Starting phenix.real_space_refine on Wed Mar 12 13:12:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ien_35387/03_2025/8ien_35387_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ien_35387/03_2025/8ien_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ien_35387/03_2025/8ien_35387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ien_35387/03_2025/8ien_35387.map" model { file = "/net/cci-nas-00/data/ceres_data/8ien_35387/03_2025/8ien_35387_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ien_35387/03_2025/8ien_35387_trim.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.39, per 1000 atoms: 0.70 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: 2.20 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.95 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: 2.75 Time building geometry restraints manager: 2.57 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: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.960 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0170 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 : 0.004 0.132 7842 Z= 0.243 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.006 0.001 TRP P 67 HIS 0.002 0.000 HIS P 190 PHE 0.015 0.001 PHE P1128 TYR 0.015 0.001 TYR P 256 ARG 0.002 0.000 ARG P1148 *********************** 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 : 0.739 Fit side-chains revert: symmetry clash REVERT: P 63 LEU cc_start: 0.2877 (mt) cc_final: 0.2586 (pt) REVERT: P 326 LEU cc_start: 0.3219 (tp) cc_final: 0.2997 (pp) REVERT: P 526 MET cc_start: -0.0095 (pmm) cc_final: -0.1444 (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: 0.0942 (mtp) outliers start: 2 outliers final: 0 residues processed: 86 average time/residue: 0.1913 time to fit residues: 23.3916 Evaluate side-chains 55 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 40 optimal weight: 0.4980 chunk 77 optimal weight: 0.2980 chunk 30 optimal weight: 0.0570 chunk 47 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.253120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.223045 restraints weight = 11482.261| |-----------------------------------------------------------------------------| r_work (start): 0.4561 rms_B_bonded: 2.60 r_work: 0.4464 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0794 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7842 Z= 0.198 Angle : 0.918 32.545 10669 Z= 0.378 Chirality : 0.042 0.144 1266 Planarity : 0.005 0.046 1339 Dihedral : 5.675 55.543 1095 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.59 % Allowed : 9.11 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.27), residues: 977 helix: 0.47 (0.24), residues: 452 sheet: -0.52 (0.60), residues: 76 loop : -2.15 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 251 HIS 0.003 0.001 HIS P 822 PHE 0.012 0.001 PHE P1128 TYR 0.023 0.001 TYR P 483 ARG 0.004 0.000 ARG P 279 *********************** 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 64 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: P 63 LEU cc_start: 0.3183 (mt) cc_final: 0.2771 (pt) REVERT: P 288 MET cc_start: -0.0059 (ptt) cc_final: -0.1136 (tpp) REVERT: P 326 LEU cc_start: 0.3782 (tp) cc_final: 0.3249 (pp) REVERT: P 477 MET cc_start: 0.1615 (tpp) cc_final: 0.1354 (mmm) REVERT: P 526 MET cc_start: -0.0818 (pmm) cc_final: -0.2129 (tmm) REVERT: P 577 MET cc_start: 0.2672 (mtp) cc_final: 0.0961 (tmm) REVERT: P 637 MET cc_start: 0.0174 (tmm) cc_final: -0.0052 (mtp) REVERT: P 978 MET cc_start: 0.2872 (mtt) cc_final: 0.1464 (mmm) outliers start: 5 outliers final: 4 residues processed: 61 average time/residue: 0.1528 time to fit residues: 14.4070 Evaluate side-chains 54 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 50 TYR Chi-restraints excluded: chain P residue 219 ASN Chi-restraints excluded: chain P residue 312 LEU 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 67 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 81 optimal weight: 0.0870 chunk 7 optimal weight: 0.0470 chunk 43 optimal weight: 0.5980 chunk 52 optimal weight: 9.9990 chunk 42 optimal weight: 0.5980 chunk 73 optimal weight: 0.1980 chunk 44 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 180 GLN ** 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 = 0.4849 r_free = 0.4849 target = 0.255004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.225112 restraints weight = 11758.557| |-----------------------------------------------------------------------------| r_work (start): 0.4577 rms_B_bonded: 2.65 r_work: 0.4478 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.4478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0896 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 7842 Z= 0.159 Angle : 0.866 30.041 10669 Z= 0.346 Chirality : 0.040 0.183 1266 Planarity : 0.004 0.044 1339 Dihedral : 5.257 59.014 1095 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.24 % Allowed : 11.83 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.27), residues: 977 helix: 0.95 (0.25), residues: 451 sheet: -0.33 (0.58), residues: 76 loop : -1.95 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 643 HIS 0.002 0.000 HIS P 780 PHE 0.010 0.001 PHE P1128 TYR 0.024 0.001 TYR P 483 ARG 0.003 0.000 ARG P 279 *********************** 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 61 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 63 LEU cc_start: 0.3191 (mt) cc_final: 0.2788 (pt) REVERT: P 288 MET cc_start: -0.0266 (ptt) cc_final: -0.1107 (tpp) REVERT: P 326 LEU cc_start: 0.4119 (tp) cc_final: 0.3013 (pp) REVERT: P 526 MET cc_start: -0.0800 (pmm) cc_final: -0.2113 (tmm) REVERT: P 577 MET cc_start: 0.2771 (mtp) cc_final: 0.0851 (tmm) REVERT: P 978 MET cc_start: 0.2427 (mtt) cc_final: 0.1511 (mmm) outliers start: 2 outliers final: 0 residues processed: 61 average time/residue: 0.1562 time to fit residues: 14.7681 Evaluate side-chains 53 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 38 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 31 optimal weight: 0.3980 chunk 12 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 255 HIS P 847 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4984 r_free = 0.4984 target = 0.270315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.252640 restraints weight = 12443.220| |-----------------------------------------------------------------------------| r_work (start): 0.4842 rms_B_bonded: 1.70 r_work: 0.4778 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.4681 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.4681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1543 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 7842 Z= 0.272 Angle : 0.988 31.324 10669 Z= 0.426 Chirality : 0.046 0.215 1266 Planarity : 0.006 0.061 1339 Dihedral : 6.250 55.761 1095 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.66 % Allowed : 14.56 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.26), residues: 977 helix: 0.25 (0.24), residues: 453 sheet: 0.07 (0.55), residues: 76 loop : -2.17 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP P1028 HIS 0.005 0.001 HIS P 390 PHE 0.025 0.002 PHE P1051 TYR 0.032 0.003 TYR P 173 ARG 0.008 0.001 ARG P 853 *********************** 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 88 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 275 LEU cc_start: 0.0962 (OUTLIER) cc_final: 0.0758 (mp) REVERT: P 288 MET cc_start: -0.1084 (ptt) cc_final: -0.1371 (tpt) REVERT: P 459 ILE cc_start: 0.0481 (OUTLIER) cc_final: -0.0099 (mt) REVERT: P 526 MET cc_start: 0.0338 (pmm) cc_final: -0.2689 (tmm) REVERT: P 573 MET cc_start: 0.3855 (ptt) cc_final: 0.3186 (ptm) REVERT: P 577 MET cc_start: 0.2856 (mtp) cc_final: 0.0972 (tmm) REVERT: P 648 GLN cc_start: 0.4965 (tp40) cc_final: 0.4466 (pt0) REVERT: P 964 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7078 (tp) outliers start: 14 outliers final: 8 residues processed: 86 average time/residue: 0.1541 time to fit residues: 19.8389 Evaluate side-chains 72 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 275 LEU Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 459 ILE Chi-restraints excluded: chain P residue 894 SER Chi-restraints excluded: chain P residue 902 VAL Chi-restraints excluded: chain P residue 964 LEU Chi-restraints excluded: chain P residue 1028 TRP Chi-restraints excluded: chain P residue 1032 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 24 optimal weight: 0.0870 chunk 65 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 84 HIS ** P 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 219 ASN P1047 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5101 r_free = 0.5101 target = 0.283648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4979 r_free = 0.4979 target = 0.268164 restraints weight = 11678.827| |-----------------------------------------------------------------------------| r_work (start): 0.4972 rms_B_bonded: 1.50 r_work: 0.4918 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4828 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.4828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1845 moved from start: 0.6696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7842 Z= 0.227 Angle : 0.947 31.718 10669 Z= 0.401 Chirality : 0.044 0.200 1266 Planarity : 0.005 0.050 1339 Dihedral : 5.768 57.296 1095 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.89 % Allowed : 17.40 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.27), residues: 977 helix: 0.46 (0.24), residues: 459 sheet: 0.19 (0.57), residues: 76 loop : -2.14 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP P1028 HIS 0.003 0.001 HIS P 772 PHE 0.022 0.002 PHE P1051 TYR 0.028 0.002 TYR P 256 ARG 0.007 0.001 ARG P 415 *********************** 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 95 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: P 210 MET cc_start: 0.5025 (tmm) cc_final: 0.4811 (tmm) REVERT: P 219 ASN cc_start: 0.4219 (t160) cc_final: 0.3890 (m-40) REVERT: P 275 LEU cc_start: 0.0301 (OUTLIER) cc_final: -0.0158 (mp) REVERT: P 327 MET cc_start: 0.2441 (mmm) cc_final: 0.2225 (mmm) REVERT: P 526 MET cc_start: 0.0129 (pmm) cc_final: -0.3049 (tmm) REVERT: P 577 MET cc_start: 0.3239 (mtp) cc_final: 0.1262 (tmm) REVERT: P 648 GLN cc_start: 0.4534 (tp40) cc_final: 0.4090 (pt0) REVERT: P 837 PHE cc_start: 0.5461 (t80) cc_final: 0.4644 (m-10) REVERT: P 964 LEU cc_start: 0.8516 (tt) cc_final: 0.8247 (tp) REVERT: P 1123 LEU cc_start: 0.3936 (mt) cc_final: 0.3721 (mt) outliers start: 16 outliers final: 9 residues processed: 92 average time/residue: 0.1507 time to fit residues: 20.8815 Evaluate side-chains 77 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 275 LEU Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 495 CYS Chi-restraints excluded: chain P residue 894 SER Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 973 THR Chi-restraints excluded: chain P residue 1028 TRP Chi-restraints excluded: chain P residue 1118 LEU Chi-restraints excluded: chain P residue 1137 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 50 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 0.0070 chunk 84 optimal weight: 0.3980 chunk 75 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 66 optimal weight: 0.0970 chunk 86 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5025 r_free = 0.5025 target = 0.276126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4890 r_free = 0.4890 target = 0.258878 restraints weight = 12443.820| |-----------------------------------------------------------------------------| r_work (start): 0.4897 rms_B_bonded: 1.90 r_work: 0.4822 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.4822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1885 moved from start: 0.7183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7842 Z= 0.171 Angle : 0.909 32.112 10669 Z= 0.373 Chirality : 0.042 0.191 1266 Planarity : 0.005 0.042 1339 Dihedral : 5.293 58.634 1095 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.49 % Allowed : 18.11 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.27), residues: 977 helix: 0.80 (0.24), residues: 458 sheet: 0.33 (0.62), residues: 69 loop : -2.01 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 175 HIS 0.003 0.001 HIS P 772 PHE 0.013 0.001 PHE P1051 TYR 0.018 0.002 TYR P 256 ARG 0.005 0.000 ARG P 164 *********************** 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 85 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.918 Fit side-chains REVERT: P 210 MET cc_start: 0.5142 (tmm) cc_final: 0.4851 (tmm) REVERT: P 327 MET cc_start: 0.2056 (mmm) cc_final: 0.1844 (mmm) REVERT: P 526 MET cc_start: 0.0218 (pmm) cc_final: -0.2630 (tmm) REVERT: P 837 PHE cc_start: 0.5615 (t80) cc_final: 0.4768 (m-80) REVERT: P 1123 LEU cc_start: 0.4606 (mt) cc_final: 0.4298 (mt) outliers start: 21 outliers final: 13 residues processed: 80 average time/residue: 0.1467 time to fit residues: 18.2597 Evaluate side-chains 77 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 275 LEU Chi-restraints excluded: chain P residue 373 THR Chi-restraints excluded: chain P residue 441 ILE Chi-restraints excluded: chain P residue 495 CYS Chi-restraints excluded: chain P residue 653 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 0 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 43 optimal weight: 0.0000 chunk 69 optimal weight: 0.0970 chunk 70 optimal weight: 0.3980 chunk 10 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 overall best weight: 0.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5036 r_free = 0.5036 target = 0.277559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.261079 restraints weight = 12500.232| |-----------------------------------------------------------------------------| r_work (start): 0.4916 rms_B_bonded: 1.83 r_work: 0.4846 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.4846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2035 moved from start: 0.7788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7842 Z= 0.182 Angle : 0.915 32.096 10669 Z= 0.379 Chirality : 0.042 0.154 1266 Planarity : 0.005 0.043 1339 Dihedral : 5.203 55.296 1095 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.89 % Allowed : 18.58 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.27), residues: 977 helix: 0.93 (0.24), residues: 458 sheet: 0.08 (0.59), residues: 71 loop : -1.95 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 175 HIS 0.004 0.001 HIS P 198 PHE 0.017 0.001 PHE P 931 TYR 0.018 0.002 TYR P 871 ARG 0.004 0.000 ARG P 164 *********************** 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 83 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.769 Fit side-chains REVERT: P 210 MET cc_start: 0.4745 (tmm) cc_final: 0.4524 (tmm) REVERT: P 327 MET cc_start: 0.2128 (mmm) cc_final: 0.1811 (mmm) REVERT: P 526 MET cc_start: 0.0350 (pmm) cc_final: -0.2591 (tmm) REVERT: P 577 MET cc_start: 0.3524 (mtp) cc_final: 0.1054 (tmm) REVERT: P 846 VAL cc_start: 0.1244 (OUTLIER) cc_final: 0.0669 (p) REVERT: P 1123 LEU cc_start: 0.4929 (mt) cc_final: 0.4634 (mt) outliers start: 16 outliers final: 13 residues processed: 79 average time/residue: 0.1398 time to fit residues: 17.5154 Evaluate side-chains 76 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 197 VAL Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 373 THR Chi-restraints excluded: chain P residue 441 ILE Chi-restraints excluded: chain P residue 495 CYS Chi-restraints excluded: chain P residue 846 VAL 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 Chi-restraints excluded: chain P residue 1050 VAL 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 43 optimal weight: 10.0000 chunk 67 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 71 optimal weight: 0.0470 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 847 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5056 r_free = 0.5056 target = 0.279803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4941 r_free = 0.4941 target = 0.264708 restraints weight = 12790.538| |-----------------------------------------------------------------------------| r_work (start): 0.4946 rms_B_bonded: 1.82 r_work: 0.4878 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work (final): 0.4878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2297 moved from start: 0.8690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7842 Z= 0.199 Angle : 0.943 32.740 10669 Z= 0.395 Chirality : 0.043 0.154 1266 Planarity : 0.005 0.042 1339 Dihedral : 5.348 58.505 1095 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.37 % Allowed : 20.00 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.27), residues: 977 helix: 0.85 (0.24), residues: 461 sheet: 0.25 (0.68), residues: 59 loop : -2.01 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 175 HIS 0.003 0.001 HIS P 772 PHE 0.012 0.001 PHE P 906 TYR 0.024 0.002 TYR P 871 ARG 0.004 0.000 ARG P 201 *********************** 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 93 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 1.122 Fit side-chains REVERT: P 257 TYR cc_start: 0.1554 (OUTLIER) cc_final: -0.1566 (m-80) REVERT: P 293 MET cc_start: 0.2829 (pmm) cc_final: 0.1994 (mtm) REVERT: P 327 MET cc_start: 0.2145 (mmm) cc_final: 0.1585 (mmm) REVERT: P 846 VAL cc_start: 0.1809 (OUTLIER) cc_final: 0.1255 (p) outliers start: 20 outliers final: 15 residues processed: 91 average time/residue: 0.1526 time to fit residues: 21.4153 Evaluate side-chains 84 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 257 TYR Chi-restraints excluded: chain P residue 261 LEU Chi-restraints excluded: chain P residue 373 THR Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 441 ILE Chi-restraints excluded: chain P residue 495 CYS Chi-restraints excluded: chain P residue 653 VAL Chi-restraints excluded: chain P residue 846 VAL Chi-restraints excluded: chain P residue 894 SER Chi-restraints excluded: chain P residue 907 THR Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 973 THR Chi-restraints excluded: chain P residue 1028 TRP Chi-restraints excluded: chain P residue 1050 VAL Chi-restraints excluded: chain P residue 1118 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 53 optimal weight: 3.9990 chunk 20 optimal weight: 0.2980 chunk 58 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 chunk 16 optimal weight: 0.4980 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 10 optimal weight: 0.3980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 881 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5070 r_free = 0.5070 target = 0.281252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4963 r_free = 0.4963 target = 0.267793 restraints weight = 12916.039| |-----------------------------------------------------------------------------| r_work (start): 0.4969 rms_B_bonded: 1.63 r_work: 0.4905 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work (final): 0.4905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2339 moved from start: 0.9213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7842 Z= 0.183 Angle : 0.936 32.670 10669 Z= 0.387 Chirality : 0.043 0.191 1266 Planarity : 0.005 0.042 1339 Dihedral : 5.217 58.038 1095 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.01 % Allowed : 21.42 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.27), residues: 977 helix: 1.06 (0.24), residues: 458 sheet: 0.31 (0.71), residues: 57 loop : -1.95 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 175 HIS 0.003 0.001 HIS P 772 PHE 0.009 0.001 PHE P1021 TYR 0.019 0.002 TYR P 256 ARG 0.004 0.000 ARG P 451 *********************** 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 89 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.831 Fit side-chains revert: symmetry clash REVERT: P 293 MET cc_start: 0.2868 (pmm) cc_final: 0.2288 (mtm) REVERT: P 327 MET cc_start: 0.2128 (mmm) cc_final: 0.1823 (mmm) REVERT: P 526 MET cc_start: 0.1655 (OUTLIER) cc_final: -0.2747 (tmm) REVERT: P 846 VAL cc_start: 0.1983 (OUTLIER) cc_final: 0.1422 (p) REVERT: P 940 TYR cc_start: 0.3868 (OUTLIER) cc_final: 0.2314 (t80) REVERT: P 1045 TYR cc_start: 0.1437 (m-80) cc_final: 0.0623 (m-80) outliers start: 17 outliers final: 13 residues processed: 85 average time/residue: 0.1617 time to fit residues: 20.4869 Evaluate side-chains 84 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 256 TYR Chi-restraints excluded: chain P residue 261 LEU Chi-restraints excluded: chain P residue 373 THR Chi-restraints excluded: chain P residue 441 ILE Chi-restraints excluded: chain P residue 495 CYS Chi-restraints excluded: chain P residue 526 MET Chi-restraints excluded: chain P residue 653 VAL Chi-restraints excluded: chain P residue 846 VAL Chi-restraints excluded: chain P residue 894 SER Chi-restraints excluded: chain P residue 907 THR Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 948 VAL Chi-restraints excluded: chain P residue 1028 TRP Chi-restraints excluded: chain P residue 1118 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 455 ASN ** P 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 881 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5079 r_free = 0.5079 target = 0.282167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4978 r_free = 0.4978 target = 0.269575 restraints weight = 12897.185| |-----------------------------------------------------------------------------| r_work (start): 0.4985 rms_B_bonded: 1.60 r_work: 0.4925 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4835 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.4835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2733 moved from start: 1.0164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7842 Z= 0.238 Angle : 1.001 33.451 10669 Z= 0.430 Chirality : 0.045 0.210 1266 Planarity : 0.006 0.042 1339 Dihedral : 5.633 58.847 1095 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.72 % Allowed : 21.18 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.27), residues: 977 helix: 0.68 (0.24), residues: 461 sheet: 0.37 (0.74), residues: 57 loop : -2.00 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP P 643 HIS 0.003 0.001 HIS P 780 PHE 0.032 0.002 PHE P1116 TYR 0.027 0.002 TYR P 871 ARG 0.007 0.001 ARG P 924 ********************** 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 105 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 257 TYR cc_start: 0.1887 (OUTLIER) cc_final: -0.1227 (m-80) REVERT: P 293 MET cc_start: 0.2915 (pmm) cc_final: 0.0958 (pmm) REVERT: P 373 THR cc_start: 0.2121 (OUTLIER) cc_final: 0.0431 (m) REVERT: P 451 ARG cc_start: 0.2273 (tpt90) cc_final: 0.1849 (mmm160) REVERT: P 526 MET cc_start: 0.1508 (OUTLIER) cc_final: 0.0808 (mpp) REVERT: P 676 MET cc_start: 0.0124 (ttm) cc_final: -0.0358 (tpp) REVERT: P 940 TYR cc_start: 0.4139 (OUTLIER) cc_final: 0.2505 (t80) REVERT: P 1119 LEU cc_start: 0.3063 (tt) cc_final: 0.2743 (tp) outliers start: 23 outliers final: 16 residues processed: 99 average time/residue: 0.1698 time to fit residues: 24.2423 Evaluate side-chains 93 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 257 TYR Chi-restraints excluded: chain P residue 261 LEU Chi-restraints excluded: chain P residue 373 THR Chi-restraints excluded: chain P residue 396 THR Chi-restraints excluded: chain P residue 441 ILE Chi-restraints excluded: chain P residue 455 ASN Chi-restraints excluded: chain P residue 495 CYS Chi-restraints excluded: chain P residue 526 MET Chi-restraints excluded: chain P residue 653 VAL Chi-restraints excluded: chain P residue 894 SER Chi-restraints excluded: chain P residue 907 THR Chi-restraints excluded: chain P residue 918 MET Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 948 VAL Chi-restraints excluded: chain P residue 973 THR Chi-restraints excluded: chain P residue 1028 TRP Chi-restraints excluded: chain P residue 1050 VAL Chi-restraints excluded: chain P residue 1118 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 28 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 84 optimal weight: 0.0670 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 455 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5090 r_free = 0.5090 target = 0.283421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4992 r_free = 0.4992 target = 0.271376 restraints weight = 12981.813| |-----------------------------------------------------------------------------| r_work (start): 0.5007 rms_B_bonded: 1.56 r_work: 0.4948 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.4860 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.4860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2641 moved from start: 1.0359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7842 Z= 0.194 Angle : 0.963 33.022 10669 Z= 0.404 Chirality : 0.043 0.200 1266 Planarity : 0.005 0.043 1339 Dihedral : 5.401 58.511 1095 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 1.89 % Allowed : 22.49 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.28), residues: 977 helix: 0.87 (0.24), residues: 463 sheet: 0.11 (0.68), residues: 64 loop : -1.95 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 175 HIS 0.003 0.001 HIS P 413 PHE 0.035 0.001 PHE P1116 TYR 0.021 0.002 TYR P 256 ARG 0.004 0.000 ARG P 487 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4207.39 seconds wall clock time: 72 minutes 40.87 seconds (4360.87 seconds total)