Starting phenix.real_space_refine on Wed Feb 12 12:44:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ien_35387/02_2025/8ien_35387_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ien_35387/02_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_35387/02_2025/8ien_35387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ien_35387/02_2025/8ien_35387.map" model { file = "/net/cci-nas-00/data/ceres_data/8ien_35387/02_2025/8ien_35387_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ien_35387/02_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-5592/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: 4.84, per 1000 atoms: 0.63 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: 1.98 Conformation dependent library (CDL) restraints added in 881.9 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: 0.84 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: 2.40 Time building geometry restraints manager: 2.28 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: 1.430 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.340 Find NCS groups from input model: 0.070 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.900 ------------------------------------------------------------------------------- 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 : 0.764 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: 0.1931 time to fit residues: 23.6592 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 : 0.860 ------------------------------------------------------------------------------- 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: 0.7980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.253457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.223715 restraints weight = 11509.482| |-----------------------------------------------------------------------------| r_work (start): 0.4563 rms_B_bonded: 2.57 r_work: 0.4469 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0828 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7842 Z= 0.194 Angle : 0.921 31.632 10669 Z= 0.381 Chirality : 0.043 0.169 1266 Planarity : 0.005 0.046 1339 Dihedral : 5.826 57.124 1095 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.59 % Allowed : 9.23 % Favored : 90.18 % 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: 0.51 (0.24), residues: 446 sheet: -0.51 (0.60), residues: 76 loop : -2.17 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 251 HIS 0.004 0.001 HIS P 822 PHE 0.012 0.002 PHE P1128 TYR 0.024 0.002 TYR P 483 ARG 0.007 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 65 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.787 Fit side-chains revert: symmetry clash REVERT: P 63 LEU cc_start: 0.3171 (mt) cc_final: 0.2761 (pt) REVERT: P 288 MET cc_start: -0.0172 (ptt) cc_final: -0.0902 (tpt) REVERT: P 326 LEU cc_start: 0.3866 (tp) cc_final: 0.3268 (pp) REVERT: P 526 MET cc_start: -0.0784 (pmm) cc_final: -0.2121 (tmm) REVERT: P 573 MET cc_start: 0.3412 (ptt) cc_final: 0.2344 (mmm) REVERT: P 577 MET cc_start: 0.2702 (mtp) cc_final: 0.0977 (tmm) REVERT: P 637 MET cc_start: -0.0145 (tmm) cc_final: -0.0572 (mtp) REVERT: P 978 MET cc_start: 0.2651 (mtt) cc_final: 0.1442 (mmm) outliers start: 5 outliers final: 4 residues processed: 61 average time/residue: 0.1548 time to fit residues: 14.5640 Evaluate side-chains 53 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 219 ASN Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 659 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 67 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 73 optimal weight: 0.0020 chunk 44 optimal weight: 0.0670 chunk 53 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 overall best weight: 0.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 180 GLN P 502 ASN ** P 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 944 GLN P 962 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4861 r_free = 0.4861 target = 0.256595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.227106 restraints weight = 11845.663| |-----------------------------------------------------------------------------| r_work (start): 0.4602 rms_B_bonded: 2.65 r_work: 0.4504 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0987 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7842 Z= 0.171 Angle : 0.883 29.587 10669 Z= 0.358 Chirality : 0.041 0.170 1266 Planarity : 0.005 0.044 1339 Dihedral : 5.406 59.366 1095 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.71 % Allowed : 12.66 % Favored : 86.63 % 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: -0.79 (0.27), residues: 977 helix: 0.81 (0.25), residues: 450 sheet: -0.31 (0.57), residues: 75 loop : -2.02 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 643 HIS 0.002 0.001 HIS P 822 PHE 0.009 0.001 PHE P1128 TYR 0.021 0.001 TYR P 483 ARG 0.006 0.000 ARG P 725 *********************** 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: 6 poor density : 57 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 63 LEU cc_start: 0.3185 (mt) cc_final: 0.2777 (pt) REVERT: P 288 MET cc_start: -0.0247 (ptt) cc_final: -0.1104 (tpp) REVERT: P 326 LEU cc_start: 0.4320 (tp) cc_final: 0.2379 (mp) REVERT: P 526 MET cc_start: -0.0049 (pmm) cc_final: -0.2460 (tmm) REVERT: P 577 MET cc_start: 0.2803 (mtp) cc_final: 0.0862 (tmm) REVERT: P 978 MET cc_start: 0.2601 (mtt) cc_final: 0.1759 (mmm) outliers start: 6 outliers final: 1 residues processed: 62 average time/residue: 0.1666 time to fit residues: 15.6616 Evaluate side-chains 54 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 38 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.0980 chunk 29 optimal weight: 4.9990 chunk 22 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1047 ASN 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 = 0.268579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.248495 restraints weight = 12312.221| |-----------------------------------------------------------------------------| r_work (start): 0.4844 rms_B_bonded: 1.88 r_work: 0.4766 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.4766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1378 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7842 Z= 0.217 Angle : 0.944 30.708 10669 Z= 0.396 Chirality : 0.043 0.153 1266 Planarity : 0.006 0.075 1339 Dihedral : 5.727 55.400 1095 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.54 % Allowed : 15.03 % Favored : 83.43 % 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: -0.92 (0.27), residues: 977 helix: 0.56 (0.24), residues: 453 sheet: 0.34 (0.56), residues: 76 loop : -2.08 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P1028 HIS 0.003 0.001 HIS P 772 PHE 0.020 0.002 PHE P 906 TYR 0.027 0.002 TYR P 256 ARG 0.006 0.001 ARG P 279 *********************** 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 87 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 275 LEU cc_start: 0.0494 (OUTLIER) cc_final: 0.0023 (mp) REVERT: P 288 MET cc_start: -0.0951 (ptt) cc_final: -0.1451 (tpp) REVERT: P 459 ILE cc_start: 0.0796 (OUTLIER) cc_final: 0.0261 (mt) REVERT: P 526 MET cc_start: 0.1435 (pmm) cc_final: 0.0841 (mpp) REVERT: P 573 MET cc_start: 0.2888 (ptt) cc_final: 0.1883 (mmm) REVERT: P 577 MET cc_start: 0.2898 (mtp) cc_final: 0.0970 (tmm) REVERT: P 721 LEU cc_start: 0.3446 (tt) cc_final: 0.2253 (mt) REVERT: P 964 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.6709 (tp) REVERT: P 1091 VAL cc_start: 0.2199 (p) cc_final: 0.1936 (t) outliers start: 13 outliers final: 7 residues processed: 82 average time/residue: 0.1657 time to fit residues: 19.9664 Evaluate side-chains 72 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 964 LEU Chi-restraints excluded: chain P residue 968 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 33 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 7 optimal weight: 0.3980 chunk 24 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 67 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** P 219 ASN P 847 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5051 r_free = 0.5051 target = 0.278185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.262551 restraints weight = 12443.847| |-----------------------------------------------------------------------------| r_work (start): 0.4985 rms_B_bonded: 1.70 r_work: 0.4925 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4839 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.4839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1971 moved from start: 0.6969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7842 Z= 0.258 Angle : 0.992 31.820 10669 Z= 0.428 Chirality : 0.045 0.162 1266 Planarity : 0.006 0.064 1339 Dihedral : 5.837 57.804 1095 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.54 % Allowed : 17.16 % Favored : 81.30 % 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: -1.26 (0.26), residues: 977 helix: 0.25 (0.24), residues: 458 sheet: 0.13 (0.60), residues: 69 loop : -2.21 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP P1028 HIS 0.006 0.001 HIS P 390 PHE 0.028 0.002 PHE P1051 TYR 0.031 0.003 TYR P 871 ARG 0.011 0.001 ARG P 279 *********************** 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 90 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 275 LEU cc_start: 0.0751 (OUTLIER) cc_final: 0.0417 (mp) REVERT: P 327 MET cc_start: 0.2487 (mmm) cc_final: 0.2143 (mmm) REVERT: P 459 ILE cc_start: 0.1690 (OUTLIER) cc_final: 0.1292 (mm) REVERT: P 526 MET cc_start: 0.1675 (pmm) cc_final: 0.0996 (mpp) REVERT: P 573 MET cc_start: 0.3027 (ptt) cc_final: 0.1863 (mmm) REVERT: P 577 MET cc_start: 0.3379 (mtp) cc_final: 0.1198 (tmm) REVERT: P 837 PHE cc_start: 0.5717 (t80) cc_final: 0.4779 (m-10) outliers start: 13 outliers final: 8 residues processed: 87 average time/residue: 0.1502 time to fit residues: 19.8130 Evaluate side-chains 76 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 275 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 459 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 50 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 0.0970 chunk 84 optimal weight: 0.1980 chunk 75 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 86 optimal weight: 0.0970 chunk 38 optimal weight: 0.8980 chunk 79 optimal weight: 0.1980 overall best weight: 0.2376 ------------------------------------------------------------------------------- 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** ** P 897 GLN ** 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 = 0.5023 r_free = 0.5023 target = 0.276022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.258238 restraints weight = 12390.125| |-----------------------------------------------------------------------------| r_work (start): 0.4893 rms_B_bonded: 1.88 r_work: 0.4822 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.4822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1838 moved from start: 0.7069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7842 Z= 0.162 Angle : 0.890 31.627 10669 Z= 0.362 Chirality : 0.040 0.148 1266 Planarity : 0.005 0.042 1339 Dihedral : 5.117 57.395 1095 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.25 % Allowed : 17.75 % Favored : 80.00 % 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 (0.27), residues: 977 helix: 0.87 (0.24), residues: 459 sheet: 0.37 (0.62), residues: 73 loop : -2.02 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P1028 HIS 0.003 0.001 HIS P 198 PHE 0.011 0.001 PHE P1051 TYR 0.015 0.001 TYR P 256 ARG 0.004 0.000 ARG P 172 *********************** 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 88 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: P 210 MET cc_start: 0.4907 (tmm) cc_final: 0.4653 (tmm) REVERT: P 526 MET cc_start: 0.1931 (pmm) cc_final: 0.0905 (mpp) REVERT: P 573 MET cc_start: 0.3355 (ptt) cc_final: 0.3092 (mmm) REVERT: P 837 PHE cc_start: 0.5596 (t80) cc_final: 0.4749 (m-80) outliers start: 19 outliers final: 11 residues processed: 83 average time/residue: 0.1357 time to fit residues: 17.6529 Evaluate side-chains 75 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 84 HIS Chi-restraints excluded: chain P residue 105 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 429 VAL Chi-restraints excluded: chain P residue 660 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 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: 0.6980 chunk 29 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 43 optimal weight: 0.0010 chunk 69 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 = 0.5037 r_free = 0.5037 target = 0.277633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.261325 restraints weight = 12560.469| |-----------------------------------------------------------------------------| r_work (start): 0.4918 rms_B_bonded: 1.85 r_work: 0.4849 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.4849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2133 moved from start: 0.8010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7842 Z= 0.206 Angle : 0.941 32.135 10669 Z= 0.395 Chirality : 0.042 0.152 1266 Planarity : 0.005 0.042 1339 Dihedral : 5.064 56.063 1095 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.25 % Allowed : 19.05 % Favored : 78.70 % 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: -0.79 (0.27), residues: 977 helix: 0.75 (0.24), residues: 459 sheet: 0.32 (0.68), residues: 63 loop : -2.06 (0.29), residues: 455 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 0.015 0.001 PHE P 906 TYR 0.025 0.002 TYR P 871 ARG 0.005 0.000 ARG P 172 *********************** 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: 19 poor density : 64 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: P 210 MET cc_start: 0.5085 (tmm) cc_final: 0.4844 (tmm) REVERT: P 526 MET cc_start: 0.2053 (pmm) cc_final: 0.0885 (mpp) REVERT: P 724 MET cc_start: 0.5803 (tpt) cc_final: 0.5399 (tpt) outliers start: 19 outliers final: 13 residues processed: 78 average time/residue: 0.1428 time to fit residues: 17.5368 Evaluate side-chains 76 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 105 VAL 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 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 660 VAL Chi-restraints excluded: chain P residue 854 MET Chi-restraints excluded: chain P residue 894 SER Chi-restraints excluded: chain P residue 940 TYR 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: 0.0030 chunk 67 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 12 optimal weight: 0.0060 chunk 88 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 0.0470 chunk 42 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 71 optimal weight: 0.0470 overall best weight: 0.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 648 GLN ** 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 = 0.5066 r_free = 0.5066 target = 0.279999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4946 r_free = 0.4946 target = 0.265051 restraints weight = 12631.467| |-----------------------------------------------------------------------------| r_work (start): 0.4925 rms_B_bonded: 1.68 r_work: 0.4867 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.4779 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.4779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1992 moved from start: 0.8054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7842 Z= 0.156 Angle : 0.897 31.638 10669 Z= 0.366 Chirality : 0.041 0.147 1266 Planarity : 0.005 0.042 1339 Dihedral : 4.774 58.885 1095 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.42 % Allowed : 20.83 % Favored : 77.75 % 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: -0.37 (0.28), residues: 977 helix: 1.19 (0.24), residues: 459 sheet: 0.31 (0.70), residues: 60 loop : -1.91 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P1028 HIS 0.003 0.001 HIS P 198 PHE 0.007 0.001 PHE P 182 TYR 0.016 0.001 TYR P 256 ARG 0.003 0.000 ARG P 172 *********************** 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 77 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: P 210 MET cc_start: 0.5166 (tmm) cc_final: 0.4894 (tmm) REVERT: P 477 MET cc_start: 0.0081 (tpt) cc_final: -0.0283 (mmm) REVERT: P 526 MET cc_start: 0.2186 (pmm) cc_final: 0.0917 (mpp) REVERT: P 648 GLN cc_start: 0.5535 (tp40) cc_final: 0.3723 (tm-30) REVERT: P 676 MET cc_start: 0.0061 (ttm) cc_final: -0.0315 (tpp) outliers start: 12 outliers final: 11 residues processed: 74 average time/residue: 0.1452 time to fit residues: 16.6078 Evaluate side-chains 73 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 256 TYR Chi-restraints excluded: chain P residue 441 ILE Chi-restraints excluded: chain P residue 660 VAL Chi-restraints excluded: chain P residue 854 MET Chi-restraints excluded: chain P residue 894 SER Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 948 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: 9.9990 chunk 20 optimal weight: 0.6980 chunk 58 optimal weight: 0.2980 chunk 35 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 0.0570 chunk 64 optimal weight: 0.0370 chunk 95 optimal weight: 3.9990 chunk 72 optimal weight: 0.0770 chunk 10 optimal weight: 9.9990 overall best weight: 0.2334 ------------------------------------------------------------------------------- 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 = 0.5040 r_free = 0.5040 target = 0.278246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4916 r_free = 0.4916 target = 0.261864 restraints weight = 12785.998| |-----------------------------------------------------------------------------| r_work (start): 0.4924 rms_B_bonded: 1.89 r_work: 0.4853 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.4853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2031 moved from start: 0.8264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7842 Z= 0.159 Angle : 0.895 31.379 10669 Z= 0.364 Chirality : 0.041 0.153 1266 Planarity : 0.005 0.042 1339 Dihedral : 4.556 58.721 1095 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.01 % Allowed : 20.83 % Favored : 77.16 % 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: -0.19 (0.28), residues: 977 helix: 1.39 (0.25), residues: 459 sheet: 0.23 (0.65), residues: 67 loop : -1.90 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 643 HIS 0.003 0.001 HIS P 198 PHE 0.008 0.001 PHE P 837 TYR 0.016 0.001 TYR P 256 ARG 0.004 0.000 ARG P 286 *********************** 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 80 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 210 MET cc_start: 0.5336 (tmm) cc_final: 0.5092 (tmm) REVERT: P 257 TYR cc_start: 0.0958 (OUTLIER) cc_final: -0.1752 (m-80) REVERT: P 357 LEU cc_start: -0.3083 (OUTLIER) cc_final: -0.3300 (mp) REVERT: P 477 MET cc_start: 0.0184 (tpt) cc_final: -0.0230 (mmm) REVERT: P 526 MET cc_start: 0.2164 (pmm) cc_final: 0.0857 (mpp) REVERT: P 573 MET cc_start: 0.2935 (OUTLIER) cc_final: 0.2315 (mmm) REVERT: P 577 MET cc_start: 0.3485 (mtp) cc_final: 0.1166 (tmm) REVERT: P 648 GLN cc_start: 0.5509 (tp40) cc_final: 0.3594 (tm-30) REVERT: P 676 MET cc_start: -0.0095 (ttm) cc_final: -0.0411 (tpp) REVERT: P 1045 TYR cc_start: 0.1303 (m-80) cc_final: 0.0768 (m-80) outliers start: 17 outliers final: 13 residues processed: 77 average time/residue: 0.1399 time to fit residues: 17.0642 Evaluate side-chains 79 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 256 TYR Chi-restraints excluded: chain P residue 257 TYR Chi-restraints excluded: chain P residue 357 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 573 MET Chi-restraints excluded: chain P residue 660 VAL Chi-restraints excluded: chain P residue 854 MET Chi-restraints excluded: chain P residue 894 SER Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 948 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 68 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 89 optimal weight: 0.3980 chunk 46 optimal weight: 7.9990 chunk 96 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 73 optimal weight: 0.0980 chunk 16 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 36 optimal weight: 0.0980 chunk 28 optimal weight: 0.8980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 508 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5063 r_free = 0.5063 target = 0.280664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4954 r_free = 0.4954 target = 0.266588 restraints weight = 12806.250| |-----------------------------------------------------------------------------| r_work (start): 0.4959 rms_B_bonded: 1.67 r_work: 0.4896 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work (final): 0.4896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2278 moved from start: 0.9081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7842 Z= 0.189 Angle : 0.931 31.911 10669 Z= 0.386 Chirality : 0.042 0.208 1266 Planarity : 0.005 0.042 1339 Dihedral : 4.760 59.921 1095 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.13 % Allowed : 20.36 % Favored : 77.51 % 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: -0.36 (0.28), residues: 977 helix: 1.21 (0.24), residues: 459 sheet: 0.21 (0.71), residues: 61 loop : -1.92 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 175 HIS 0.003 0.001 HIS P 772 PHE 0.014 0.001 PHE P 906 TYR 0.021 0.002 TYR P 871 ARG 0.004 0.000 ARG P 164 ********************** 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 90 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 257 TYR cc_start: 0.1431 (OUTLIER) cc_final: -0.1623 (m-80) REVERT: P 357 LEU cc_start: -0.2929 (OUTLIER) cc_final: -0.3208 (mp) REVERT: P 477 MET cc_start: 0.0286 (tpt) cc_final: -0.1292 (ppp) REVERT: P 508 GLN cc_start: 0.0634 (OUTLIER) cc_final: -0.1278 (mp10) REVERT: P 526 MET cc_start: 0.2237 (pmm) cc_final: 0.0940 (mpp) REVERT: P 648 GLN cc_start: 0.5461 (tp40) cc_final: 0.3534 (tm-30) REVERT: P 940 TYR cc_start: 0.3595 (OUTLIER) cc_final: 0.1875 (t80) REVERT: P 1045 TYR cc_start: 0.1531 (m-80) cc_final: 0.0894 (m-80) outliers start: 18 outliers final: 13 residues processed: 88 average time/residue: 0.1580 time to fit residues: 21.0448 Evaluate side-chains 81 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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 257 TYR Chi-restraints excluded: chain P residue 357 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 508 GLN Chi-restraints excluded: chain P residue 660 VAL Chi-restraints excluded: chain P residue 854 MET Chi-restraints excluded: chain P residue 894 SER Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 948 VAL Chi-restraints excluded: chain P residue 1006 LEU 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: 0.7980 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 0.0870 chunk 71 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 84 optimal weight: 0.0670 chunk 34 optimal weight: 7.9990 chunk 36 optimal weight: 0.1980 chunk 77 optimal weight: 0.0670 chunk 60 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.2034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5064 r_free = 0.5064 target = 0.280791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4952 r_free = 0.4952 target = 0.266753 restraints weight = 12825.803| |-----------------------------------------------------------------------------| r_work (start): 0.4956 rms_B_bonded: 1.65 r_work: 0.4900 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.4815 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.4815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2366 moved from start: 0.9139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.279 7842 Z= 0.397 Angle : 1.193 59.162 10669 Z= 0.599 Chirality : 0.046 0.702 1266 Planarity : 0.005 0.046 1339 Dihedral : 4.766 59.922 1095 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.01 % Allowed : 21.30 % Favored : 76.69 % Cbeta Deviations : 0.11 % 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: -0.36 (0.28), residues: 977 helix: 1.20 (0.24), residues: 459 sheet: 0.07 (0.67), residues: 68 loop : -1.90 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 175 HIS 0.003 0.001 HIS P 772 PHE 0.013 0.001 PHE P 906 TYR 0.019 0.002 TYR P 871 ARG 0.003 0.000 ARG P 164 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4027.29 seconds wall clock time: 72 minutes 8.44 seconds (4328.44 seconds total)