Starting phenix.real_space_refine on Thu Aug 6 20:00:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zqh_60385/08_2026/8zqh_60385.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zqh_60385/08_2026/8zqh_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 { model { file = "/net/cci-nas-00/data/ceres_data/8zqh_60385/08_2026/8zqh_60385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zqh_60385/08_2026/8zqh_60385.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zqh_60385/08_2026/8zqh_60385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zqh_60385/08_2026/8zqh_60385.map" } 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-2.2rc3-6140/lib/python3.11/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: 2.68, per 1000 atoms: 0.16 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: 1.57 Conformation dependent library (CDL) restraints added in 584.5 milliseconds 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: 3.40 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: 4.46 Time building geometry restraints manager: 2.18 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=" C1' DT C -5 " pdb=" N1 DT C -5 " ideal model delta sigma weight residual 1.468 1.517 -0.049 1.40e-02 5.10e+03 1.21e+01 bond pdb=" C1' DT C 8 " pdb=" N1 DT C 8 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.40e+00 bond pdb=" C3' DT C -12 " pdb=" C2' DT C -12 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.57e+00 bond pdb=" C3' DC C -11 " pdb=" C2' DC C -11 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.71e+00 bond pdb=" N3 DA C -2 " pdb=" C4 DA C -2 " ideal model delta sigma weight residual 1.344 1.329 0.015 6.00e-03 2.78e+04 6.15e+00 ... (remaining 17509 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 31450 2.96 - 5.92: 95 5.92 - 8.88: 0 8.88 - 11.84: 0 11.84 - 14.80: 1 Bond angle restraints: 31546 Sorted by residual: angle pdb=" O5' A B 12 " pdb=" C5' A B 12 " pdb=" C4' A B 12 " ideal model delta sigma weight residual 109.40 112.80 -3.40 8.00e-01 1.56e+00 1.81e+01 angle pdb=" N3 DT D 5 " pdb=" C4 DT D 5 " pdb=" O4 DT D 5 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT C -10 " pdb=" C4 DT C -10 " pdb=" O4 DT C -10 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT C 8 " pdb=" C4 DT C 8 " pdb=" O4 DT C 8 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT C -13 " pdb=" C4 DT C -13 " pdb=" O4 DT C -13 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.66e+01 ... (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 - 0.041: 1046 0.041 - 0.082: 240 0.082 - 0.123: 109 0.123 - 0.165: 23 0.165 - 0.206: 7 Chirality restraints: 1425 Sorted by residual: chirality pdb=" C3' DT D 5 " pdb=" C4' DT D 5 " pdb=" O3' DT D 5 " pdb=" C2' DT D 5 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C3' DA C 4 " pdb=" C4' DA C 4 " pdb=" O3' DA C 4 " pdb=" C2' DA C 4 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 9.88e-01 chirality pdb=" C3' DA C -1 " pdb=" C4' DA C -1 " pdb=" O3' DA C -1 " pdb=" C2' DA C -1 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.03e-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: 3.720 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: 0.090 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.830 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:1.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 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= 0.309 Angle : 0.687 14.796 12887 Z= 0.502 Chirality : 0.046 0.206 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 are 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/Z covalent geometry : bond 0.00448 / 0.31 ( 9311) covalent geometry : angle 0.68739 / 0.50 (12887) hydrogen bonds : bond 0.15657 / 16.04 ( 452) hydrogen bonds : angle 6.04308 / 8.11 ( 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 : 0.449 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 outliers start: 1 outliers final: 0 residues processed: 118 average time/residue: 0.4038 time to fit residues: 57.8465 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 : 0.455 ------------------------------------------------------------------------------- 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... A 632 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.094597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.061778 restraints weight = 65972.671| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.34 r_work: 0.2829 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 9311 Z= 0.199 Angle : 0.615 14.974 12887 Z= 0.347 Chirality : 0.038 0.161 1425 Planarity : 0.007 0.168 1410 Dihedral : 20.026 178.408 2058 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.30 % Favored : 95.47 % Rotamer: Outliers : 0.89 % Allowed : 15.69 % 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 are not related in a simple way. whole: -0.20 (0.28), residues: 906 helix: 1.48 (0.26), residues: 403 sheet: -0.58 (0.41), residues: 154 loop : -1.89 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 49 TYR 0.011 0.001 TYR A 22 PHE 0.012 0.001 PHE A 64 TRP 0.008 0.001 TRP A 720 HIS 0.004 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.20 ( 9311) covalent geometry : angle 0.61511 / 0.35 (12887) hydrogen bonds : bond 0.06415 / 6.83 ( 452) hydrogen bonds : angle 4.93356 / 6.50 ( 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 68 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.446 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 20 ASP cc_start: 0.8752 (t0) cc_final: 0.8504 (t0) outliers start: 7 outliers final: 6 residues processed: 67 average time/residue: 0.2568 time to fit residues: 23.2388 Evaluate side-chains 62 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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 406 GLU 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: 1.9990 chunk 30 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.092036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.058996 restraints weight = 66827.453| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 3.26 r_work: 0.2770 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 9311 Z= 0.259 Angle : 0.606 15.924 12887 Z= 0.337 Chirality : 0.038 0.147 1425 Planarity : 0.007 0.171 1410 Dihedral : 19.924 179.386 2058 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.19 % Favored : 95.58 % Rotamer: Outliers : 1.40 % Allowed : 14.80 % 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 are not related in a simple way. whole: -0.23 (0.28), residues: 906 helix: 1.53 (0.25), residues: 408 sheet: -0.69 (0.40), residues: 152 loop : -2.01 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 49 TYR 0.009 0.001 TYR A 542 PHE 0.014 0.001 PHE A 571 TRP 0.010 0.001 TRP A 229 HIS 0.005 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.26 ( 9311) covalent geometry : angle 0.60592 / 0.34 (12887) hydrogen bonds : bond 0.05340 / 5.73 ( 452) hydrogen bonds : angle 4.58399 / 6.03 ( 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 71 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.403 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 798 TYR cc_start: 0.9614 (OUTLIER) cc_final: 0.9331 (t80) outliers start: 11 outliers final: 4 residues processed: 70 average time/residue: 0.2660 time to fit residues: 24.7492 Evaluate side-chains 60 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 441 PHE 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: 0.9980 chunk 6 optimal weight: 0.5980 chunk 2 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 632 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.092768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.059432 restraints weight = 66460.389| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 3.33 r_work: 0.2782 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 9311 Z= 0.149 Angle : 0.551 15.135 12887 Z= 0.305 Chirality : 0.036 0.146 1425 Planarity : 0.006 0.169 1410 Dihedral : 19.948 179.368 2058 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.53 % Favored : 95.25 % Rotamer: Outliers : 1.53 % Allowed : 14.67 % 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 are not related in a simple way. whole: 0.00 (0.28), residues: 906 helix: 1.79 (0.26), residues: 408 sheet: -0.81 (0.39), residues: 164 loop : -1.89 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 49 TYR 0.016 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/Z covalent geometry : bond 0.00311 / 0.15 ( 9311) covalent geometry : angle 0.55070 / 0.31 (12887) hydrogen bonds : bond 0.04839 / 5.19 ( 452) hydrogen bonds : angle 4.33046 / 5.72 ( 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 69 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.395 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: A 20 ASP cc_start: 0.8914 (t0) cc_final: 0.8669 (t0) REVERT: A 730 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8446 (mm-30) REVERT: A 798 TYR cc_start: 0.9582 (OUTLIER) cc_final: 0.9335 (t80) outliers start: 12 outliers final: 8 residues processed: 66 average time/residue: 0.2233 time to fit residues: 19.5427 Evaluate side-chains 62 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 208 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 724 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.091399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.058445 restraints weight = 66446.658| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 3.21 r_work: 0.2761 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 9311 Z= 0.232 Angle : 0.575 15.473 12887 Z= 0.317 Chirality : 0.037 0.138 1425 Planarity : 0.006 0.170 1410 Dihedral : 19.877 179.699 2058 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.97 % Favored : 94.81 % Rotamer: Outliers : 1.02 % Allowed : 15.94 % Favored : 83.04 % 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 are not related in a simple way. whole: 0.02 (0.29), residues: 906 helix: 1.87 (0.25), residues: 410 sheet: -0.88 (0.39), residues: 164 loop : -1.94 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 49 TYR 0.010 0.001 TYR A 125 PHE 0.013 0.001 PHE A 571 TRP 0.010 0.001 TRP A 229 HIS 0.004 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.23 ( 9311) covalent geometry : angle 0.57517 / 0.32 (12887) hydrogen bonds : bond 0.04733 / 5.09 ( 452) hydrogen bonds : angle 4.29425 / 5.71 ( 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 60 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.445 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 730 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8412 (mm-30) REVERT: A 742 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8462 (mt-10) REVERT: A 798 TYR cc_start: 0.9594 (OUTLIER) cc_final: 0.9342 (t80) outliers start: 8 outliers final: 7 residues processed: 57 average time/residue: 0.2806 time to fit residues: 21.2840 Evaluate side-chains 60 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 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 774 ASP Chi-restraints excluded: chain A residue 798 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 2 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 70 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.091548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.058647 restraints weight = 66189.321| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.22 r_work: 0.2767 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9311 Z= 0.171 Angle : 0.540 14.965 12887 Z= 0.299 Chirality : 0.036 0.140 1425 Planarity : 0.006 0.169 1410 Dihedral : 19.964 179.308 2058 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.19 % Favored : 95.47 % Rotamer: Outliers : 1.15 % Allowed : 15.69 % Favored : 83.16 % 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 are not related in a simple way. whole: 0.17 (0.29), residues: 906 helix: 2.04 (0.26), residues: 409 sheet: -0.86 (0.39), residues: 166 loop : -1.90 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 49 TYR 0.012 0.001 TYR A 22 PHE 0.013 0.001 PHE A 571 TRP 0.008 0.001 TRP A 229 HIS 0.003 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 ( 9311) covalent geometry : angle 0.54043 / 0.30 (12887) hydrogen bonds : bond 0.04422 / 4.74 ( 452) hydrogen bonds : angle 4.12120 / 5.45 ( 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 60 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.457 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 730 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8422 (mm-30) REVERT: A 742 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8446 (mt-10) REVERT: A 798 TYR cc_start: 0.9575 (OUTLIER) cc_final: 0.9263 (t80) outliers start: 9 outliers final: 6 residues processed: 58 average time/residue: 0.2682 time to fit residues: 20.8827 Evaluate side-chains 57 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 208 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 18 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 0.0970 chunk 2 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 644 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.092343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.059379 restraints weight = 66359.925| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.22 r_work: 0.2778 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 9311 Z= 0.123 Angle : 0.524 14.508 12887 Z= 0.288 Chirality : 0.035 0.139 1425 Planarity : 0.006 0.167 1410 Dihedral : 19.970 179.332 2058 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.30 % Favored : 95.47 % Rotamer: Outliers : 1.15 % Allowed : 15.82 % Favored : 83.04 % 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 are not related in a simple way. whole: 0.35 (0.29), residues: 906 helix: 2.17 (0.26), residues: 412 sheet: -0.79 (0.40), residues: 166 loop : -1.81 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 49 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 0.003 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 9311) covalent geometry : angle 0.52372 / 0.29 (12887) hydrogen bonds : bond 0.04206 / 4.52 ( 452) hydrogen bonds : angle 3.97413 / 5.25 ( 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 61 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.467 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 730 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8404 (mm-30) REVERT: A 732 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8733 (mm-30) REVERT: A 742 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8441 (mt-10) REVERT: A 798 TYR cc_start: 0.9562 (OUTLIER) cc_final: 0.9248 (t80) outliers start: 9 outliers final: 7 residues processed: 58 average time/residue: 0.2915 time to fit residues: 22.3526 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 : 0.453 ------------------------------------------------------------------------------- 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 140 LYS 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 798 TYR 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: 4.9990 chunk 43 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 0.0030 chunk 78 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 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: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.091461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.058499 restraints weight = 66544.202| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.23 r_work: 0.2761 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3187 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= 0.174 Angle : 0.533 14.615 12887 Z= 0.293 Chirality : 0.036 0.136 1425 Planarity : 0.006 0.167 1410 Dihedral : 19.959 179.332 2058 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.30 % Favored : 95.36 % Rotamer: Outliers : 1.40 % Allowed : 15.56 % Favored : 83.04 % 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 are not related in a simple way. whole: 0.39 (0.29), residues: 906 helix: 2.23 (0.25), residues: 412 sheet: -0.80 (0.40), residues: 166 loop : -1.80 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 49 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 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 ( 9311) covalent geometry : angle 0.53314 / 0.29 (12887) hydrogen bonds : bond 0.04235 / 4.56 ( 452) hydrogen bonds : angle 3.98796 / 5.28 ( 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 63 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.464 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 244 ARG cc_start: 0.8047 (tmm-80) cc_final: 0.7751 (ttp80) REVERT: A 444 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: A 520 ILE cc_start: 0.8906 (mm) cc_final: 0.8655 (mm) REVERT: A 732 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8806 (tp30) REVERT: A 742 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8456 (mt-10) REVERT: A 798 TYR cc_start: 0.9575 (OUTLIER) cc_final: 0.9267 (t80) outliers start: 11 outliers final: 9 residues processed: 61 average time/residue: 0.2642 time to fit residues: 21.5388 Evaluate side-chains 62 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 208 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 228 SER 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 800 SER Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 879 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 46 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.091927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.058971 restraints weight = 66624.844| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.26 r_work: 0.2778 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 9311 Z= 0.134 Angle : 0.521 14.362 12887 Z= 0.286 Chirality : 0.035 0.137 1425 Planarity : 0.006 0.167 1410 Dihedral : 20.002 179.225 2058 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.30 % Favored : 95.47 % Rotamer: Outliers : 1.53 % Allowed : 15.43 % Favored : 83.04 % 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 are not related in a simple way. whole: 0.57 (0.29), residues: 906 helix: 2.37 (0.26), residues: 410 sheet: -0.81 (0.39), residues: 166 loop : -1.62 (0.35), residues: 330 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 0.010 0.001 PHE A 571 TRP 0.009 0.001 TRP A 229 HIS 0.003 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 9311) covalent geometry : angle 0.52125 / 0.29 (12887) hydrogen bonds : bond 0.04135 / 4.45 ( 452) hydrogen bonds : angle 3.89793 / 5.16 ( 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 63 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.440 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 244 ARG cc_start: 0.8044 (tmm-80) cc_final: 0.7749 (ttp80) REVERT: A 444 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.7837 (mp0) REVERT: A 520 ILE cc_start: 0.8907 (mm) cc_final: 0.8663 (mm) REVERT: A 742 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8422 (mt-10) REVERT: A 798 TYR cc_start: 0.9563 (OUTLIER) cc_final: 0.9249 (t80) outliers start: 12 outliers final: 10 residues processed: 60 average time/residue: 0.2733 time to fit residues: 22.0057 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 : 0.457 ------------------------------------------------------------------------------- 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 208 GLU Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 228 SER 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 800 SER 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: 3.9990 chunk 4 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.091593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.058722 restraints weight = 66568.826| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.21 r_work: 0.2775 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 9311 Z= 0.153 Angle : 0.524 14.299 12887 Z= 0.287 Chirality : 0.035 0.136 1425 Planarity : 0.006 0.166 1410 Dihedral : 20.004 179.249 2058 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.53 % Favored : 95.14 % Rotamer: Outliers : 1.40 % Allowed : 15.56 % Favored : 83.04 % 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 are not related in a simple way. whole: 0.58 (0.29), residues: 906 helix: 2.40 (0.26), residues: 410 sheet: -0.82 (0.39), residues: 166 loop : -1.63 (0.35), residues: 330 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 0.010 0.001 PHE A 571 TRP 0.009 0.001 TRP A 229 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 9311) covalent geometry : angle 0.52359 / 0.29 (12887) hydrogen bonds : bond 0.04117 / 4.44 ( 452) hydrogen bonds : angle 3.88071 / 5.14 ( 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: 11 poor density : 50 time to evaluate : 0.443 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 244 ARG cc_start: 0.8090 (tmm-80) cc_final: 0.7790 (ttp80) REVERT: A 444 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.7773 (mp0) REVERT: A 520 ILE cc_start: 0.8868 (mm) cc_final: 0.8619 (mm) REVERT: A 742 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8452 (mt-10) REVERT: A 798 TYR cc_start: 0.9549 (OUTLIER) cc_final: 0.9242 (t80) outliers start: 11 outliers final: 9 residues processed: 59 average time/residue: 0.2775 time to fit residues: 21.8541 Evaluate side-chains 60 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 208 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 228 SER 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 800 SER 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 25 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.092304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.059446 restraints weight = 66434.330| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 3.24 r_work: 0.2787 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 9311 Z= 0.116 Angle : 0.508 13.992 12887 Z= 0.279 Chirality : 0.035 0.137 1425 Planarity : 0.006 0.166 1410 Dihedral : 20.041 179.112 2058 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.19 % Favored : 95.58 % Rotamer: Outliers : 1.28 % Allowed : 15.94 % Favored : 82.78 % 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 are not related in a simple way. whole: 0.71 (0.29), residues: 906 helix: 2.52 (0.26), residues: 410 sheet: -0.75 (0.40), residues: 166 loop : -1.57 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 179 TYR 0.011 0.001 TYR A 22 PHE 0.010 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/Z covalent geometry : bond 0.00249 / 0.12 ( 9311) covalent geometry : angle 0.50813 / 0.28 (12887) hydrogen bonds : bond 0.03986 / 4.31 ( 452) hydrogen bonds : angle 3.78739 / 5.01 ( 1241) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4195.53 seconds wall clock time: 72 minutes 1.10 seconds (4321.10 seconds total)