Starting phenix.real_space_refine on Thu Sep 18 13:23:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zqh_60385/09_2025/8zqh_60385.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zqh_60385/09_2025/8zqh_60385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zqh_60385/09_2025/8zqh_60385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zqh_60385/09_2025/8zqh_60385.map" model { file = "/net/cci-nas-00/data/ceres_data/8zqh_60385/09_2025/8zqh_60385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zqh_60385/09_2025/8zqh_60385.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 6 Type Number sf(0) Gaussians P 74 5.49 5 S 25 5.16 5 C 5379 2.51 5 N 1643 2.21 5 O 1861 1.98 5 H 8203 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17185 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 1510 Classifications: {'RNA': 47} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 21, 'rna3p_pyr': 21} Link IDs: {'rna2p': 5, 'rna3p': 41} Chain breaks: 1 Chain: "C" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 607 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain breaks: 1 Chain: "A" Number of atoms: 14812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 908, 14812 Classifications: {'peptide': 908} Link IDs: {'PTRANS': 32, 'TRANS': 875} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 256 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Time building chain proxies: 3.32, per 1000 atoms: 0.19 Number of scatterers: 17185 At special positions: 0 Unit cell: (93.06, 102.3, 112.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 25 16.00 P 74 15.00 O 1861 8.00 N 1643 7.00 C 5379 6.00 H 8203 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 417.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1716 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 7 sheets defined 50.6% alpha, 16.4% beta 28 base pairs and 40 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'A' and resid 15 through 40 removed outlier: 3.567A pdb=" N LEU A 37 " --> pdb=" O MET A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 69 removed outlier: 3.590A pdb=" N THR A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 88 Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.535A pdb=" N LEU A 110 " --> pdb=" O SER A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 137 through 147 Processing helix chain 'A' and resid 152 through 158 removed outlier: 3.968A pdb=" N LYS A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 169 removed outlier: 4.282A pdb=" N ARG A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 187 through 200 Processing helix chain 'A' and resid 211 through 253 removed outlier: 3.798A pdb=" N GLY A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 272 Processing helix chain 'A' and resid 277 through 286 Processing helix chain 'A' and resid 293 through 301 removed outlier: 4.715A pdb=" N ARG A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLY A 299 " --> pdb=" O GLU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 314 through 329 Processing helix chain 'A' and resid 447 through 459 removed outlier: 3.567A pdb=" N ALA A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 553 removed outlier: 4.197A pdb=" N ARG A 541 " --> pdb=" O PHE A 537 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A 548 " --> pdb=" O ARG A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 566 removed outlier: 3.513A pdb=" N LEU A 563 " --> pdb=" O GLU A 559 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 571 Processing helix chain 'A' and resid 578 through 606 removed outlier: 3.667A pdb=" N ARG A 582 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG A 583 " --> pdb=" O ALA A 579 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 609 No H-bonds generated for 'chain 'A' and resid 607 through 609' Processing helix chain 'A' and resid 610 through 616 removed outlier: 4.371A pdb=" N ASP A 614 " --> pdb=" O SER A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 642 removed outlier: 4.257A pdb=" N PHE A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 690 Processing helix chain 'A' and resid 711 through 719 removed outlier: 3.504A pdb=" N ASN A 714 " --> pdb=" O ARG A 711 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 715 " --> pdb=" O LYS A 712 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LEU A 716 " --> pdb=" O GLU A 713 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU A 717 " --> pdb=" O ASN A 714 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER A 718 " --> pdb=" O SER A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 736 removed outlier: 3.759A pdb=" N VAL A 725 " --> pdb=" O ALA A 721 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 726 " --> pdb=" O PRO A 722 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG A 728 " --> pdb=" O MET A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 796 removed outlier: 3.646A pdb=" N ALA A 786 " --> pdb=" O ALA A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 832 Processing helix chain 'A' and resid 854 through 864 removed outlier: 4.446A pdb=" N LEU A 858 " --> pdb=" O GLU A 854 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS A 864 " --> pdb=" O GLN A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 899 removed outlier: 3.862A pdb=" N GLU A 886 " --> pdb=" O GLU A 882 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 349 through 352 removed outlier: 4.406A pdb=" N LYS A 422 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N ASP A 438 " --> pdb=" O LYS A 422 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ILE A 424 " --> pdb=" O PHE A 436 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N PHE A 436 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU A 426 " --> pdb=" O TYR A 434 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TYR A 434 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG A 428 " --> pdb=" O ARG A 432 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ARG A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N TYR A 433 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 7 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU A 10 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE A 369 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 349 through 352 removed outlier: 5.052A pdb=" N THR A 408 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ASN A 392 " --> pdb=" O THR A 408 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 44 through 47 removed outlier: 3.537A pdb=" N TYR A 44 " --> pdb=" O VAL A 56 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 513 through 517 removed outlier: 3.939A pdb=" N SER A 513 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 488 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N MET A 475 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N GLU A 697 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE A 477 " --> pdb=" O GLU A 697 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL A 694 " --> pdb=" O TRP A 741 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL A 743 " --> pdb=" O VAL A 694 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N MET A 696 " --> pdb=" O VAL A 743 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 499 through 503 removed outlier: 4.524A pdb=" N ILE A 499 " --> pdb=" O PHE A 511 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL A 503 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N GLU A 507 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 760 through 761 Processing sheet with id=AA7, first strand: chain 'A' and resid 803 through 809 removed outlier: 3.723A pdb=" N ARG A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER A 845 " --> pdb=" O THR A 841 " (cutoff:3.500A) 385 hydrogen bonds defined for protein. 1107 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 71 hydrogen bonds 134 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 40 stacking parallelities Total time for adding SS restraints: 4.20 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8192 1.03 - 1.23: 49 1.23 - 1.42: 4138 1.42 - 1.62: 5096 1.62 - 1.81: 39 Bond restraints: 17514 Sorted by residual: bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.43e+00 bond pdb=" CB PRO A 203 " pdb=" CG PRO A 203 " ideal model delta sigma weight residual 1.492 1.569 -0.077 5.00e-02 4.00e+02 2.39e+00 bond pdb=" N MET A 1 " pdb=" H MET A 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" CA GLY A 352 " pdb=" C GLY A 352 " ideal model delta sigma weight residual 1.519 1.507 0.012 8.90e-03 1.26e+04 1.83e+00 bond pdb=" CA PHE A 390 " pdb=" C PHE A 390 " ideal model delta sigma weight residual 1.530 1.517 0.013 1.11e-02 8.12e+03 1.31e+00 ... (remaining 17509 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 31464 2.96 - 5.92: 81 5.92 - 8.88: 0 8.88 - 11.84: 0 11.84 - 14.80: 1 Bond angle restraints: 31546 Sorted by residual: angle pdb=" C PHE A 202 " pdb=" N PRO A 203 " pdb=" CD PRO A 203 " ideal model delta sigma weight residual 125.00 110.20 14.80 4.10e+00 5.95e-02 1.30e+01 angle pdb=" N VAL A 764 " pdb=" CA VAL A 764 " pdb=" C VAL A 764 " ideal model delta sigma weight residual 111.56 108.80 2.76 8.60e-01 1.35e+00 1.03e+01 angle pdb=" CA PRO A 203 " pdb=" N PRO A 203 " pdb=" CD PRO A 203 " ideal model delta sigma weight residual 112.00 107.76 4.24 1.40e+00 5.10e-01 9.17e+00 angle pdb=" N ASP A 74 " pdb=" CA ASP A 74 " pdb=" C ASP A 74 " ideal model delta sigma weight residual 112.72 109.68 3.04 1.28e+00 6.10e-01 5.64e+00 angle pdb=" N VAL A 76 " pdb=" CA VAL A 76 " pdb=" C VAL A 76 " ideal model delta sigma weight residual 111.91 109.81 2.10 8.90e-01 1.26e+00 5.59e+00 ... (remaining 31541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.67: 7658 35.67 - 71.33: 427 71.33 - 107.00: 33 107.00 - 142.66: 1 142.66 - 178.33: 2 Dihedral angle restraints: 8121 sinusoidal: 4999 harmonic: 3122 Sorted by residual: dihedral pdb=" CA PHE A 202 " pdb=" C PHE A 202 " pdb=" N PRO A 203 " pdb=" CA PRO A 203 " ideal model delta harmonic sigma weight residual 180.00 -138.25 -41.75 0 5.00e+00 4.00e-02 6.97e+01 dihedral pdb=" O4' U B -32 " pdb=" C1' U B -32 " pdb=" N1 U B -32 " pdb=" C2 U B -32 " ideal model delta sinusoidal sigma weight residual -128.00 50.33 -178.33 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA ARG A 122 " pdb=" C ARG A 122 " pdb=" N PRO A 123 " pdb=" CA PRO A 123 " ideal model delta harmonic sigma weight residual 180.00 154.22 25.78 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 8118 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 891 0.030 - 0.060: 380 0.060 - 0.090: 99 0.090 - 0.120: 44 0.120 - 0.149: 11 Chirality restraints: 1425 Sorted by residual: chirality pdb=" CA ILE A 780 " pdb=" N ILE A 780 " pdb=" C ILE A 780 " pdb=" CB ILE A 780 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA ILE A 903 " pdb=" N ILE A 903 " pdb=" C ILE A 903 " pdb=" CB ILE A 903 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA ILE A 424 " pdb=" N ILE A 424 " pdb=" C ILE A 424 " pdb=" CB ILE A 424 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 ... (remaining 1422 not shown) Planarity restraints: 2342 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 202 " 0.110 5.00e-02 4.00e+02 1.66e-01 4.42e+01 pdb=" N PRO A 203 " -0.287 5.00e-02 4.00e+02 pdb=" CA PRO A 203 " 0.096 5.00e-02 4.00e+02 pdb=" CD PRO A 203 " 0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 72 " -0.046 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO A 73 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 73 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 73 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 568 " -0.042 5.00e-02 4.00e+02 6.42e-02 6.59e+00 pdb=" N PRO A 569 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 569 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 569 " -0.036 5.00e-02 4.00e+02 ... (remaining 2339 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 346 2.08 - 2.71: 26883 2.71 - 3.34: 48258 3.34 - 3.97: 61439 3.97 - 4.60: 95814 Nonbonded interactions: 232740 Sorted by model distance: nonbonded pdb=" OE1 GLU A 17 " pdb=" H GLU A 17 " model vdw 1.446 2.450 nonbonded pdb=" OP2 U B -32 " pdb=" HH TYR A 666 " model vdw 1.582 2.450 nonbonded pdb=" OE2 GLU A 463 " pdb="HH11 ARG A 465 " model vdw 1.588 2.450 nonbonded pdb="HH11 ARG A 27 " pdb=" OE2 GLU A 208 " model vdw 1.594 2.450 nonbonded pdb=" OE2 GLU A 133 " pdb=" H ASP A 173 " model vdw 1.600 2.450 ... (remaining 232735 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.330 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: 0.100 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.940 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 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 0.077 9311 Z= 0.199 Angle : 0.631 14.796 12887 Z= 0.356 Chirality : 0.039 0.149 1425 Planarity : 0.007 0.166 1410 Dihedral : 20.127 178.331 3935 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.64 % Favored : 95.14 % Rotamer: Outliers : 0.13 % Allowed : 16.45 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.28), residues: 906 helix: 1.07 (0.26), residues: 395 sheet: -0.67 (0.45), residues: 142 loop : -1.78 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 582 TYR 0.014 0.002 TYR A 872 PHE 0.018 0.002 PHE A 436 TRP 0.009 0.001 TRP A 328 HIS 0.004 0.001 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 9311) covalent geometry : angle 0.63086 (12887) hydrogen bonds : bond 0.15657 ( 452) hydrogen bonds : angle 6.04308 ( 1241) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 118 average time/residue: 0.4159 time to fit residues: 58.2018 Evaluate side-chains 64 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.093941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.061089 restraints weight = 66095.030| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.29 r_work: 0.2814 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 9311 Z= 0.211 Angle : 0.626 15.285 12887 Z= 0.337 Chirality : 0.038 0.140 1425 Planarity : 0.007 0.169 1410 Dihedral : 19.939 178.909 2058 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.30 % Favored : 95.47 % Rotamer: Outliers : 1.40 % Allowed : 15.18 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.28), residues: 906 helix: 1.64 (0.26), residues: 408 sheet: -0.57 (0.41), residues: 154 loop : -1.91 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 179 TYR 0.011 0.001 TYR A 22 PHE 0.013 0.001 PHE A 571 TRP 0.008 0.001 TRP A 720 HIS 0.007 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 9311) covalent geometry : angle 0.62554 (12887) hydrogen bonds : bond 0.05113 ( 452) hydrogen bonds : angle 4.69256 ( 1241) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8859 (t0) cc_final: 0.8613 (t0) REVERT: A 756 ASP cc_start: 0.7940 (t0) cc_final: 0.7551 (t0) outliers start: 11 outliers final: 9 residues processed: 74 average time/residue: 0.2589 time to fit residues: 25.5298 Evaluate side-chains 67 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 724 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 39 optimal weight: 0.5980 chunk 30 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 778 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.092721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.059591 restraints weight = 66485.144| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.33 r_work: 0.2787 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9311 Z= 0.191 Angle : 0.580 15.145 12887 Z= 0.311 Chirality : 0.037 0.140 1425 Planarity : 0.006 0.169 1410 Dihedral : 19.826 178.592 2058 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.53 % Favored : 96.25 % Rotamer: Outliers : 1.53 % Allowed : 15.05 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.28), residues: 906 helix: 1.90 (0.26), residues: 409 sheet: -0.71 (0.39), residues: 164 loop : -1.87 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 625 TYR 0.017 0.001 TYR A 125 PHE 0.012 0.001 PHE A 571 TRP 0.009 0.001 TRP A 229 HIS 0.004 0.001 HIS A 26 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 9311) covalent geometry : angle 0.58012 (12887) hydrogen bonds : bond 0.04566 ( 452) hydrogen bonds : angle 4.32553 ( 1241) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8920 (t0) cc_final: 0.8634 (t0) REVERT: A 53 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8096 (mp0) REVERT: A 696 MET cc_start: 0.9365 (ttp) cc_final: 0.9124 (ttp) REVERT: A 705 ASP cc_start: 0.9127 (m-30) cc_final: 0.8804 (m-30) REVERT: A 742 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8486 (mt-10) REVERT: A 798 TYR cc_start: 0.9571 (OUTLIER) cc_final: 0.9307 (t80) outliers start: 12 outliers final: 6 residues processed: 70 average time/residue: 0.3113 time to fit residues: 27.7529 Evaluate side-chains 61 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 774 ASP Chi-restraints excluded: chain A residue 798 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 45 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.089928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.057117 restraints weight = 67074.533| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 3.25 r_work: 0.2736 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 9311 Z= 0.279 Angle : 0.622 15.608 12887 Z= 0.334 Chirality : 0.039 0.148 1425 Planarity : 0.006 0.171 1410 Dihedral : 19.824 179.524 2058 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.52 % Favored : 94.26 % Rotamer: Outliers : 1.66 % Allowed : 14.54 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.28), residues: 906 helix: 1.83 (0.25), residues: 409 sheet: -0.96 (0.40), residues: 164 loop : -2.00 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 49 TYR 0.013 0.002 TYR A 417 PHE 0.018 0.001 PHE A 571 TRP 0.010 0.001 TRP A 328 HIS 0.005 0.001 HIS A 26 Details of bonding type rmsd covalent geometry : bond 0.00595 ( 9311) covalent geometry : angle 0.62229 (12887) hydrogen bonds : bond 0.04627 ( 452) hydrogen bonds : angle 4.34219 ( 1241) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8100 (mp0) REVERT: A 742 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8454 (mt-10) REVERT: A 798 TYR cc_start: 0.9594 (OUTLIER) cc_final: 0.9269 (t80) outliers start: 13 outliers final: 6 residues processed: 65 average time/residue: 0.2990 time to fit residues: 24.8542 Evaluate side-chains 58 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 774 ASP Chi-restraints excluded: chain A residue 798 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 66 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.091258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.058316 restraints weight = 66348.479| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.21 r_work: 0.2763 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 9311 Z= 0.158 Angle : 0.562 14.889 12887 Z= 0.300 Chirality : 0.037 0.140 1425 Planarity : 0.006 0.169 1410 Dihedral : 19.876 178.463 2058 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.30 % Favored : 95.47 % Rotamer: Outliers : 1.66 % Allowed : 15.05 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.29), residues: 906 helix: 2.10 (0.25), residues: 410 sheet: -0.85 (0.39), residues: 166 loop : -1.85 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 225 TYR 0.011 0.001 TYR A 22 PHE 0.011 0.001 PHE A 571 TRP 0.009 0.001 TRP A 229 HIS 0.003 0.001 HIS A 26 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9311) covalent geometry : angle 0.56206 (12887) hydrogen bonds : bond 0.04085 ( 452) hydrogen bonds : angle 4.06121 ( 1241) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8137 (mp0) REVERT: A 520 ILE cc_start: 0.8908 (mm) cc_final: 0.8699 (mm) REVERT: A 742 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8422 (mt-10) REVERT: A 798 TYR cc_start: 0.9566 (OUTLIER) cc_final: 0.9262 (t80) outliers start: 13 outliers final: 9 residues processed: 59 average time/residue: 0.3256 time to fit residues: 24.7042 Evaluate side-chains 61 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 774 ASP Chi-restraints excluded: chain A residue 798 TYR Chi-restraints excluded: chain A residue 877 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 2 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.091155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.058363 restraints weight = 66230.145| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 3.24 r_work: 0.2765 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9311 Z= 0.154 Angle : 0.547 14.513 12887 Z= 0.291 Chirality : 0.036 0.153 1425 Planarity : 0.006 0.167 1410 Dihedral : 19.889 178.639 2058 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.30 % Favored : 94.48 % Rotamer: Outliers : 1.53 % Allowed : 15.05 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.29), residues: 906 helix: 2.32 (0.25), residues: 409 sheet: -0.80 (0.40), residues: 166 loop : -1.62 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 179 TYR 0.011 0.001 TYR A 22 PHE 0.012 0.001 PHE A 485 TRP 0.010 0.001 TRP A 229 HIS 0.003 0.001 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9311) covalent geometry : angle 0.54720 (12887) hydrogen bonds : bond 0.03941 ( 452) hydrogen bonds : angle 3.92788 ( 1241) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8117 (mp0) REVERT: A 244 ARG cc_start: 0.8065 (tmm-80) cc_final: 0.7751 (ttp80) REVERT: A 444 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.7803 (mp0) REVERT: A 732 GLU cc_start: 0.8991 (tp30) cc_final: 0.8760 (mm-30) REVERT: A 742 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8402 (mt-10) REVERT: A 798 TYR cc_start: 0.9556 (OUTLIER) cc_final: 0.9248 (t80) outliers start: 12 outliers final: 7 residues processed: 61 average time/residue: 0.3252 time to fit residues: 25.3151 Evaluate side-chains 60 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 798 TYR Chi-restraints excluded: chain A residue 879 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 18 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 25 optimal weight: 0.0170 chunk 26 optimal weight: 1.9990 overall best weight: 1.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.090916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.058197 restraints weight = 67058.028| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 3.22 r_work: 0.2760 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 9311 Z= 0.161 Angle : 0.545 14.356 12887 Z= 0.290 Chirality : 0.036 0.156 1425 Planarity : 0.006 0.167 1410 Dihedral : 19.916 178.422 2058 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.30 % Favored : 95.47 % Rotamer: Outliers : 1.91 % Allowed : 14.54 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.29), residues: 906 helix: 2.41 (0.25), residues: 409 sheet: -0.83 (0.40), residues: 166 loop : -1.61 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 225 TYR 0.011 0.001 TYR A 22 PHE 0.010 0.001 PHE A 571 TRP 0.009 0.001 TRP A 229 HIS 0.004 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 9311) covalent geometry : angle 0.54542 (12887) hydrogen bonds : bond 0.03892 ( 452) hydrogen bonds : angle 3.88955 ( 1241) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8127 (mp0) REVERT: A 244 ARG cc_start: 0.8106 (tmm-80) cc_final: 0.7787 (ttp80) REVERT: A 444 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.7789 (mp0) REVERT: A 732 GLU cc_start: 0.9022 (tp30) cc_final: 0.8812 (mm-30) REVERT: A 742 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8390 (mt-10) REVERT: A 798 TYR cc_start: 0.9548 (OUTLIER) cc_final: 0.9237 (t80) outliers start: 15 outliers final: 10 residues processed: 61 average time/residue: 0.3302 time to fit residues: 25.4924 Evaluate side-chains 60 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 798 TYR Chi-restraints excluded: chain A residue 877 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.090961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.058224 restraints weight = 66472.782| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.26 r_work: 0.2768 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 9311 Z= 0.157 Angle : 0.541 14.174 12887 Z= 0.287 Chirality : 0.036 0.155 1425 Planarity : 0.006 0.166 1410 Dihedral : 19.919 178.440 2058 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.64 % Favored : 95.14 % Rotamer: Outliers : 1.66 % Allowed : 14.92 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.30), residues: 906 helix: 2.50 (0.25), residues: 410 sheet: -0.82 (0.40), residues: 166 loop : -1.52 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 179 TYR 0.011 0.001 TYR A 22 PHE 0.012 0.001 PHE A 571 TRP 0.010 0.001 TRP A 229 HIS 0.003 0.001 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 9311) covalent geometry : angle 0.54144 (12887) hydrogen bonds : bond 0.03853 ( 452) hydrogen bonds : angle 3.83796 ( 1241) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8133 (mp0) REVERT: A 244 ARG cc_start: 0.8133 (tmm-80) cc_final: 0.7818 (ttp80) REVERT: A 444 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.7828 (mp0) REVERT: A 742 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8402 (mt-10) outliers start: 13 outliers final: 10 residues processed: 58 average time/residue: 0.3064 time to fit residues: 22.8621 Evaluate side-chains 59 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 877 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 46 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 0.3980 chunk 40 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.090932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.058191 restraints weight = 66969.872| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.22 r_work: 0.2768 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9311 Z= 0.151 Angle : 0.533 14.096 12887 Z= 0.283 Chirality : 0.036 0.152 1425 Planarity : 0.006 0.166 1410 Dihedral : 19.893 178.417 2058 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.30 % Favored : 95.47 % Rotamer: Outliers : 1.79 % Allowed : 14.54 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.30), residues: 906 helix: 2.54 (0.25), residues: 410 sheet: -0.78 (0.40), residues: 166 loop : -1.51 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 225 TYR 0.010 0.001 TYR A 22 PHE 0.010 0.001 PHE A 485 TRP 0.009 0.001 TRP A 229 HIS 0.003 0.001 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9311) covalent geometry : angle 0.53336 (12887) hydrogen bonds : bond 0.03831 ( 452) hydrogen bonds : angle 3.80348 ( 1241) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8146 (mp0) REVERT: A 244 ARG cc_start: 0.8149 (tmm-80) cc_final: 0.7850 (ttp80) REVERT: A 444 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: A 742 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8387 (mt-10) outliers start: 14 outliers final: 12 residues processed: 58 average time/residue: 0.3239 time to fit residues: 24.0925 Evaluate side-chains 60 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 879 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 70 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 62 optimal weight: 0.0870 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.091002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.058217 restraints weight = 66459.095| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 3.16 r_work: 0.2773 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9311 Z= 0.149 Angle : 0.532 13.999 12887 Z= 0.283 Chirality : 0.036 0.151 1425 Planarity : 0.006 0.166 1410 Dihedral : 19.873 178.407 2058 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.19 % Favored : 95.58 % Rotamer: Outliers : 1.79 % Allowed : 14.67 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.30), residues: 906 helix: 2.58 (0.25), residues: 410 sheet: -0.75 (0.40), residues: 166 loop : -1.53 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 225 TYR 0.011 0.001 TYR A 22 PHE 0.010 0.001 PHE A 485 TRP 0.009 0.001 TRP A 229 HIS 0.003 0.001 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9311) covalent geometry : angle 0.53207 (12887) hydrogen bonds : bond 0.03849 ( 452) hydrogen bonds : angle 3.77896 ( 1241) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8137 (mp0) REVERT: A 244 ARG cc_start: 0.8184 (tmm-80) cc_final: 0.7882 (ttp80) REVERT: A 444 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.7911 (mp0) REVERT: A 656 ASN cc_start: 0.9271 (m110) cc_final: 0.8991 (m110) REVERT: A 742 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8364 (mt-10) outliers start: 14 outliers final: 11 residues processed: 58 average time/residue: 0.3300 time to fit residues: 24.4585 Evaluate side-chains 60 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 877 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 25 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.089751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.057208 restraints weight = 67274.058| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 3.15 r_work: 0.2743 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 9311 Z= 0.216 Angle : 0.564 14.290 12887 Z= 0.300 Chirality : 0.037 0.156 1425 Planarity : 0.006 0.166 1410 Dihedral : 19.846 178.506 2058 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.74 % Favored : 94.04 % Rotamer: Outliers : 1.66 % Allowed : 14.92 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.29), residues: 906 helix: 2.46 (0.25), residues: 410 sheet: -0.77 (0.41), residues: 166 loop : -1.62 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 179 TYR 0.011 0.001 TYR A 22 PHE 0.012 0.001 PHE A 571 TRP 0.009 0.001 TRP A 229 HIS 0.004 0.001 HIS A 26 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 9311) covalent geometry : angle 0.56448 (12887) hydrogen bonds : bond 0.04155 ( 452) hydrogen bonds : angle 3.90784 ( 1241) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4515.45 seconds wall clock time: 77 minutes 18.33 seconds (4638.33 seconds total)