Starting phenix.real_space_refine on Wed Mar 12 18:39:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ies_35392/03_2025/8ies_35392.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ies_35392/03_2025/8ies_35392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ies_35392/03_2025/8ies_35392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ies_35392/03_2025/8ies_35392.map" model { file = "/net/cci-nas-00/data/ceres_data/8ies_35392/03_2025/8ies_35392.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ies_35392/03_2025/8ies_35392.cif" } resolution = 3.73 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= 0.002 sd= 0.056 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 2 5.49 5 Mg 1 5.21 5 S 53 5.16 5 C 5129 2.51 5 N 1367 2.21 5 O 1408 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 30 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: 7965 Number of models: 1 Model: "" Number of chains: 2 Chain: "P" Number of atoms: 7932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 7932 Classifications: {'peptide': 1026} Link IDs: {'PTRANS': 69, 'TRANS': 956} Chain breaks: 4 Chain: "P" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.40, per 1000 atoms: 0.68 Number of scatterers: 7965 At special positions: 0 Unit cell: (96.36, 91.98, 131.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 53 16.00 P 2 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1408 8.00 N 1367 7.00 C 5129 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 950.9 milliseconds 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1916 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 8 sheets defined 41.2% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'P' and resid 49 through 58 removed outlier: 4.344A pdb=" N VAL P 53 " --> pdb=" O GLY P 49 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TRP P 55 " --> pdb=" O HIS P 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 59 through 64 removed outlier: 3.555A pdb=" N LEU P 62 " --> pdb=" O GLY P 59 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU P 63 " --> pdb=" O ILE P 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 76 removed outlier: 3.592A pdb=" N VAL P 73 " --> pdb=" O PRO P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 194 through 199 Processing helix chain 'P' and resid 227 through 234 removed outlier: 3.925A pdb=" N ASP P 234 " --> pdb=" O GLN P 230 " (cutoff:3.500A) Processing helix chain 'P' and resid 238 through 253 removed outlier: 3.586A pdb=" N GLY P 242 " --> pdb=" O ASN P 238 " (cutoff:3.500A) Processing helix chain 'P' and resid 258 through 287 removed outlier: 3.934A pdb=" N LEU P 285 " --> pdb=" O GLN P 281 " (cutoff:3.500A) Processing helix chain 'P' and resid 402 through 412 Processing helix chain 'P' and resid 423 through 450 removed outlier: 3.792A pdb=" N LYS P 427 " --> pdb=" O LYS P 423 " (cutoff:3.500A) Processing helix chain 'P' and resid 456 through 467 removed outlier: 4.015A pdb=" N ARG P 460 " --> pdb=" O GLU P 456 " (cutoff:3.500A) Processing helix chain 'P' and resid 472 through 478 removed outlier: 3.507A pdb=" N MET P 477 " --> pdb=" O LEU P 473 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR P 478 " --> pdb=" O PRO P 474 " (cutoff:3.500A) Processing helix chain 'P' and resid 478 through 489 removed outlier: 3.984A pdb=" N LEU P 482 " --> pdb=" O THR P 478 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG P 489 " --> pdb=" O GLN P 485 " (cutoff:3.500A) Processing helix chain 'P' and resid 503 through 507 removed outlier: 3.621A pdb=" N LEU P 507 " --> pdb=" O GLY P 504 " (cutoff:3.500A) Processing helix chain 'P' and resid 550 through 557 Processing helix chain 'P' and resid 571 through 580 Processing helix chain 'P' and resid 609 through 612 Processing helix chain 'P' and resid 656 through 662 removed outlier: 4.256A pdb=" N GLY P 662 " --> pdb=" O GLU P 658 " (cutoff:3.500A) Processing helix chain 'P' and resid 672 through 682 removed outlier: 3.737A pdb=" N GLN P 678 " --> pdb=" O ALA P 674 " (cutoff:3.500A) Processing helix chain 'P' and resid 696 through 704 removed outlier: 3.548A pdb=" N ALA P 704 " --> pdb=" O SER P 700 " (cutoff:3.500A) Processing helix chain 'P' and resid 732 through 741 Processing helix chain 'P' and resid 753 through 765 removed outlier: 3.874A pdb=" N CYS P 764 " --> pdb=" O VAL P 760 " (cutoff:3.500A) Processing helix chain 'P' and resid 826 through 832 Processing helix chain 'P' and resid 840 through 847 removed outlier: 3.559A pdb=" N VAL P 844 " --> pdb=" O LEU P 840 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL P 846 " --> pdb=" O PRO P 842 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN P 847 " --> pdb=" O LYS P 843 " (cutoff:3.500A) Processing helix chain 'P' and resid 858 through 868 Processing helix chain 'P' and resid 882 through 887 removed outlier: 3.932A pdb=" N LEU P 886 " --> pdb=" O ASP P 882 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS P 887 " --> pdb=" O CYS P 883 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 882 through 887' Processing helix chain 'P' and resid 915 through 952 Processing helix chain 'P' and resid 959 through 969 removed outlier: 4.052A pdb=" N PHE P 963 " --> pdb=" O GLY P 959 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU P 964 " --> pdb=" O ASP P 960 " (cutoff:3.500A) Processing helix chain 'P' and resid 971 through 977 Processing helix chain 'P' and resid 998 through 1025 Processing helix chain 'P' and resid 1046 through 1066 removed outlier: 4.159A pdb=" N VAL P1050 " --> pdb=" O GLU P1046 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE P1056 " --> pdb=" O SER P1052 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN P1057 " --> pdb=" O LEU P1053 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR P1058 " --> pdb=" O SER P1054 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU P1059 " --> pdb=" O SER P1055 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA P1063 " --> pdb=" O LEU P1059 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL P1065 " --> pdb=" O LEU P1061 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER P1066 " --> pdb=" O ALA P1062 " (cutoff:3.500A) Processing helix chain 'P' and resid 1078 through 1094 Processing helix chain 'P' and resid 1117 through 1136 removed outlier: 4.148A pdb=" N LEU P1123 " --> pdb=" O LEU P1119 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE P1132 " --> pdb=" O PHE P1128 " (cutoff:3.500A) Processing helix chain 'P' and resid 1141 through 1147 Processing helix chain 'P' and resid 1157 through 1167 Processing sheet with id=AA1, first strand: chain 'P' and resid 39 through 43 removed outlier: 4.355A pdb=" N GLY P 39 " --> pdb=" O ILE P 92 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE P 92 " --> pdb=" O GLY P 39 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU P 88 " --> pdb=" O SER P 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 105 through 106 removed outlier: 6.495A pdb=" N ARG P 164 " --> pdb=" O TRP P 175 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TRP P 175 " --> pdb=" O ARG P 164 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR P 166 " --> pdb=" O TYR P 173 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR P 173 " --> pdb=" O TYR P 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 297 through 298 removed outlier: 4.028A pdb=" N VAL P 297 " --> pdb=" O GLU P 305 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU P 305 " --> pdb=" O VAL P 297 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'P' and resid 317 through 318 removed outlier: 3.616A pdb=" N ALA P 393 " --> pdb=" O LEU P 318 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU P 392 " --> pdb=" O VAL P 334 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL P 334 " --> pdb=" O LEU P 392 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 338 through 340 Processing sheet with id=AA6, first strand: chain 'P' and resid 823 through 825 removed outlier: 6.237A pdb=" N LEU P 823 " --> pdb=" O GLY P 848 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL P 850 " --> pdb=" O LEU P 823 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ALA P 746 " --> pdb=" O THR P 849 " (cutoff:3.500A) removed outlier: 9.148A pdb=" N PHE P 851 " --> pdb=" O ALA P 746 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N MET P 748 " --> pdb=" O PHE P 851 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N ILE P 893 " --> pdb=" O VAL P 873 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N MET P 875 " --> pdb=" O ILE P 893 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'P' and resid 528 through 530 removed outlier: 5.119A pdb=" N LEU P 718 " --> pdb=" O SER P 692 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N SER P 692 " --> pdb=" O LEU P 718 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY P 720 " --> pdb=" O LEU P 690 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU P 722 " --> pdb=" O VAL P 688 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA P 651 " --> pdb=" O LYS P 693 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS P 626 " --> pdb=" O VAL P 640 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA P 642 " --> pdb=" O VAL P 624 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N VAL P 624 " --> pdb=" O ALA P 642 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 584 through 586 removed outlier: 4.073A pdb=" N VAL P 584 " --> pdb=" O MET P 615 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN P 613 " --> pdb=" O GLU P 586 " (cutoff:3.500A) 300 hydrogen bonds defined for protein. 873 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: 2.34 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2557 1.34 - 1.46: 1664 1.46 - 1.58: 3832 1.58 - 1.69: 3 1.69 - 1.81: 83 Bond restraints: 8139 Sorted by residual: bond pdb=" F1 ALF P1201 " pdb="AL ALF P1201 " ideal model delta sigma weight residual 1.684 1.785 -0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" F2 ALF P1201 " pdb="AL ALF P1201 " ideal model delta sigma weight residual 1.685 1.785 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" F3 ALF P1201 " pdb="AL ALF P1201 " ideal model delta sigma weight residual 1.685 1.784 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" F4 ALF P1201 " pdb="AL ALF P1201 " ideal model delta sigma weight residual 1.686 1.785 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" C LEU P1142 " pdb=" N PRO P1143 " ideal model delta sigma weight residual 1.335 1.355 -0.020 1.28e-02 6.10e+03 2.52e+00 ... (remaining 8134 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.25: 11088 14.25 - 28.50: 4 28.50 - 42.75: 0 42.75 - 56.99: 0 56.99 - 71.24: 2 Bond angle restraints: 11094 Sorted by residual: angle pdb=" F1 ALF P1201 " pdb="AL ALF P1201 " pdb=" F2 ALF P1201 " ideal model delta sigma weight residual 108.68 179.92 -71.24 3.00e+00 1.11e-01 5.64e+02 angle pdb=" F3 ALF P1201 " pdb="AL ALF P1201 " pdb=" F4 ALF P1201 " ideal model delta sigma weight residual 109.63 179.96 -70.33 3.00e+00 1.11e-01 5.50e+02 angle pdb=" F2 ALF P1201 " pdb="AL ALF P1201 " pdb=" F4 ALF P1201 " 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 P1201 " pdb="AL ALF P1201 " pdb=" F3 ALF P1201 " ideal model delta sigma weight residual 109.69 89.98 19.71 3.00e+00 1.11e-01 4.32e+01 angle pdb=" F2 ALF P1201 " pdb="AL ALF P1201 " pdb=" F3 ALF P1201 " ideal model delta sigma weight residual 109.59 90.02 19.57 3.00e+00 1.11e-01 4.25e+01 ... (remaining 11089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.02: 4699 27.02 - 54.05: 204 54.05 - 81.07: 10 81.07 - 108.10: 0 108.10 - 135.12: 3 Dihedral angle restraints: 4916 sinusoidal: 1948 harmonic: 2968 Sorted by residual: dihedral pdb=" O2A ADP P1203 " pdb=" O3A ADP P1203 " pdb=" PA ADP P1203 " pdb=" PB ADP P1203 " ideal model delta sinusoidal sigma weight residual -60.00 75.12 -135.12 1 2.00e+01 2.50e-03 4.10e+01 dihedral pdb=" C5' ADP P1203 " pdb=" O5' ADP P1203 " pdb=" PA ADP P1203 " pdb=" O2A ADP P1203 " ideal model delta sinusoidal sigma weight residual -60.00 67.58 -127.57 1 2.00e+01 2.50e-03 3.86e+01 dihedral pdb=" O1B ADP P1203 " pdb=" O3A ADP P1203 " pdb=" PB ADP P1203 " pdb=" PA ADP P1203 " ideal model delta sinusoidal sigma weight residual -60.00 66.52 -126.52 1 2.00e+01 2.50e-03 3.83e+01 ... (remaining 4913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 754 0.026 - 0.053: 351 0.053 - 0.079: 116 0.079 - 0.105: 78 0.105 - 0.132: 19 Chirality restraints: 1318 Sorted by residual: chirality pdb=" CA ILE P 350 " pdb=" N ILE P 350 " pdb=" C ILE P 350 " pdb=" CB ILE P 350 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA VAL P 469 " pdb=" N VAL P 469 " pdb=" C VAL P 469 " pdb=" CB VAL P 469 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.00e-01 chirality pdb=" CA VAL P 313 " pdb=" N VAL P 313 " pdb=" C VAL P 313 " pdb=" CB VAL P 313 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.69e-01 ... (remaining 1315 not shown) Planarity restraints: 1395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU P 617 " -0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO P 618 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO P 618 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO P 618 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL P 999 " 0.019 5.00e-02 4.00e+02 2.82e-02 1.27e+00 pdb=" N PRO P1000 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO P1000 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO P1000 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR P 567 " 0.018 5.00e-02 4.00e+02 2.65e-02 1.13e+00 pdb=" N PRO P 568 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO P 568 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO P 568 " 0.015 5.00e-02 4.00e+02 ... (remaining 1392 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1960 2.79 - 3.32: 6981 3.32 - 3.85: 12303 3.85 - 4.37: 12953 4.37 - 4.90: 23214 Nonbonded interactions: 57411 Sorted by model distance: nonbonded pdb=" O THR P 515 " pdb=" F2 ALF P1201 " model vdw 2.268 2.990 nonbonded pdb=" N GLY P 879 " pdb="MG MG P1202 " model vdw 2.270 2.250 nonbonded pdb=" O ARG P 553 " pdb=" OG1 THR P 557 " model vdw 2.290 3.040 nonbonded pdb=" OG1 THR P 647 " pdb=" OE1 GLN P 648 " model vdw 2.307 3.040 nonbonded pdb=" O ASP P 967 " pdb=" OG1 THR P 972 " model vdw 2.309 3.040 ... (remaining 57406 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 group one per residue 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: 1.800 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: 0.050 Set scattering table: 0.080 Process input model: 22.110 Find NCS groups from input model: 0.070 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 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 : 0.003 0.101 8139 Z= 0.181 Angle : 1.160 71.242 11094 Z= 0.454 Chirality : 0.039 0.132 1318 Planarity : 0.003 0.038 1395 Dihedral : 13.702 135.121 3000 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -3.84 (0.22), residues: 1016 helix: -0.87 (0.24), residues: 396 sheet: -2.51 (0.53), residues: 79 loop : -4.08 (0.19), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.000 TRP P 55 HIS 0.001 0.000 HIS P 51 PHE 0.003 0.000 PHE P1128 TYR 0.003 0.000 TYR P 241 ARG 0.001 0.000 ARG P 201 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: P 40 TYR cc_start: 0.4402 (m-80) cc_final: 0.3237 (m-80) REVERT: P 437 LEU cc_start: 0.8732 (pp) cc_final: 0.8469 (mp) REVERT: P 641 VAL cc_start: 0.8123 (t) cc_final: 0.7740 (p) REVERT: P 942 LEU cc_start: 0.9024 (tp) cc_final: 0.8574 (tp) REVERT: P 1012 VAL cc_start: 0.7641 (t) cc_final: 0.7411 (t) REVERT: P 1046 GLU cc_start: 0.7213 (mp0) cc_final: 0.6795 (mp0) REVERT: P 1164 ARG cc_start: 0.8838 (tmm160) cc_final: 0.8636 (ptm-80) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.2726 time to fit residues: 71.8570 Evaluate side-chains 118 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 51 HIS P 84 HIS P 101 GLN P 534 GLN P 755 GLN P 822 HIS P 858 GLN P1026 GLN P1033 ASN P1169 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.169041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.139356 restraints weight = 16862.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.143016 restraints weight = 10050.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.145456 restraints weight = 7173.296| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8139 Z= 0.211 Angle : 0.934 30.754 11094 Z= 0.380 Chirality : 0.044 0.243 1318 Planarity : 0.005 0.033 1395 Dihedral : 6.755 136.088 1125 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 1.71 % Allowed : 15.03 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.59 (0.25), residues: 1016 helix: 0.58 (0.28), residues: 394 sheet: -2.35 (0.55), residues: 75 loop : -3.61 (0.21), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP P 55 HIS 0.007 0.001 HIS P 84 PHE 0.012 0.001 PHE P 512 TYR 0.027 0.002 TYR P 241 ARG 0.005 0.001 ARG P 627 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: P 437 LEU cc_start: 0.8709 (pp) cc_final: 0.8411 (mp) REVERT: P 1046 GLU cc_start: 0.7319 (mp0) cc_final: 0.7066 (mp0) outliers start: 15 outliers final: 10 residues processed: 146 average time/residue: 0.2103 time to fit residues: 41.7254 Evaluate side-chains 121 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain P residue 408 VAL Chi-restraints excluded: chain P residue 464 LEU Chi-restraints excluded: chain P residue 525 VAL Chi-restraints excluded: chain P residue 634 LEU Chi-restraints excluded: chain P residue 735 VAL Chi-restraints excluded: chain P residue 873 VAL Chi-restraints excluded: chain P residue 946 ILE Chi-restraints excluded: chain P residue 986 VAL Chi-restraints excluded: chain P residue 1138 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 87 optimal weight: 0.9990 chunk 53 optimal weight: 0.0050 chunk 85 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 89 optimal weight: 0.0670 chunk 94 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 67 optimal weight: 0.0570 chunk 73 optimal weight: 1.9990 overall best weight: 0.3450 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 101 GLN P 897 GLN P1057 GLN P1127 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.167203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.137263 restraints weight = 16952.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.140850 restraints weight = 10310.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.143303 restraints weight = 7427.733| |-----------------------------------------------------------------------------| r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8139 Z= 0.150 Angle : 0.888 30.055 11094 Z= 0.350 Chirality : 0.042 0.180 1318 Planarity : 0.004 0.055 1395 Dihedral : 6.432 137.314 1125 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 1.71 % Allowed : 18.45 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.10 (0.26), residues: 1016 helix: 1.10 (0.29), residues: 389 sheet: -1.76 (0.59), residues: 75 loop : -3.45 (0.22), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP P 45 HIS 0.002 0.000 HIS P 84 PHE 0.011 0.001 PHE P 246 TYR 0.011 0.001 TYR P 183 ARG 0.004 0.000 ARG P 164 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.783 Fit side-chains REVERT: P 437 LEU cc_start: 0.8714 (pp) cc_final: 0.8408 (mp) REVERT: P 893 ILE cc_start: 0.8304 (mm) cc_final: 0.7686 (mm) outliers start: 15 outliers final: 5 residues processed: 128 average time/residue: 0.1682 time to fit residues: 31.1627 Evaluate side-chains 112 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 373 THR Chi-restraints excluded: chain P residue 464 LEU Chi-restraints excluded: chain P residue 735 VAL Chi-restraints excluded: chain P residue 873 VAL Chi-restraints excluded: chain P residue 1138 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 98 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 58 optimal weight: 0.0770 chunk 76 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 32 optimal weight: 0.0980 chunk 94 optimal weight: 4.9990 chunk 14 optimal weight: 0.0020 overall best weight: 0.7948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 413 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.158342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.127867 restraints weight = 16556.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.130130 restraints weight = 11402.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.131243 restraints weight = 8184.645| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8139 Z= 0.205 Angle : 0.927 31.336 11094 Z= 0.376 Chirality : 0.044 0.140 1318 Planarity : 0.005 0.063 1395 Dihedral : 6.232 118.093 1125 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 2.73 % Allowed : 20.73 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.88 (0.27), residues: 1016 helix: 1.26 (0.29), residues: 391 sheet: -1.99 (0.54), residues: 81 loop : -3.26 (0.23), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP P 45 HIS 0.004 0.001 HIS P 559 PHE 0.011 0.001 PHE P 837 TYR 0.024 0.001 TYR P 183 ARG 0.010 0.001 ARG P 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.879 Fit side-chains REVERT: P 267 SER cc_start: 0.7988 (m) cc_final: 0.7736 (p) REVERT: P 293 MET cc_start: 0.7269 (OUTLIER) cc_final: 0.6618 (ptp) REVERT: P 353 LEU cc_start: 0.8310 (tp) cc_final: 0.8098 (mp) REVERT: P 437 LEU cc_start: 0.8719 (pp) cc_final: 0.8373 (mp) REVERT: P 893 ILE cc_start: 0.8695 (mm) cc_final: 0.8424 (mm) outliers start: 24 outliers final: 16 residues processed: 144 average time/residue: 0.1829 time to fit residues: 37.3355 Evaluate side-chains 124 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 293 MET Chi-restraints excluded: chain P residue 318 LEU Chi-restraints excluded: chain P residue 373 THR Chi-restraints excluded: chain P residue 424 HIS Chi-restraints excluded: chain P residue 464 LEU Chi-restraints excluded: chain P residue 585 LEU Chi-restraints excluded: chain P residue 634 LEU Chi-restraints excluded: chain P residue 687 VAL Chi-restraints excluded: chain P residue 735 VAL Chi-restraints excluded: chain P residue 759 THR Chi-restraints excluded: chain P residue 773 LEU Chi-restraints excluded: chain P residue 873 VAL Chi-restraints excluded: chain P residue 903 VAL Chi-restraints excluded: chain P residue 986 VAL Chi-restraints excluded: chain P residue 1049 VAL Chi-restraints excluded: chain P residue 1138 LEU Chi-restraints excluded: chain P residue 1149 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 6 optimal weight: 0.2980 chunk 91 optimal weight: 1.9990 chunk 58 optimal weight: 0.0970 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 47 optimal weight: 0.0770 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 219 ASN ** 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 = 0.4245 r_free = 0.4245 target = 0.158137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.128006 restraints weight = 16503.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.130445 restraints weight = 10244.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.131741 restraints weight = 7877.282| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8139 Z= 0.151 Angle : 0.892 29.908 11094 Z= 0.353 Chirality : 0.043 0.155 1318 Planarity : 0.004 0.059 1395 Dihedral : 5.929 117.155 1125 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.05 % Allowed : 21.98 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.70 (0.27), residues: 1016 helix: 1.29 (0.29), residues: 399 sheet: -1.68 (0.55), residues: 81 loop : -3.15 (0.23), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP P 45 HIS 0.003 0.000 HIS P 822 PHE 0.013 0.001 PHE P1056 TYR 0.009 0.001 TYR P 183 ARG 0.003 0.000 ARG P 740 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.893 Fit side-chains REVERT: P 40 TYR cc_start: 0.5427 (OUTLIER) cc_final: 0.3640 (m-80) REVERT: P 293 MET cc_start: 0.7050 (OUTLIER) cc_final: 0.6495 (ptp) REVERT: P 404 LYS cc_start: 0.9133 (tppt) cc_final: 0.8836 (tppt) REVERT: P 437 LEU cc_start: 0.8681 (pp) cc_final: 0.8399 (mp) REVERT: P 861 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7129 (tp30) REVERT: P 893 ILE cc_start: 0.8764 (mm) cc_final: 0.8408 (mm) outliers start: 18 outliers final: 11 residues processed: 124 average time/residue: 0.1614 time to fit residues: 29.4105 Evaluate side-chains 116 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 40 TYR Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 293 MET Chi-restraints excluded: chain P residue 424 HIS Chi-restraints excluded: chain P residue 464 LEU Chi-restraints excluded: chain P residue 735 VAL Chi-restraints excluded: chain P residue 773 LEU Chi-restraints excluded: chain P residue 873 VAL Chi-restraints excluded: chain P residue 903 VAL Chi-restraints excluded: chain P residue 963 PHE Chi-restraints excluded: chain P residue 978 MET Chi-restraints excluded: chain P residue 1096 VAL Chi-restraints excluded: chain P residue 1138 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 56 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 0.0070 chunk 27 optimal weight: 6.9990 chunk 23 optimal weight: 0.0270 chunk 80 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 485 GLN P 491 GLN P 753 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.152973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.123033 restraints weight = 16382.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.124909 restraints weight = 11514.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.126695 restraints weight = 8248.916| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8139 Z= 0.193 Angle : 0.920 30.431 11094 Z= 0.370 Chirality : 0.043 0.152 1318 Planarity : 0.004 0.054 1395 Dihedral : 5.679 108.570 1125 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 2.39 % Allowed : 23.46 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.53 (0.27), residues: 1016 helix: 1.42 (0.29), residues: 392 sheet: -1.60 (0.56), residues: 81 loop : -2.98 (0.24), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP P 100 HIS 0.002 0.001 HIS P 836 PHE 0.038 0.001 PHE P 243 TYR 0.007 0.001 TYR P 166 ARG 0.004 0.000 ARG P1158 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.972 Fit side-chains REVERT: P 293 MET cc_start: 0.7281 (OUTLIER) cc_final: 0.6521 (ptp) REVERT: P 437 LEU cc_start: 0.8757 (pp) cc_final: 0.8378 (mp) REVERT: P 766 MET cc_start: 0.4612 (pmm) cc_final: 0.4215 (pmm) REVERT: P 854 MET cc_start: 0.8809 (mmp) cc_final: 0.8446 (mmp) REVERT: P 893 ILE cc_start: 0.8816 (mm) cc_final: 0.8496 (mm) REVERT: P 1046 GLU cc_start: 0.7172 (mp0) cc_final: 0.6691 (pm20) outliers start: 21 outliers final: 12 residues processed: 123 average time/residue: 0.2191 time to fit residues: 40.1869 Evaluate side-chains 110 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 293 MET Chi-restraints excluded: chain P residue 318 LEU Chi-restraints excluded: chain P residue 424 HIS Chi-restraints excluded: chain P residue 435 LEU Chi-restraints excluded: chain P residue 464 LEU Chi-restraints excluded: chain P residue 653 VAL Chi-restraints excluded: chain P residue 735 VAL Chi-restraints excluded: chain P residue 773 LEU Chi-restraints excluded: chain P residue 873 VAL Chi-restraints excluded: chain P residue 903 VAL Chi-restraints excluded: chain P residue 978 MET Chi-restraints excluded: chain P residue 1138 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 20 optimal weight: 1.9990 chunk 100 optimal weight: 0.0970 chunk 96 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 75 optimal weight: 0.0770 chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 0.0040 overall best weight: 0.8352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 84 HIS ** P 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.149693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.120765 restraints weight = 16483.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.120987 restraints weight = 11404.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.122344 restraints weight = 9912.631| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.6140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8139 Z= 0.203 Angle : 0.931 30.342 11094 Z= 0.375 Chirality : 0.044 0.165 1318 Planarity : 0.004 0.058 1395 Dihedral : 5.423 100.683 1125 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 2.05 % Allowed : 23.92 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.34 (0.27), residues: 1016 helix: 1.43 (0.29), residues: 401 sheet: -1.04 (0.64), residues: 71 loop : -2.87 (0.24), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP P 45 HIS 0.008 0.001 HIS P 84 PHE 0.018 0.001 PHE P 243 TYR 0.008 0.001 TYR P 940 ARG 0.006 0.000 ARG P 725 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: P 40 TYR cc_start: 0.5196 (OUTLIER) cc_final: 0.3478 (m-80) REVERT: P 293 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.6648 (ptp) REVERT: P 766 MET cc_start: 0.4996 (pmm) cc_final: 0.4570 (pmm) REVERT: P 854 MET cc_start: 0.8816 (mmp) cc_final: 0.8538 (mmp) REVERT: P 861 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7458 (tp30) REVERT: P 894 SER cc_start: 0.8673 (m) cc_final: 0.8162 (t) outliers start: 18 outliers final: 13 residues processed: 112 average time/residue: 0.2088 time to fit residues: 34.0505 Evaluate side-chains 111 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 40 TYR Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 293 MET Chi-restraints excluded: chain P residue 355 THR Chi-restraints excluded: chain P residue 424 HIS Chi-restraints excluded: chain P residue 464 LEU Chi-restraints excluded: chain P residue 551 LEU Chi-restraints excluded: chain P residue 653 VAL Chi-restraints excluded: chain P residue 724 MET Chi-restraints excluded: chain P residue 735 VAL Chi-restraints excluded: chain P residue 759 THR Chi-restraints excluded: chain P residue 873 VAL Chi-restraints excluded: chain P residue 903 VAL Chi-restraints excluded: chain P residue 978 MET Chi-restraints excluded: chain P residue 1138 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 92 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 47 optimal weight: 0.3980 chunk 32 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 491 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.149022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.120371 restraints weight = 16317.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.119991 restraints weight = 10740.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.121431 restraints weight = 10013.179| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.6404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8139 Z= 0.191 Angle : 0.931 30.145 11094 Z= 0.373 Chirality : 0.043 0.150 1318 Planarity : 0.004 0.055 1395 Dihedral : 5.366 104.129 1125 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 2.28 % Allowed : 24.37 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.25 (0.28), residues: 1016 helix: 1.52 (0.29), residues: 400 sheet: -1.00 (0.65), residues: 71 loop : -2.82 (0.24), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 45 HIS 0.002 0.001 HIS P 390 PHE 0.022 0.001 PHE P 243 TYR 0.008 0.001 TYR P 183 ARG 0.003 0.000 ARG P 279 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.810 Fit side-chains REVERT: P 40 TYR cc_start: 0.5269 (OUTLIER) cc_final: 0.3609 (m-80) REVERT: P 293 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.6818 (ptp) REVERT: P 766 MET cc_start: 0.4899 (pmm) cc_final: 0.4514 (pmm) REVERT: P 854 MET cc_start: 0.8822 (mmp) cc_final: 0.8544 (mmp) REVERT: P 861 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7432 (tp30) REVERT: P 894 SER cc_start: 0.8750 (m) cc_final: 0.8227 (t) REVERT: P 1046 GLU cc_start: 0.7212 (mp0) cc_final: 0.6917 (pm20) outliers start: 20 outliers final: 13 residues processed: 113 average time/residue: 0.1772 time to fit residues: 28.7055 Evaluate side-chains 112 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 40 TYR Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 293 MET Chi-restraints excluded: chain P residue 355 THR Chi-restraints excluded: chain P residue 424 HIS Chi-restraints excluded: chain P residue 464 LEU Chi-restraints excluded: chain P residue 551 LEU Chi-restraints excluded: chain P residue 653 VAL Chi-restraints excluded: chain P residue 735 VAL Chi-restraints excluded: chain P residue 759 THR Chi-restraints excluded: chain P residue 873 VAL Chi-restraints excluded: chain P residue 903 VAL Chi-restraints excluded: chain P residue 978 MET Chi-restraints excluded: chain P residue 986 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 78 optimal weight: 1.9990 chunk 49 optimal weight: 0.0870 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 74 optimal weight: 0.4980 chunk 55 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 2 optimal weight: 20.0000 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 491 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 = 0.4128 r_free = 0.4128 target = 0.148716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.119553 restraints weight = 16623.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.120017 restraints weight = 11630.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.120963 restraints weight = 10007.235| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.6613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8139 Z= 0.177 Angle : 0.925 29.991 11094 Z= 0.372 Chirality : 0.043 0.173 1318 Planarity : 0.004 0.057 1395 Dihedral : 5.328 109.822 1125 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 1.82 % Allowed : 25.28 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1016 helix: 1.49 (0.29), residues: 405 sheet: -0.95 (0.63), residues: 71 loop : -2.70 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP P 45 HIS 0.002 0.001 HIS P 390 PHE 0.021 0.001 PHE P 243 TYR 0.015 0.001 TYR P 386 ARG 0.004 0.000 ARG P 544 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.959 Fit side-chains REVERT: P 40 TYR cc_start: 0.5056 (OUTLIER) cc_final: 0.3439 (m-80) REVERT: P 243 PHE cc_start: 0.8247 (t80) cc_final: 0.7967 (t80) REVERT: P 293 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.6648 (ptp) REVERT: P 485 GLN cc_start: 0.8025 (tt0) cc_final: 0.7774 (mt0) REVERT: P 546 LEU cc_start: 0.7270 (mt) cc_final: 0.6900 (pp) REVERT: P 766 MET cc_start: 0.4917 (pmm) cc_final: 0.4565 (pmm) REVERT: P 854 MET cc_start: 0.8811 (mmp) cc_final: 0.8556 (mmp) REVERT: P 861 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7413 (tp30) REVERT: P 894 SER cc_start: 0.8654 (m) cc_final: 0.8104 (t) REVERT: P 1046 GLU cc_start: 0.7118 (mp0) cc_final: 0.6910 (pm20) outliers start: 16 outliers final: 12 residues processed: 114 average time/residue: 0.1836 time to fit residues: 29.8638 Evaluate side-chains 113 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 40 TYR Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 293 MET Chi-restraints excluded: chain P residue 355 THR Chi-restraints excluded: chain P residue 424 HIS Chi-restraints excluded: chain P residue 551 LEU Chi-restraints excluded: chain P residue 653 VAL Chi-restraints excluded: chain P residue 724 MET Chi-restraints excluded: chain P residue 735 VAL Chi-restraints excluded: chain P residue 759 THR Chi-restraints excluded: chain P residue 903 VAL Chi-restraints excluded: chain P residue 978 MET Chi-restraints excluded: chain P residue 986 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 47 optimal weight: 0.0170 chunk 2 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 14 optimal weight: 0.0370 chunk 42 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 overall best weight: 0.9500 ------------------------------------------------------------------------------- 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 = 0.4096 r_free = 0.4096 target = 0.146051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.116441 restraints weight = 16294.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.117736 restraints weight = 10980.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.119025 restraints weight = 8772.572| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.6934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8139 Z= 0.219 Angle : 0.956 30.358 11094 Z= 0.393 Chirality : 0.044 0.158 1318 Planarity : 0.005 0.081 1395 Dihedral : 5.491 118.512 1125 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 1.59 % Allowed : 25.85 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.16 (0.27), residues: 1016 helix: 1.44 (0.28), residues: 403 sheet: -1.03 (0.63), residues: 72 loop : -2.65 (0.24), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP P 55 HIS 0.002 0.001 HIS P 390 PHE 0.019 0.001 PHE P 243 TYR 0.011 0.001 TYR P 183 ARG 0.007 0.000 ARG P 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: P 40 TYR cc_start: 0.4973 (OUTLIER) cc_final: 0.3285 (m-80) REVERT: P 84 HIS cc_start: 0.7797 (t-90) cc_final: 0.7548 (t-170) REVERT: P 243 PHE cc_start: 0.8234 (t80) cc_final: 0.7994 (t80) REVERT: P 293 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.6777 (ptp) REVERT: P 546 LEU cc_start: 0.7473 (mt) cc_final: 0.6841 (pp) REVERT: P 766 MET cc_start: 0.4926 (pmm) cc_final: 0.4549 (pmm) REVERT: P 854 MET cc_start: 0.8811 (mmp) cc_final: 0.8538 (mmp) REVERT: P 861 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7513 (tp30) REVERT: P 894 SER cc_start: 0.8718 (m) cc_final: 0.8215 (t) REVERT: P 1020 TYR cc_start: 0.7420 (t80) cc_final: 0.7159 (t80) outliers start: 14 outliers final: 12 residues processed: 116 average time/residue: 0.1786 time to fit residues: 29.7246 Evaluate side-chains 121 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 40 TYR Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 293 MET Chi-restraints excluded: chain P residue 355 THR Chi-restraints excluded: chain P residue 424 HIS Chi-restraints excluded: chain P residue 551 LEU Chi-restraints excluded: chain P residue 653 VAL Chi-restraints excluded: chain P residue 724 MET Chi-restraints excluded: chain P residue 735 VAL Chi-restraints excluded: chain P residue 759 THR Chi-restraints excluded: chain P residue 903 VAL Chi-restraints excluded: chain P residue 978 MET Chi-restraints excluded: chain P residue 986 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 7 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 21 optimal weight: 0.3980 chunk 23 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 85 optimal weight: 0.2980 chunk 13 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4111 r_free = 0.4111 target = 0.147166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.117411 restraints weight = 16313.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.118745 restraints weight = 11592.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.120385 restraints weight = 8659.695| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.7055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8139 Z= 0.175 Angle : 0.940 29.853 11094 Z= 0.381 Chirality : 0.044 0.233 1318 Planarity : 0.005 0.068 1395 Dihedral : 5.494 121.347 1125 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 1.82 % Allowed : 26.88 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.06 (0.27), residues: 1016 helix: 1.47 (0.28), residues: 404 sheet: -0.87 (0.63), residues: 72 loop : -2.57 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP P 55 HIS 0.001 0.000 HIS P 190 PHE 0.020 0.001 PHE P 243 TYR 0.015 0.001 TYR P 183 ARG 0.003 0.000 ARG P 279 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2807.28 seconds wall clock time: 51 minutes 25.59 seconds (3085.59 seconds total)