 ... (remaining 4737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 996 0.044 - 0.088: 197 0.088 - 0.132: 69 0.132 - 0.176: 2 0.176 - 0.220: 2 Chirality restraints: 1266 Sorted by residual: chirality pdb=" CA SER P 425 " pdb=" N SER P 425 " pdb=" C SER P 425 " pdb=" CB SER P 425 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA HIS P 424 " pdb=" N HIS P 424 " pdb=" C HIS P 424 " pdb=" CB HIS P 424 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.50e-01 chirality pdb=" CA PRO P 618 " pdb=" N PRO P 618 " pdb=" C PRO P 618 " pdb=" CB PRO P 618 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.31e-01 ... (remaining 1263 not shown) Planarity restraints: 1339 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO P 618 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO P 619 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO P 619 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO P 619 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET P 426 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C MET P 426 " -0.030 2.00e-02 2.50e+03 pdb=" O MET P 426 " 0.011 2.00e-02 2.50e+03 pdb=" N LYS P 427 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU P1042 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.07e+00 pdb=" N PRO P1043 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO P1043 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO P1043 " -0.019 5.00e-02 4.00e+02 ... (remaining 1336 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 215 2.71 - 3.26: 7394 3.26 - 3.81: 11972 3.81 - 4.35: 14110 4.35 - 4.90: 24051 Nonbonded interactions: 57742 Sorted by model distance: nonbonded pdb="MG MG P1201 " pdb=" F1 ALF P1202 " model vdw 2.168 2.120 nonbonded pdb=" CG2 VAL P 467 " pdb=" C12 SPM P1204 " model vdw 2.241 3.860 nonbonded pdb=" OD2 ASP P 513 " pdb="MG MG P1201 " model vdw 2.252 2.170 nonbonded pdb=" O THR P 515 " pdb="MG MG P1201 " model vdw 2.280 2.170 nonbonded pdb=" CZ3 TRP P 251 " pdb=" C9 SPM P1204 " model vdw 2.282 3.740 ... (remaining 57737 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.100 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0001 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 : 0.009 0.737 7844 Z= 0.880 Angle : 1.211 71.295 10669 Z= 0.486 Chirality : 0.040 0.220 1266 Planarity : 0.004 0.050 1339 Dihedral : 14.043 88.379 2894 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.02 % Favored : 94.88 % Rotamer: Outliers : 0.24 % Allowed : 2.49 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -2.18 (0.25), residues: 977 helix: -0.46 (0.23), residues: 450 sheet: -1.34 (0.62), residues: 61 loop : -2.50 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P1148 TYR 0.015 0.001 TYR P 256 PHE 0.015 0.001 PHE P1128 TRP 0.006 0.001 TRP P 67 HIS 0.002 0.000 HIS P 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.21 ( 7842) covalent geometry : angle 1.21135 / 0.49 (10669) hydrogen bonds : bond 0.17266 / 11.63 ( 362) hydrogen bonds : angle 5.73938 / 3.99 ( 1071) Misc. bond : bond 0.53561 / 28.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.173 Fit side-chains revert: symmetry clash REVERT: P 63 LEU cc_start: 0.2877 (mt) cc_final: 0.2583 (pt) REVERT: P 526 MET cc_start: -0.0095 (pmm) cc_final: -0.1442 (tpp) REVERT: P 577 MET cc_start: 0.1892 (mtp) cc_final: 0.0826 (tmm) REVERT: P 637 MET cc_start: 0.1190 (tmm) cc_final: 0.0944 (mtp) outliers start: 2 outliers final: 0 residues processed: 86 average time/residue: 0.0605 time to fit residues: 7.6586 Evaluate side-chains 54 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.4980 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.0060 chunk 45 optimal weight: 0.8980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 101 GLN P 198 HIS ** P 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 219 ASN P 281 GLN P 559 HIS ** P 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 944 GLN P1127 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.253319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.223555 restraints weight = 11592.833| |-----------------------------------------------------------------------------| r_work (start): 0.4565 rms_B_bonded: 2.59 r_work: 0.4470 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0642 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7844 Z= 0.149 Angle : 0.924 32.847 10669 Z= 0.381 Chirality : 0.042 0.144 1266 Planarity : 0.005 0.045 1339 Dihedral : 5.782 57.580 1095 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.24 % Allowed : 9.70 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -1.19 (0.26), residues: 977 helix: 0.39 (0.24), residues: 451 sheet: -0.50 (0.61), residues: 76 loop : -2.14 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 279 TYR 0.025 0.002 TYR P 483 PHE 0.011 0.002 PHE P1128 TRP 0.018 0.001 TRP P 251 HIS 0.004 0.001 HIS P 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 ( 7842) covalent geometry : angle 0.92424 / 0.38 (10669) hydrogen bonds : bond 0.03862 / 2.62 ( 362) hydrogen bonds : angle 4.36303 / 3.05 ( 1071) Misc. bond : bond 0.00536 / 0.28 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 63 LEU cc_start: 0.3162 (mt) cc_final: 0.2755 (pt) REVERT: P 288 MET cc_start: -0.0401 (ptt) cc_final: -0.1166 (tpt) REVERT: P 477 MET cc_start: 0.1560 (tpp) cc_final: 0.1283 (mmm) REVERT: P 526 MET cc_start: -0.0751 (pmm) cc_final: -0.2151 (tmm) REVERT: P 573 MET cc_start: 0.3629 (ptt) cc_final: 0.2461 (mmm) REVERT: P 577 MET cc_start: 0.2677 (mtp) cc_final: 0.0963 (tmm) REVERT: P 637 MET cc_start: -0.0125 (tmm) cc_final: -0.0421 (mtp) REVERT: P 978 MET cc_start: 0.2636 (mtt) cc_final: 0.1387 (mmm) outliers start: 2 outliers final: 2 residues processed: 62 average time/residue: 0.0540 time to fit residues: 5.3494 Evaluate side-chains 52 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 219 ASN Chi-restraints excluded: chain P residue 429 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 5 optimal weight: 0.5980 chunk 63 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 66 optimal weight: 0.0970 chunk 27 optimal weight: 0.0000 chunk 87 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 overall best weight: 0.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 81 ASN ** P 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 944 GLN P 962 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.255447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.225631 restraints weight = 11691.865| |-----------------------------------------------------------------------------| r_work (start): 0.4580 rms_B_bonded: 2.66 r_work: 0.4480 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0761 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7844 Z= 0.115 Angle : 0.871 29.581 10669 Z= 0.351 Chirality : 0.040 0.148 1266 Planarity : 0.004 0.044 1339 Dihedral : 5.325 58.212 1095 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.95 % Allowed : 12.07 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -0.70 (0.27), residues: 977 helix: 0.94 (0.25), residues: 448 sheet: -0.35 (0.58), residues: 76 loop : -2.01 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 279 TYR 0.025 0.001 TYR P 483 PHE 0.009 0.001 PHE P1128 TRP 0.006 0.001 TRP P 643 HIS 0.007 0.001 HIS P 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 ( 7842) covalent geometry : angle 0.87055 / 0.35 (10669) hydrogen bonds : bond 0.03042 / 2.04 ( 362) hydrogen bonds : angle 4.07206 / 2.83 ( 1071) Misc. bond : bond 0.00236 / 0.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 63 LEU cc_start: 0.3197 (mt) cc_final: 0.2796 (pt) REVERT: P 288 MET cc_start: -0.0289 (ptt) cc_final: -0.1113 (tpp) REVERT: P 526 MET cc_start: -0.0214 (pmm) cc_final: -0.2522 (tmm) REVERT: P 577 MET cc_start: 0.2754 (mtp) cc_final: 0.0847 (tmm) REVERT: P 978 MET cc_start: 0.2521 (mtt) cc_final: 0.1711 (mmm) outliers start: 8 outliers final: 2 residues processed: 61 average time/residue: 0.0498 time to fit residues: 4.7705 Evaluate side-chains 52 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 275 LEU Chi-restraints excluded: chain P residue 724 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 28 optimal weight: 0.8980 chunk 20 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 70.3051 > 50:) chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 chunk 51 optimal weight: 0.2980 chunk 43 optimal weight: 0.1980 chunk 12 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 219 ASN ** P 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1047 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4948 r_free = 0.4948 target = 0.265279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.243116 restraints weight = 12272.931| |-----------------------------------------------------------------------------| r_work (start): 0.4838 rms_B_bonded: 1.94 r_work: 0.4767 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.4767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1006 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7844 Z= 0.139 Angle : 0.909 30.003 10669 Z= 0.377 Chirality : 0.042 0.242 1266 Planarity : 0.005 0.042 1339 Dihedral : 5.705 58.030 1095 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.42 % Allowed : 14.20 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -0.67 (0.27), residues: 977 helix: 0.85 (0.25), residues: 449 sheet: 0.25 (0.57), residues: 73 loop : -1.96 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 279 TYR 0.021 0.002 TYR P 256 PHE 0.014 0.001 PHE P 906 TRP 0.009 0.001 TRP P1028 HIS 0.008 0.001 HIS P 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 ( 7842) covalent geometry : angle 0.90855 / 0.38 (10669) hydrogen bonds : bond 0.03477 / 2.37 ( 362) hydrogen bonds : angle 4.14025 / 2.88 ( 1071) Misc. bond : bond 0.00282 / 0.14 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 275 LEU cc_start: 0.0692 (OUTLIER) cc_final: 0.0197 (mp) REVERT: P 459 ILE cc_start: 0.1112 (OUTLIER) cc_final: 0.0784 (pt) REVERT: P 483 TYR cc_start: 0.1938 (m-80) cc_final: -0.0242 (m-10) REVERT: P 526 MET cc_start: 0.1068 (pmm) cc_final: 0.0614 (mpp) REVERT: P 577 MET cc_start: 0.2709 (mtp) cc_final: 0.0785 (tmm) REVERT: P 648 GLN cc_start: 0.4739 (tp40) cc_final: 0.4313 (pt0) REVERT: P 675 GLN cc_start: 0.5093 (tm-30) cc_final: 0.4476 (mp10) REVERT: P 964 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.5934 (tp) outliers start: 12 outliers final: 4 residues processed: 75 average time/residue: 0.0579 time to fit residues: 6.7030 Evaluate side-chains 68 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 219 ASN Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 275 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 459 ILE Chi-restraints excluded: chain P residue 964 LEU Chi-restraints excluded: chain P residue 1028 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 82 optimal weight: 0.9980 chunk 97 optimal weight: 0.0000 chunk 44 optimal weight: 4.9990 chunk 48 optimal weight: 0.0060 chunk 90 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 8 optimal weight: 0.3980 chunk 23 optimal weight: 0.0370 chunk 6 optimal weight: 0.6980 overall best weight: 0.2278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 219 ASN ** P 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4953 r_free = 0.4953 target = 0.266074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.244194 restraints weight = 12101.755| |-----------------------------------------------------------------------------| r_work (start): 0.4851 rms_B_bonded: 1.93 r_work: 0.4784 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work (final): 0.4784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1005 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7844 Z= 0.106 Angle : 0.872 30.199 10669 Z= 0.348 Chirality : 0.040 0.147 1266 Planarity : 0.004 0.042 1339 Dihedral : 5.477 57.432 1095 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.07 % Allowed : 16.09 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -0.40 (0.28), residues: 977 helix: 1.09 (0.25), residues: 454 sheet: 0.43 (0.57), residues: 73 loop : -1.89 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 636 TYR 0.017 0.001 TYR P 936 PHE 0.007 0.001 PHE P1051 TRP 0.007 0.001 TRP P1028 HIS 0.006 0.001 HIS P 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 ( 7842) covalent geometry : angle 0.87166 / 0.35 (10669) hydrogen bonds : bond 0.02905 / 1.95 ( 362) hydrogen bonds : angle 3.93043 / 2.72 ( 1071) Misc. bond : bond 0.00154 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 526 MET cc_start: 0.1029 (pmm) cc_final: 0.0686 (mpp) REVERT: P 577 MET cc_start: 0.2656 (mtp) cc_final: 0.0747 (tmm) REVERT: P 675 GLN cc_start: 0.4965 (tm-30) cc_final: 0.4507 (mp10) REVERT: P 964 LEU cc_start: 0.7367 (tt) cc_final: 0.6271 (tp) outliers start: 9 outliers final: 6 residues processed: 69 average time/residue: 0.0466 time to fit residues: 5.1898 Evaluate side-chains 63 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 275 LEU Chi-restraints excluded: chain P residue 380 ILE Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 894 SER Chi-restraints excluded: chain P residue 902 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 94 optimal weight: 0.5980 chunk 53 optimal weight: 9.9990 chunk 26 optimal weight: 0.0970 chunk 39 optimal weight: 0.0980 chunk 30 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 90 optimal weight: 0.0970 chunk 98 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 847 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4971 r_free = 0.4971 target = 0.268362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.247860 restraints weight = 12220.017| |-----------------------------------------------------------------------------| r_work (start): 0.4876 rms_B_bonded: 1.88 r_work: 0.4807 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work (final): 0.4807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1139 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7844 Z= 0.107 Angle : 0.871 29.971 10669 Z= 0.349 Chirality : 0.040 0.146 1266 Planarity : 0.005 0.042 1339 Dihedral : 5.066 56.228 1095 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.18 % Allowed : 17.99 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -0.31 (0.28), residues: 977 helix: 1.16 (0.25), residues: 454 sheet: 0.49 (0.58), residues: 75 loop : -1.85 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 286 TYR 0.015 0.001 TYR P 256 PHE 0.007 0.001 PHE P1051 TRP 0.014 0.001 TRP P1028 HIS 0.007 0.001 HIS P 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 ( 7842) covalent geometry : angle 0.87063 / 0.35 (10669) hydrogen bonds : bond 0.02881 / 1.95 ( 362) hydrogen bonds : angle 3.89388 / 2.69 ( 1071) Misc. bond : bond 0.00153 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 526 MET cc_start: 0.1323 (pmm) cc_final: 0.0800 (mpp) REVERT: P 577 MET cc_start: 0.2736 (mtp) cc_final: 0.0792 (tmm) REVERT: P 937 MET cc_start: 0.3111 (mmt) cc_final: 0.1916 (mmt) REVERT: P 964 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.6892 (tp) REVERT: P 1091 VAL cc_start: 0.1829 (p) cc_final: 0.1464 (t) outliers start: 10 outliers final: 7 residues processed: 70 average time/residue: 0.0496 time to fit residues: 5.6933 Evaluate side-chains 67 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 197 VAL Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain P residue 902 VAL Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 964 LEU Chi-restraints excluded: chain P residue 1028 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 89 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 82 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 202 HIS P 219 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5045 r_free = 0.5045 target = 0.278292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4928 r_free = 0.4928 target = 0.263502 restraints weight = 12509.769| |-----------------------------------------------------------------------------| r_work (start): 0.4932 rms_B_bonded: 1.64 r_work: 0.4874 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.4785 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.4785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2037 moved from start: 0.7560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7844 Z= 0.177 Angle : 1.029 33.204 10669 Z= 0.447 Chirality : 0.046 0.169 1266 Planarity : 0.006 0.065 1339 Dihedral : 5.943 57.302 1095 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 1.89 % Allowed : 17.75 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -1.36 (0.26), residues: 977 helix: 0.08 (0.23), residues: 459 sheet: 0.16 (0.64), residues: 59 loop : -2.12 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 544 TYR 0.038 0.003 TYR P 871 PHE 0.025 0.002 PHE P1051 TRP 0.018 0.002 TRP P1028 HIS 0.005 0.001 HIS P 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.18 ( 7842) covalent geometry : angle 1.02889 / 0.45 (10669) hydrogen bonds : bond 0.04831 / 3.14 ( 362) hydrogen bonds : angle 4.98999 / 3.44 ( 1071) Misc. bond : bond 0.00225 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: P 526 MET cc_start: 0.2374 (pmm) cc_final: 0.1088 (mpp) REVERT: P 648 GLN cc_start: 0.5125 (tp-100) cc_final: 0.3387 (tt0) REVERT: P 837 PHE cc_start: 0.5768 (t80) cc_final: 0.4821 (m-10) REVERT: P 937 MET cc_start: 0.5555 (mmt) cc_final: 0.4097 (mmt) REVERT: P 1123 LEU cc_start: 0.5039 (mt) cc_final: 0.4572 (mt) outliers start: 16 outliers final: 13 residues processed: 91 average time/residue: 0.0492 time to fit residues: 6.8736 Evaluate side-chains 79 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 197 VAL Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain P residue 327 MET Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 441 ILE Chi-restraints excluded: chain P residue 854 MET Chi-restraints excluded: chain P residue 894 SER Chi-restraints excluded: chain P residue 902 VAL Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 1028 TRP Chi-restraints excluded: chain P residue 1118 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.0020 chunk 45 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 26 optimal weight: 0.0670 chunk 97 optimal weight: 0.0170 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 85 optimal weight: 0.0040 chunk 2 optimal weight: 0.0980 chunk 50 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.0376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 180 GLN P 219 ASN P 881 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5055 r_free = 0.5055 target = 0.278324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4932 r_free = 0.4932 target = 0.263261 restraints weight = 12510.190| |-----------------------------------------------------------------------------| r_work (start): 0.4913 rms_B_bonded: 1.63 r_work: 0.4854 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.4764 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.4764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1710 moved from start: 0.7389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7844 Z= 0.115 Angle : 0.911 31.560 10669 Z= 0.371 Chirality : 0.041 0.151 1266 Planarity : 0.005 0.041 1339 Dihedral : 5.115 59.696 1095 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.30 % Allowed : 19.64 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -0.39 (0.28), residues: 977 helix: 1.05 (0.25), residues: 458 sheet: 0.61 (0.68), residues: 54 loop : -1.78 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 172 TYR 0.020 0.001 TYR P 952 PHE 0.007 0.001 PHE P1056 TRP 0.007 0.001 TRP P 643 HIS 0.009 0.001 HIS P 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 7842) covalent geometry : angle 0.91110 / 0.37 (10669) hydrogen bonds : bond 0.03107 / 2.06 ( 362) hydrogen bonds : angle 4.06312 / 2.78 ( 1071) Misc. bond : bond 0.00088 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: P 293 MET cc_start: 0.2030 (pmm) cc_final: 0.1440 (mtt) REVERT: P 526 MET cc_start: 0.1638 (pmm) cc_final: 0.0638 (mpp) REVERT: P 937 MET cc_start: 0.5272 (mmt) cc_final: 0.4341 (mmp) REVERT: P 1123 LEU cc_start: 0.4759 (mt) cc_final: 0.4429 (mt) outliers start: 11 outliers final: 9 residues processed: 81 average time/residue: 0.0509 time to fit residues: 6.3425 Evaluate side-chains 80 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 854 MET Chi-restraints excluded: chain P residue 894 SER Chi-restraints excluded: chain P residue 902 VAL Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 1028 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 7 optimal weight: 0.6980 chunk 40 optimal weight: 0.0370 chunk 44 optimal weight: 0.0770 chunk 54 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 9 optimal weight: 0.0470 chunk 5 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.3114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5032 r_free = 0.5032 target = 0.277195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4903 r_free = 0.4903 target = 0.260630 restraints weight = 12640.412| |-----------------------------------------------------------------------------| r_work (start): 0.4910 rms_B_bonded: 1.87 r_work: 0.4837 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.4837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1845 moved from start: 0.7722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7844 Z= 0.117 Angle : 0.904 31.352 10669 Z= 0.369 Chirality : 0.041 0.151 1266 Planarity : 0.005 0.044 1339 Dihedral : 4.839 57.782 1095 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.54 % Allowed : 20.00 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -0.24 (0.28), residues: 977 helix: 1.18 (0.25), residues: 458 sheet: 0.73 (0.71), residues: 54 loop : -1.73 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 172 TYR 0.021 0.002 TYR P 952 PHE 0.008 0.001 PHE P 963 TRP 0.007 0.001 TRP P 175 HIS 0.008 0.001 HIS P 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 ( 7842) covalent geometry : angle 0.90390 / 0.37 (10669) hydrogen bonds : bond 0.03116 / 2.04 ( 362) hydrogen bonds : angle 4.03117 / 2.76 ( 1071) Misc. bond : bond 0.00115 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: P 293 MET cc_start: 0.2279 (pmm) cc_final: 0.1785 (mtm) REVERT: P 526 MET cc_start: 0.1545 (pmm) cc_final: 0.0540 (mpp) REVERT: P 648 GLN cc_start: 0.5512 (tp40) cc_final: 0.3674 (tm-30) REVERT: P 1009 MET cc_start: 0.5139 (mmt) cc_final: 0.4855 (mmt) REVERT: P 1123 LEU cc_start: 0.4880 (mt) cc_final: 0.4532 (mt) outliers start: 13 outliers final: 11 residues processed: 80 average time/residue: 0.0404 time to fit residues: 5.2660 Evaluate side-chains 77 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 197 VAL Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 441 ILE Chi-restraints excluded: chain P residue 854 MET Chi-restraints excluded: chain P residue 894 SER Chi-restraints excluded: chain P residue 902 VAL Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 1028 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 69 optimal weight: 0.0570 chunk 77 optimal weight: 0.3980 chunk 74 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 53 optimal weight: 0.0970 chunk 88 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 73 optimal weight: 0.1980 chunk 41 optimal weight: 0.3980 chunk 36 optimal weight: 0.8980 overall best weight: 0.2296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5036 r_free = 0.5036 target = 0.277664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.261282 restraints weight = 12698.903| |-----------------------------------------------------------------------------| r_work (start): 0.4914 rms_B_bonded: 1.89 r_work: 0.4843 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.4843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1831 moved from start: 0.7958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 7844 Z= 0.112 Angle : 0.903 31.269 10669 Z= 0.368 Chirality : 0.041 0.147 1266 Planarity : 0.005 0.044 1339 Dihedral : 4.563 56.528 1095 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.42 % Allowed : 20.36 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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 (0.28), residues: 977 helix: 1.38 (0.25), residues: 459 sheet: 0.75 (0.65), residues: 61 loop : -1.64 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 286 TYR 0.015 0.001 TYR P 256 PHE 0.008 0.001 PHE P 963 TRP 0.008 0.001 TRP P 643 HIS 0.009 0.001 HIS P 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 7842) covalent geometry : angle 0.90275 / 0.37 (10669) hydrogen bonds : bond 0.03010 / 1.95 ( 362) hydrogen bonds : angle 3.96066 / 2.71 ( 1071) Misc. bond : bond 0.00099 / 0.05 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: P 293 MET cc_start: 0.2109 (pmm) cc_final: 0.1771 (mtm) REVERT: P 526 MET cc_start: 0.1519 (pmm) cc_final: 0.0519 (mpp) REVERT: P 648 GLN cc_start: 0.5463 (tp40) cc_final: 0.3565 (tm-30) REVERT: P 1009 MET cc_start: 0.5070 (mmt) cc_final: 0.4853 (mmt) outliers start: 12 outliers final: 12 residues processed: 74 average time/residue: 0.0466 time to fit residues: 5.4562 Evaluate side-chains 76 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 197 VAL Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 441 ILE Chi-restraints excluded: chain P residue 854 MET Chi-restraints excluded: chain P residue 894 SER Chi-restraints excluded: chain P residue 902 VAL Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 948 VAL Chi-restraints excluded: chain P residue 1028 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 68 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 8 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 847 GLN P 881 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5074 r_free = 0.5074 target = 0.281932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4980 r_free = 0.4980 target = 0.269740 restraints weight = 12894.218| |-----------------------------------------------------------------------------| r_work (start): 0.4990 rms_B_bonded: 1.56 r_work: 0.4928 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.4841 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.4841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2566 moved from start: 0.9735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7844 Z= 0.182 Angle : 1.027 33.351 10669 Z= 0.450 Chirality : 0.046 0.196 1266 Planarity : 0.006 0.050 1339 Dihedral : 5.452 42.441 1095 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 1.66 % Allowed : 20.24 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -0.83 (0.27), residues: 977 helix: 0.58 (0.24), residues: 459 sheet: 0.74 (0.76), residues: 49 loop : -1.91 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 460 TYR 0.045 0.003 TYR P 871 PHE 0.016 0.002 PHE P 906 TRP 0.018 0.002 TRP P 175 HIS 0.009 0.001 HIS P 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 ( 7842) covalent geometry : angle 1.02744 / 0.45 (10669) hydrogen bonds : bond 0.04475 / 2.99 ( 362) hydrogen bonds : angle 4.84449 / 3.32 ( 1071) Misc. bond : bond 0.00199 / 0.10 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1606.00 seconds wall clock time: 28 minutes 7.37 seconds (1687.37 seconds total)