Starting phenix.real_space_refine on Sat Sep 12 07:56:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6x5a_22047/09_2026/6x5a_22047.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x5a_22047/09_2026/6x5a_22047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6x5a_22047/09_2026/6x5a_22047.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6x5a_22047/09_2026/6x5a_22047.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x5a_22047/09_2026/6x5a_22047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x5a_22047/09_2026/6x5a_22047.map" model { file = "/net/cci-nas-00/data/ceres_data/6x5a_22047/09_2026/6x5a_22047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x5a_22047/09_2026/6x5a_22047.cif" } resolution = 4.36 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= 0.002 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 Zn 1 6.06 5 P 288 5.49 5 S 23 5.16 5 C 8541 2.51 5 N 2764 2.21 5 O 3346 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14963 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 809 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 637 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 809 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 645 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2954 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2985 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 2993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2993 Classifications: {'peptide': 362} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 345} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.20, per 1000 atoms: 0.21 Number of scatterers: 14963 At special positions: 0 Unit cell: (129.47, 116.63, 133.75, 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) Zn 1 29.99 S 23 16.00 P 288 15.00 O 3346 8.00 N 2764 7.00 C 8541 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 551.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 601 " pdb="ZN ZN K 601 " - pdb=" NE2 HIS K 378 " 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 13 sheets defined 62.9% alpha, 8.2% beta 142 base pairs and 253 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.687A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.715A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.524A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.254A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.836A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 72 removed outlier: 3.878A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.592A pdb=" N MET D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.858A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.687A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.715A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.524A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.048A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.599A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.628A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.845A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.502A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 57 through 84 removed outlier: 3.629A pdb=" N ASN H 63 " --> pdb=" O MET H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 123 removed outlier: 3.575A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 183 removed outlier: 3.906A pdb=" N GLU K 166 " --> pdb=" O LYS K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 248 through 250 No H-bonds generated for 'chain 'K' and resid 248 through 250' Processing helix chain 'K' and resid 258 through 276 Processing helix chain 'K' and resid 319 through 323 Processing helix chain 'K' and resid 333 through 342 removed outlier: 3.666A pdb=" N ARG K 337 " --> pdb=" O GLY K 333 " (cutoff:3.500A) Processing helix chain 'K' and resid 367 through 377 Processing helix chain 'K' and resid 393 through 412 Processing helix chain 'K' and resid 419 through 434 removed outlier: 4.352A pdb=" N VAL K 423 " --> pdb=" O CYS K 419 " (cutoff:3.500A) Processing helix chain 'K' and resid 436 through 440 Processing helix chain 'K' and resid 441 through 443 No H-bonds generated for 'chain 'K' and resid 441 through 443' Processing helix chain 'K' and resid 444 through 462 removed outlier: 3.510A pdb=" N THR K 462 " --> pdb=" O GLU K 458 " (cutoff:3.500A) Processing helix chain 'K' and resid 482 through 499 Processing helix chain 'K' and resid 500 through 506 removed outlier: 6.087A pdb=" N ILE K 503 " --> pdb=" O GLY K 500 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS K 506 " --> pdb=" O ILE K 503 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.886A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.451A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.255A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.295A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 removed outlier: 3.527A pdb=" N ILE G 78 " --> pdb=" O GLY H 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 192 through 195 removed outlier: 3.978A pdb=" N MET K 215 " --> pdb=" O LEU K 195 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N PHE K 212 " --> pdb=" O ASP K 307 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ILE K 309 " --> pdb=" O PHE K 212 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL K 214 " --> pdb=" O ILE K 309 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ALA K 311 " --> pdb=" O VAL K 214 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N PHE K 216 " --> pdb=" O ALA K 311 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLU K 313 " --> pdb=" O PHE K 216 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU K 218 " --> pdb=" O GLU K 313 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU K 310 " --> pdb=" O PRO K 349 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 192 through 195 removed outlier: 3.978A pdb=" N MET K 215 " --> pdb=" O LEU K 195 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N PHE K 212 " --> pdb=" O ASP K 307 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ILE K 309 " --> pdb=" O PHE K 212 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL K 214 " --> pdb=" O ILE K 309 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ALA K 311 " --> pdb=" O VAL K 214 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N PHE K 216 " --> pdb=" O ALA K 311 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLU K 313 " --> pdb=" O PHE K 216 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU K 218 " --> pdb=" O GLU K 313 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL K 294 " --> pdb=" O ILE K 308 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR K 295 " --> pdb=" O GLU K 285 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 252 through 253 529 hydrogen bonds defined for protein. 1545 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 363 hydrogen bonds 722 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 253 stacking parallelities Total time for adding SS restraints: 3.90 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3189 1.33 - 1.45: 4638 1.45 - 1.57: 7387 1.57 - 1.69: 577 1.69 - 1.81: 38 Bond restraints: 15829 Sorted by residual: bond pdb=" C3' DT J 57 " pdb=" O3' DT J 57 " ideal model delta sigma weight residual 1.435 1.361 0.074 1.30e-02 5.92e+03 3.28e+01 bond pdb=" C3' DA J 58 " pdb=" O3' DA J 58 " ideal model delta sigma weight residual 1.435 1.374 0.061 1.30e-02 5.92e+03 2.21e+01 bond pdb=" C3' DG J 67 " pdb=" O3' DG J 67 " ideal model delta sigma weight residual 1.435 1.374 0.061 1.30e-02 5.92e+03 2.19e+01 bond pdb=" C3' DG I 49 " pdb=" O3' DG I 49 " ideal model delta sigma weight residual 1.435 1.375 0.060 1.30e-02 5.92e+03 2.14e+01 bond pdb=" C3' DT J 56 " pdb=" O3' DT J 56 " ideal model delta sigma weight residual 1.435 1.375 0.060 1.30e-02 5.92e+03 2.11e+01 ... (remaining 15824 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 21805 2.42 - 4.84: 726 4.84 - 7.25: 48 7.25 - 9.67: 10 9.67 - 12.09: 2 Bond angle restraints: 22591 Sorted by residual: angle pdb=" O4' DG I 127 " pdb=" C4' DG I 127 " pdb=" C3' DG I 127 " ideal model delta sigma weight residual 106.00 102.54 3.46 6.00e-01 2.78e+00 3.32e+01 angle pdb=" O4' DA J 116 " pdb=" C1' DA J 116 " pdb=" N9 DA J 116 " ideal model delta sigma weight residual 108.00 104.40 3.60 7.00e-01 2.04e+00 2.65e+01 angle pdb=" N3 DT J 82 " pdb=" C4 DT J 82 " pdb=" O4 DT J 82 " ideal model delta sigma weight residual 119.90 122.68 -2.78 6.00e-01 2.78e+00 2.15e+01 angle pdb=" CA ARG K 299 " pdb=" CB ARG K 299 " pdb=" CG ARG K 299 " ideal model delta sigma weight residual 114.10 123.36 -9.26 2.00e+00 2.50e-01 2.14e+01 angle pdb=" O4' DA J 132 " pdb=" C4' DA J 132 " pdb=" C3' DA J 132 " ideal model delta sigma weight residual 106.00 103.25 2.75 6.00e-01 2.78e+00 2.10e+01 ... (remaining 22586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.36: 7272 35.36 - 70.72: 1526 70.72 - 106.08: 23 106.08 - 141.43: 1 141.43 - 176.79: 2 Dihedral angle restraints: 8824 sinusoidal: 5557 harmonic: 3267 Sorted by residual: dihedral pdb=" CA LYS K 353 " pdb=" C LYS K 353 " pdb=" N ASP K 354 " pdb=" CA ASP K 354 " ideal model delta harmonic sigma weight residual 180.00 -137.45 -42.55 0 5.00e+00 4.00e-02 7.24e+01 dihedral pdb=" CA LYS A 37 " pdb=" C LYS A 37 " pdb=" N PRO A 38 " pdb=" CA PRO A 38 " ideal model delta harmonic sigma weight residual -180.00 -153.69 -26.31 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA LYS E 37 " pdb=" C LYS E 37 " pdb=" N PRO E 38 " pdb=" CA PRO E 38 " ideal model delta harmonic sigma weight residual 180.00 -153.70 -26.30 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 8821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1539 0.045 - 0.090: 708 0.090 - 0.135: 235 0.135 - 0.180: 51 0.180 - 0.226: 7 Chirality restraints: 2540 Sorted by residual: chirality pdb=" CG LEU K 415 " pdb=" CB LEU K 415 " pdb=" CD1 LEU K 415 " pdb=" CD2 LEU K 415 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB ILE B 50 " pdb=" CA ILE B 50 " pdb=" CG1 ILE B 50 " pdb=" CG2 ILE B 50 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA LYS K 409 " pdb=" N LYS K 409 " pdb=" C LYS K 409 " pdb=" CB LYS K 409 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 2537 not shown) Planarity restraints: 1858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU E 59 " -0.020 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" CD GLU E 59 " 0.071 2.00e-02 2.50e+03 pdb=" OE1 GLU E 59 " -0.026 2.00e-02 2.50e+03 pdb=" OE2 GLU E 59 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 59 " -0.020 2.00e-02 2.50e+03 4.08e-02 1.67e+01 pdb=" CD GLU A 59 " 0.071 2.00e-02 2.50e+03 pdb=" OE1 GLU A 59 " -0.026 2.00e-02 2.50e+03 pdb=" OE2 GLU A 59 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO F 32 " 0.019 2.00e-02 2.50e+03 3.71e-02 1.37e+01 pdb=" C PRO F 32 " -0.064 2.00e-02 2.50e+03 pdb=" O PRO F 32 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA F 33 " 0.022 2.00e-02 2.50e+03 ... (remaining 1855 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 535 2.67 - 3.22: 13722 3.22 - 3.78: 27799 3.78 - 4.34: 35201 4.34 - 4.90: 51239 Nonbonded interactions: 128496 Sorted by model distance: nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.107 3.040 nonbonded pdb=" N LYS B 79 " pdb=" OP1 DA J 101 " model vdw 2.125 3.120 nonbonded pdb=" NH2 ARG E 42 " pdb=" OP1 DG J 68 " model vdw 2.154 3.120 nonbonded pdb=" NH2 ARG A 69 " pdb=" OP2 DA J 90 " model vdw 2.171 3.120 nonbonded pdb=" O2 DC I 94 " pdb=" N2 DG J 52 " model vdw 2.174 2.496 ... (remaining 128491 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 102) } ncs_group { reference = (chain 'C' and resid 10 through 116) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 31 through 124) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 19.420 Find NCS groups from input model: 0.140 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 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 : 0.008 0.263 15830 Z= 0.672 Angle : 0.977 12.088 22591 Z= 0.738 Chirality : 0.057 0.226 2540 Planarity : 0.007 0.057 1858 Dihedral : 26.988 176.793 6712 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.15 % Favored : 93.67 % Rotamer: Outliers : 1.66 % Allowed : 10.27 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.94 (0.22), residues: 1105 helix: -0.44 (0.18), residues: 676 sheet: -1.46 (0.63), residues: 52 loop : -2.76 (0.28), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG K 299 TYR 0.021 0.002 TYR B 72 PHE 0.029 0.002 PHE K 476 TRP 0.026 0.003 TRP K 440 HIS 0.010 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00803 / 0.67 (15829) covalent geometry : angle 0.97670 / 0.74 (22591) hydrogen bonds : bond 0.13469 / 8.62 ( 889) hydrogen bonds : angle 4.78508 / 3.42 ( 2267) metal coordination : bond 0.26343 / 13.86 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 260 time to evaluate : 0.430 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: A 50 GLU cc_start: 0.9314 (mt-10) cc_final: 0.8751 (mt-10) REVERT: A 54 TYR cc_start: 0.8712 (m-80) cc_final: 0.8175 (m-80) REVERT: A 55 GLN cc_start: 0.8998 (mt0) cc_final: 0.8104 (tt0) REVERT: A 56 LYS cc_start: 0.8777 (ttmt) cc_final: 0.8549 (mmmt) REVERT: A 67 PHE cc_start: 0.8178 (t80) cc_final: 0.7798 (t80) REVERT: A 73 GLU cc_start: 0.8897 (pt0) cc_final: 0.8488 (pt0) REVERT: A 85 GLN cc_start: 0.9574 (mt0) cc_final: 0.8999 (mp10) REVERT: A 107 THR cc_start: 0.9260 (p) cc_final: 0.9051 (p) REVERT: B 72 TYR cc_start: 0.9327 (m-80) cc_final: 0.9046 (m-10) REVERT: B 88 TYR cc_start: 0.9301 (m-10) cc_final: 0.8407 (m-10) REVERT: C 38 ASN cc_start: 0.8638 (m-40) cc_final: 0.8252 (t0) REVERT: D 59 MET cc_start: 0.8549 (tpp) cc_final: 0.8135 (tmm) REVERT: D 83 TYR cc_start: 0.8520 (m-10) cc_final: 0.7346 (m-10) REVERT: E 46 VAL cc_start: 0.8073 (t) cc_final: 0.7365 (t) REVERT: E 50 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8610 (mt-10) REVERT: E 85 GLN cc_start: 0.8770 (mt0) cc_final: 0.8505 (mt0) REVERT: E 106 ASP cc_start: 0.9206 (m-30) cc_final: 0.8904 (m-30) REVERT: F 37 LEU cc_start: 0.9393 (mt) cc_final: 0.9182 (tt) REVERT: F 58 LEU cc_start: 0.9354 (tp) cc_final: 0.9126 (tt) REVERT: F 74 GLU cc_start: 0.8841 (pt0) cc_final: 0.8619 (pt0) REVERT: G 38 ASN cc_start: 0.8907 (m110) cc_final: 0.8350 (m110) REVERT: G 90 ASP cc_start: 0.8807 (t70) cc_final: 0.8581 (t0) REVERT: G 99 LYS cc_start: 0.9002 (mtmm) cc_final: 0.8613 (mmmm) REVERT: H 113 GLU cc_start: 0.9316 (mm-30) cc_final: 0.9098 (mm-30) REVERT: K 215 MET cc_start: 0.7058 (mtt) cc_final: 0.6730 (mpp) REVERT: K 430 MET cc_start: -0.0038 (tpt) cc_final: -0.0256 (ttt) REVERT: K 467 HIS cc_start: 0.7160 (t-90) cc_final: 0.6875 (t-90) outliers start: 16 outliers final: 4 residues processed: 272 average time/residue: 0.1427 time to fit residues: 54.5314 Evaluate side-chains 133 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 129 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 40.0000 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 30.0000 chunk 55 optimal weight: 10.0000 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 24 GLN C 31 HIS ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN E 68 GLN F 75 HIS F 93 GLN G 31 HIS G 84 GLN G 89 ASN H 47 GLN H 95 GLN K 183 GLN ** K 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.053608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.033728 restraints weight = 141171.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.034238 restraints weight = 81666.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.034432 restraints weight = 58874.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.034734 restraints weight = 50854.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.034847 restraints weight = 45573.707| |-----------------------------------------------------------------------------| r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 15830 Z= 0.242 Angle : 0.823 10.799 22591 Z= 0.451 Chirality : 0.051 0.261 2540 Planarity : 0.006 0.064 1858 Dihedral : 30.644 176.778 4405 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.21 % Allowed : 5.60 % Favored : 94.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 (0.24), residues: 1105 helix: 0.91 (0.19), residues: 682 sheet: -1.08 (0.70), residues: 50 loop : -2.31 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 158 TYR 0.020 0.002 TYR K 495 PHE 0.016 0.002 PHE K 251 TRP 0.014 0.002 TRP K 440 HIS 0.013 0.002 HIS K 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.24 (15829) covalent geometry : angle 0.82322 / 0.45 (22591) hydrogen bonds : bond 0.07459 / 5.02 ( 889) hydrogen bonds : angle 4.09715 / 2.91 ( 2267) metal coordination : bond 0.01604 / 0.84 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 163 time to evaluate : 0.450 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: A 50 GLU cc_start: 0.9431 (mt-10) cc_final: 0.8809 (mp0) REVERT: A 54 TYR cc_start: 0.8972 (m-80) cc_final: 0.8367 (m-80) REVERT: A 55 GLN cc_start: 0.9080 (mt0) cc_final: 0.8206 (tt0) REVERT: A 56 LYS cc_start: 0.8910 (ttmt) cc_final: 0.8617 (mmmt) REVERT: A 85 GLN cc_start: 0.9598 (mt0) cc_final: 0.9253 (mp10) REVERT: A 97 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8143 (mt-10) REVERT: B 84 MET cc_start: 0.8588 (mmp) cc_final: 0.7697 (tpp) REVERT: B 88 TYR cc_start: 0.9205 (m-10) cc_final: 0.8435 (m-80) REVERT: C 38 ASN cc_start: 0.8691 (m-40) cc_final: 0.8299 (p0) REVERT: E 50 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8625 (mt-10) REVERT: E 81 ASP cc_start: 0.6037 (t70) cc_final: 0.4868 (t0) REVERT: E 120 MET cc_start: 0.8893 (mmp) cc_final: 0.8521 (mmm) REVERT: F 37 LEU cc_start: 0.9591 (mt) cc_final: 0.9389 (tt) REVERT: G 38 ASN cc_start: 0.9060 (m110) cc_final: 0.8125 (p0) REVERT: G 51 LEU cc_start: 0.9596 (tp) cc_final: 0.9200 (pp) REVERT: G 99 LYS cc_start: 0.9137 (mtmm) cc_final: 0.8782 (mmmt) REVERT: H 71 GLU cc_start: 0.9427 (tm-30) cc_final: 0.9212 (tm-30) REVERT: K 215 MET cc_start: 0.6927 (mtt) cc_final: 0.6599 (mpp) REVERT: K 326 LEU cc_start: 0.4890 (tp) cc_final: 0.4078 (tp) REVERT: K 369 HIS cc_start: 0.6662 (p-80) cc_final: 0.6054 (p-80) REVERT: K 467 HIS cc_start: 0.7253 (t-90) cc_final: 0.7025 (t-90) outliers start: 2 outliers final: 0 residues processed: 165 average time/residue: 0.1339 time to fit residues: 31.7238 Evaluate side-chains 108 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 42 optimal weight: 6.9990 chunk 80 optimal weight: 40.0000 chunk 75 optimal weight: 40.0000 chunk 85 optimal weight: 50.0000 chunk 79 optimal weight: 40.0000 chunk 48 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 38 optimal weight: 0.1980 chunk 59 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN K 359 GLN ** K 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.053890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.034007 restraints weight = 140623.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.034571 restraints weight = 80123.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.034764 restraints weight = 57211.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.035075 restraints weight = 49744.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.035215 restraints weight = 44303.339| |-----------------------------------------------------------------------------| r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15830 Z= 0.174 Angle : 0.693 9.172 22591 Z= 0.388 Chirality : 0.046 0.316 2540 Planarity : 0.005 0.045 1858 Dihedral : 30.558 175.575 4405 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.62 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.21 (0.25), residues: 1105 helix: 1.39 (0.20), residues: 682 sheet: -1.15 (0.70), residues: 50 loop : -2.12 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 177 TYR 0.025 0.002 TYR K 468 PHE 0.018 0.002 PHE K 251 TRP 0.005 0.001 TRP K 440 HIS 0.009 0.002 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.17 (15829) covalent geometry : angle 0.69308 / 0.39 (22591) hydrogen bonds : bond 0.05971 / 4.04 ( 889) hydrogen bonds : angle 3.81165 / 2.72 ( 2267) metal coordination : bond 0.00628 / 0.33 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.326 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: A 50 GLU cc_start: 0.9455 (mt-10) cc_final: 0.8820 (mp0) REVERT: A 54 TYR cc_start: 0.8964 (m-80) cc_final: 0.8306 (m-80) REVERT: A 55 GLN cc_start: 0.9056 (mt0) cc_final: 0.8142 (tt0) REVERT: A 56 LYS cc_start: 0.8921 (ttmt) cc_final: 0.8624 (mmmt) REVERT: A 85 GLN cc_start: 0.9627 (mt0) cc_final: 0.9298 (mp10) REVERT: B 31 LYS cc_start: 0.9306 (tmmt) cc_final: 0.9070 (ttpp) REVERT: B 61 PHE cc_start: 0.9322 (t80) cc_final: 0.9121 (t80) REVERT: B 84 MET cc_start: 0.8474 (mmp) cc_final: 0.7479 (tpp) REVERT: B 88 TYR cc_start: 0.9194 (m-10) cc_final: 0.8286 (m-80) REVERT: E 106 ASP cc_start: 0.9103 (m-30) cc_final: 0.8878 (m-30) REVERT: G 24 GLN cc_start: 0.7191 (mp10) cc_final: 0.6909 (mp10) REVERT: G 38 ASN cc_start: 0.8956 (m110) cc_final: 0.8566 (p0) REVERT: G 51 LEU cc_start: 0.9604 (tp) cc_final: 0.9239 (pp) REVERT: G 92 GLU cc_start: 0.7630 (tt0) cc_final: 0.7416 (tt0) REVERT: G 99 LYS cc_start: 0.9140 (mtmm) cc_final: 0.8760 (mmmt) REVERT: H 71 GLU cc_start: 0.9439 (tm-30) cc_final: 0.9162 (tm-30) REVERT: K 201 TYR cc_start: 0.4242 (m-10) cc_final: 0.3414 (m-10) REVERT: K 215 MET cc_start: 0.6858 (mtt) cc_final: 0.6543 (mpp) REVERT: K 326 LEU cc_start: 0.4809 (tp) cc_final: 0.3989 (tp) REVERT: K 369 HIS cc_start: 0.6943 (p-80) cc_final: 0.6703 (p-80) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1294 time to fit residues: 30.4940 Evaluate side-chains 107 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 92 optimal weight: 40.0000 chunk 47 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 97 optimal weight: 40.0000 chunk 18 optimal weight: 0.5980 chunk 132 optimal weight: 30.0000 chunk 107 optimal weight: 30.0000 chunk 68 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 89 optimal weight: 50.0000 chunk 39 optimal weight: 0.8980 overall best weight: 4.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN D 63 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS ** K 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.052950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.033245 restraints weight = 141906.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.033793 restraints weight = 81661.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.034093 restraints weight = 59593.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.034316 restraints weight = 49309.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.034459 restraints weight = 44827.989| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 15830 Z= 0.191 Angle : 0.707 11.138 22591 Z= 0.393 Chirality : 0.046 0.328 2540 Planarity : 0.005 0.045 1858 Dihedral : 30.522 177.364 4405 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.29 (0.26), residues: 1105 helix: 1.40 (0.20), residues: 684 sheet: -1.17 (0.73), residues: 50 loop : -1.98 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 222 TYR 0.036 0.002 TYR K 468 PHE 0.034 0.002 PHE K 266 TRP 0.010 0.002 TRP K 440 HIS 0.009 0.002 HIS K 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.19 (15829) covalent geometry : angle 0.70691 / 0.39 (22591) hydrogen bonds : bond 0.06752 / 4.56 ( 889) hydrogen bonds : angle 3.85583 / 2.75 ( 2267) metal coordination : bond 0.00032 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.427 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: A 50 GLU cc_start: 0.9472 (mt-10) cc_final: 0.8987 (mp0) REVERT: A 54 TYR cc_start: 0.9057 (m-80) cc_final: 0.8449 (m-80) REVERT: A 56 LYS cc_start: 0.8968 (ttmt) cc_final: 0.8699 (mmmt) REVERT: B 31 LYS cc_start: 0.9321 (tmmt) cc_final: 0.9058 (ttpp) REVERT: B 84 MET cc_start: 0.8424 (mmp) cc_final: 0.7431 (tpp) REVERT: B 88 TYR cc_start: 0.9142 (m-10) cc_final: 0.8222 (m-80) REVERT: E 106 ASP cc_start: 0.9192 (m-30) cc_final: 0.8938 (m-30) REVERT: E 120 MET cc_start: 0.9139 (mmp) cc_final: 0.8830 (mmm) REVERT: G 38 ASN cc_start: 0.8956 (m110) cc_final: 0.8478 (p0) REVERT: G 51 LEU cc_start: 0.9645 (tp) cc_final: 0.9263 (pp) REVERT: G 78 ILE cc_start: 0.9463 (pt) cc_final: 0.8917 (mt) REVERT: G 99 LYS cc_start: 0.9215 (mtmm) cc_final: 0.8607 (mmmt) REVERT: H 71 GLU cc_start: 0.9420 (tm-30) cc_final: 0.9065 (tm-30) REVERT: H 93 GLU cc_start: 0.9229 (mp0) cc_final: 0.8772 (mp0) REVERT: H 108 LYS cc_start: 0.9375 (mmtm) cc_final: 0.9133 (pttt) REVERT: K 215 MET cc_start: 0.6729 (mtt) cc_final: 0.6420 (mpp) REVERT: K 467 HIS cc_start: 0.7033 (t-90) cc_final: 0.6814 (t-90) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1271 time to fit residues: 27.6962 Evaluate side-chains 95 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 66 optimal weight: 0.9990 chunk 91 optimal weight: 40.0000 chunk 81 optimal weight: 40.0000 chunk 67 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 97 optimal weight: 40.0000 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 HIS ** K 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.053356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.033592 restraints weight = 142336.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.034150 restraints weight = 81185.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.034487 restraints weight = 58599.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.034671 restraints weight = 48693.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.034808 restraints weight = 44564.950| |-----------------------------------------------------------------------------| r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15830 Z= 0.149 Angle : 0.650 7.438 22591 Z= 0.367 Chirality : 0.045 0.333 2540 Planarity : 0.004 0.057 1858 Dihedral : 30.466 177.229 4405 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.48 (0.26), residues: 1105 helix: 1.56 (0.20), residues: 684 sheet: -1.00 (0.75), residues: 50 loop : -1.92 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 497 TYR 0.017 0.001 TYR K 346 PHE 0.027 0.002 PHE B 61 TRP 0.004 0.001 TRP K 318 HIS 0.007 0.001 HIS K 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.15 (15829) covalent geometry : angle 0.64980 / 0.37 (22591) hydrogen bonds : bond 0.05100 / 3.48 ( 889) hydrogen bonds : angle 3.67026 / 2.61 ( 2267) metal coordination : bond 0.00107 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9602 (mt-10) cc_final: 0.9050 (mt-10) REVERT: A 54 TYR cc_start: 0.8962 (m-80) cc_final: 0.8319 (m-80) REVERT: A 55 GLN cc_start: 0.9028 (mt0) cc_final: 0.8293 (tt0) REVERT: A 56 LYS cc_start: 0.9061 (ttmt) cc_final: 0.8711 (mmmt) REVERT: B 31 LYS cc_start: 0.9319 (tmmt) cc_final: 0.9115 (ttpp) REVERT: B 84 MET cc_start: 0.8416 (mmp) cc_final: 0.7341 (tpp) REVERT: B 88 TYR cc_start: 0.9131 (m-10) cc_final: 0.8072 (m-80) REVERT: C 38 ASN cc_start: 0.8658 (m-40) cc_final: 0.8415 (p0) REVERT: C 39 TYR cc_start: 0.9017 (m-80) cc_final: 0.8347 (m-80) REVERT: C 110 ASN cc_start: 0.8566 (m110) cc_final: 0.8357 (m110) REVERT: G 38 ASN cc_start: 0.8844 (m110) cc_final: 0.7778 (p0) REVERT: G 51 LEU cc_start: 0.9627 (tp) cc_final: 0.9242 (pp) REVERT: G 99 LYS cc_start: 0.9101 (mtmm) cc_final: 0.8529 (mmmt) REVERT: H 71 GLU cc_start: 0.9404 (tm-30) cc_final: 0.9018 (tm-30) REVERT: H 93 GLU cc_start: 0.9226 (mp0) cc_final: 0.8754 (mp0) REVERT: H 108 LYS cc_start: 0.9341 (mmtm) cc_final: 0.9135 (pttt) REVERT: K 201 TYR cc_start: 0.4209 (m-10) cc_final: 0.3673 (m-10) REVERT: K 215 MET cc_start: 0.6617 (mtt) cc_final: 0.6319 (mpp) REVERT: K 369 HIS cc_start: 0.7342 (p-80) cc_final: 0.6914 (p-80) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1320 time to fit residues: 28.9164 Evaluate side-chains 100 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 110 optimal weight: 0.9980 chunk 59 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 126 optimal weight: 7.9990 chunk 135 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 96 optimal weight: 40.0000 chunk 90 optimal weight: 40.0000 chunk 68 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 250 HIS ** K 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.053153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.033160 restraints weight = 140070.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.033649 restraints weight = 81265.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.033822 restraints weight = 59403.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.034126 restraints weight = 51728.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.034249 restraints weight = 47019.000| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 15830 Z= 0.166 Angle : 0.660 8.927 22591 Z= 0.370 Chirality : 0.045 0.326 2540 Planarity : 0.004 0.043 1858 Dihedral : 30.367 177.760 4405 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.54 (0.25), residues: 1105 helix: 1.58 (0.20), residues: 684 sheet: -1.13 (0.74), residues: 52 loop : -1.82 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 39 TYR 0.022 0.001 TYR K 468 PHE 0.019 0.002 PHE K 251 TRP 0.005 0.001 TRP K 431 HIS 0.009 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.17 (15829) covalent geometry : angle 0.66045 / 0.37 (22591) hydrogen bonds : bond 0.05936 / 4.04 ( 889) hydrogen bonds : angle 3.66992 / 2.62 ( 2267) metal coordination : bond 0.00045 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9588 (mt-10) cc_final: 0.9319 (mt-10) REVERT: A 55 GLN cc_start: 0.9008 (mt0) cc_final: 0.8279 (tt0) REVERT: A 56 LYS cc_start: 0.9067 (ttmt) cc_final: 0.8730 (mmmt) REVERT: A 92 LEU cc_start: 0.9459 (tt) cc_final: 0.9244 (tt) REVERT: C 38 ASN cc_start: 0.8760 (m-40) cc_final: 0.8473 (p0) REVERT: C 39 TYR cc_start: 0.9032 (m-80) cc_final: 0.8409 (m-80) REVERT: D 59 MET cc_start: 0.8757 (tpt) cc_final: 0.8411 (tpt) REVERT: E 81 ASP cc_start: 0.6636 (t70) cc_final: 0.6180 (t70) REVERT: E 106 ASP cc_start: 0.9205 (m-30) cc_final: 0.8980 (m-30) REVERT: F 53 GLU cc_start: 0.8829 (mp0) cc_final: 0.8410 (mp0) REVERT: F 59 LYS cc_start: 0.9432 (mmmm) cc_final: 0.9229 (tppp) REVERT: G 38 ASN cc_start: 0.8872 (m110) cc_final: 0.7773 (p0) REVERT: G 51 LEU cc_start: 0.9632 (tp) cc_final: 0.9282 (pp) REVERT: G 99 LYS cc_start: 0.9122 (mtmm) cc_final: 0.8566 (mmmt) REVERT: H 71 GLU cc_start: 0.9433 (tm-30) cc_final: 0.9051 (tm-30) REVERT: H 93 GLU cc_start: 0.9228 (mp0) cc_final: 0.8748 (mp0) REVERT: H 108 LYS cc_start: 0.9368 (mmtm) cc_final: 0.9015 (ptmm) REVERT: K 215 MET cc_start: 0.6528 (mtt) cc_final: 0.6238 (mpp) REVERT: K 369 HIS cc_start: 0.6273 (p-80) cc_final: 0.5525 (p-80) REVERT: K 467 HIS cc_start: 0.6951 (t-90) cc_final: 0.6709 (t-90) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1251 time to fit residues: 26.7301 Evaluate side-chains 101 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 53 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 94 optimal weight: 40.0000 chunk 17 optimal weight: 30.0000 chunk 27 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 73 optimal weight: 40.0000 chunk 34 optimal weight: 9.9990 chunk 99 optimal weight: 30.0000 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN K 250 HIS ** K 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.051172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.031662 restraints weight = 148328.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.032125 restraints weight = 85971.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.032332 restraints weight = 63710.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.032670 restraints weight = 53181.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.032732 restraints weight = 49236.538| |-----------------------------------------------------------------------------| r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 15830 Z= 0.268 Angle : 0.776 10.684 22591 Z= 0.426 Chirality : 0.048 0.332 2540 Planarity : 0.006 0.057 1858 Dihedral : 30.621 179.631 4405 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.25 (0.25), residues: 1105 helix: 1.30 (0.19), residues: 685 sheet: -1.35 (0.72), residues: 52 loop : -1.80 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 29 TYR 0.017 0.002 TYR K 346 PHE 0.016 0.002 PHE K 251 TRP 0.009 0.002 TRP K 431 HIS 0.014 0.003 HIS K 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.27 (15829) covalent geometry : angle 0.77625 / 0.43 (22591) hydrogen bonds : bond 0.09382 / 6.31 ( 889) hydrogen bonds : angle 4.09864 / 2.97 ( 2267) metal coordination : bond 0.00074 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9598 (mt-10) cc_final: 0.9338 (mt-10) REVERT: A 55 GLN cc_start: 0.9062 (mt0) cc_final: 0.8528 (mt0) REVERT: A 56 LYS cc_start: 0.9053 (ttmt) cc_final: 0.8758 (mmmt) REVERT: C 39 TYR cc_start: 0.9152 (m-80) cc_final: 0.8431 (m-80) REVERT: E 106 ASP cc_start: 0.9288 (m-30) cc_final: 0.9040 (m-30) REVERT: E 120 MET cc_start: 0.9195 (mmp) cc_final: 0.8865 (mmm) REVERT: F 74 GLU cc_start: 0.8938 (tp30) cc_final: 0.8736 (tp30) REVERT: G 38 ASN cc_start: 0.8926 (m110) cc_final: 0.8718 (m110) REVERT: G 99 LYS cc_start: 0.9193 (mtmm) cc_final: 0.8602 (mmmt) REVERT: H 71 GLU cc_start: 0.9428 (tm-30) cc_final: 0.9053 (tm-30) REVERT: H 108 LYS cc_start: 0.9406 (mmtm) cc_final: 0.9071 (ttpt) REVERT: K 407 GLN cc_start: 0.1907 (mt0) cc_final: 0.1504 (pt0) REVERT: K 467 HIS cc_start: 0.6811 (t-90) cc_final: 0.6610 (t-90) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1310 time to fit residues: 25.9119 Evaluate side-chains 92 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 70 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 98 optimal weight: 40.0000 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 53 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.052530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.032778 restraints weight = 143401.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.033252 restraints weight = 82134.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.033425 restraints weight = 59532.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.033760 restraints weight = 51860.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.033869 restraints weight = 46579.916| |-----------------------------------------------------------------------------| r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15830 Z= 0.143 Angle : 0.666 9.032 22591 Z= 0.373 Chirality : 0.046 0.346 2540 Planarity : 0.005 0.048 1858 Dihedral : 30.620 179.468 4405 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.52 (0.26), residues: 1105 helix: 1.49 (0.20), residues: 684 sheet: -1.04 (0.77), residues: 50 loop : -1.66 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 131 TYR 0.027 0.002 TYR B 51 PHE 0.021 0.002 PHE B 61 TRP 0.004 0.001 TRP K 363 HIS 0.006 0.001 HIS K 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 (15829) covalent geometry : angle 0.66552 / 0.37 (22591) hydrogen bonds : bond 0.05036 / 3.46 ( 889) hydrogen bonds : angle 3.72167 / 2.69 ( 2267) metal coordination : bond 0.00282 / 0.15 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9591 (mt-10) cc_final: 0.9311 (mt-10) REVERT: A 55 GLN cc_start: 0.8969 (mt0) cc_final: 0.8447 (mt0) REVERT: A 56 LYS cc_start: 0.9034 (ttmt) cc_final: 0.8712 (mmmt) REVERT: B 84 MET cc_start: 0.8322 (mmp) cc_final: 0.7913 (mmt) REVERT: B 88 TYR cc_start: 0.8917 (m-10) cc_final: 0.8551 (m-80) REVERT: B 90 LEU cc_start: 0.9627 (mm) cc_final: 0.9399 (tp) REVERT: C 39 TYR cc_start: 0.9082 (m-80) cc_final: 0.8378 (m-80) REVERT: D 57 LYS cc_start: 0.9373 (mtpp) cc_final: 0.9164 (mmmm) REVERT: E 106 ASP cc_start: 0.9239 (m-30) cc_final: 0.8987 (m-30) REVERT: E 120 MET cc_start: 0.9148 (mmp) cc_final: 0.8767 (mmm) REVERT: F 59 LYS cc_start: 0.9494 (mmmm) cc_final: 0.9198 (tppp) REVERT: G 51 LEU cc_start: 0.9577 (tp) cc_final: 0.9299 (pp) REVERT: G 99 LYS cc_start: 0.9130 (mtmm) cc_final: 0.8603 (mmmt) REVERT: H 71 GLU cc_start: 0.9380 (tm-30) cc_final: 0.8927 (tm-30) REVERT: H 108 LYS cc_start: 0.9332 (mmtm) cc_final: 0.9068 (ptmm) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1294 time to fit residues: 26.0515 Evaluate side-chains 93 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 12 optimal weight: 0.9990 chunk 81 optimal weight: 40.0000 chunk 107 optimal weight: 0.8980 chunk 116 optimal weight: 40.0000 chunk 124 optimal weight: 7.9990 chunk 120 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 112 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 63 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.052267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.032596 restraints weight = 144553.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.033090 restraints weight = 83076.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.033267 restraints weight = 59894.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.033617 restraints weight = 52027.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.033724 restraints weight = 46774.693| |-----------------------------------------------------------------------------| r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15830 Z= 0.152 Angle : 0.665 8.517 22591 Z= 0.370 Chirality : 0.044 0.332 2540 Planarity : 0.005 0.055 1858 Dihedral : 30.471 179.887 4405 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.63 (0.26), residues: 1105 helix: 1.55 (0.20), residues: 687 sheet: -0.87 (0.78), residues: 51 loop : -1.63 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 299 TYR 0.021 0.001 TYR B 51 PHE 0.013 0.001 PHE K 216 TRP 0.005 0.001 TRP K 431 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 (15829) covalent geometry : angle 0.66456 / 0.37 (22591) hydrogen bonds : bond 0.05592 / 3.82 ( 889) hydrogen bonds : angle 3.69231 / 2.67 ( 2267) metal coordination : bond 0.00054 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9594 (mt-10) cc_final: 0.9328 (mt-10) REVERT: A 55 GLN cc_start: 0.8980 (mt0) cc_final: 0.8461 (mt0) REVERT: A 56 LYS cc_start: 0.9040 (ttmt) cc_final: 0.8715 (mmmt) REVERT: B 84 MET cc_start: 0.8428 (mmp) cc_final: 0.7568 (tpp) REVERT: B 90 LEU cc_start: 0.9636 (mm) cc_final: 0.9410 (tp) REVERT: C 39 TYR cc_start: 0.9074 (m-80) cc_final: 0.8385 (m-80) REVERT: D 57 LYS cc_start: 0.9407 (mtpp) cc_final: 0.9178 (mmmm) REVERT: E 106 ASP cc_start: 0.9296 (m-30) cc_final: 0.9040 (m-30) REVERT: E 120 MET cc_start: 0.9170 (mmp) cc_final: 0.8795 (mmm) REVERT: F 59 LYS cc_start: 0.9495 (mmmm) cc_final: 0.9184 (tppp) REVERT: G 51 LEU cc_start: 0.9596 (tp) cc_final: 0.9320 (pp) REVERT: G 99 LYS cc_start: 0.9119 (mtmm) cc_final: 0.8574 (mmmt) REVERT: H 71 GLU cc_start: 0.9363 (tm-30) cc_final: 0.8923 (tm-30) REVERT: H 108 LYS cc_start: 0.9315 (mmtm) cc_final: 0.9026 (ptmm) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1204 time to fit residues: 23.9620 Evaluate side-chains 92 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 125 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 78 optimal weight: 40.0000 chunk 131 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 53 optimal weight: 0.0030 chunk 44 optimal weight: 6.9990 chunk 75 optimal weight: 40.0000 chunk 62 optimal weight: 3.9990 chunk 69 optimal weight: 0.2980 chunk 37 optimal weight: 10.0000 overall best weight: 3.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.052296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.032465 restraints weight = 141995.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.032979 restraints weight = 81586.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.033157 restraints weight = 59451.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.033441 restraints weight = 51914.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.033535 restraints weight = 46591.117| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15830 Z= 0.154 Angle : 0.660 7.838 22591 Z= 0.370 Chirality : 0.044 0.329 2540 Planarity : 0.005 0.065 1858 Dihedral : 30.480 179.361 4405 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.70 (0.26), residues: 1105 helix: 1.58 (0.20), residues: 687 sheet: -0.86 (0.79), residues: 51 loop : -1.53 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 92 TYR 0.020 0.001 TYR B 51 PHE 0.019 0.002 PHE B 61 TRP 0.008 0.001 TRP K 431 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 (15829) covalent geometry : angle 0.65979 / 0.37 (22591) hydrogen bonds : bond 0.05449 / 3.73 ( 889) hydrogen bonds : angle 3.69886 / 2.67 ( 2267) metal coordination : bond 0.00045 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9594 (mt-10) cc_final: 0.9337 (mt-10) REVERT: A 55 GLN cc_start: 0.8968 (mt0) cc_final: 0.8509 (mt0) REVERT: A 56 LYS cc_start: 0.9032 (ttmt) cc_final: 0.8686 (mmmt) REVERT: B 84 MET cc_start: 0.8452 (mmp) cc_final: 0.7627 (tpp) REVERT: C 39 TYR cc_start: 0.9103 (m-80) cc_final: 0.8401 (m-80) REVERT: D 57 LYS cc_start: 0.9427 (mtpp) cc_final: 0.9196 (mmmm) REVERT: E 90 MET cc_start: 0.8709 (tmm) cc_final: 0.8470 (tmm) REVERT: E 106 ASP cc_start: 0.9267 (m-30) cc_final: 0.9005 (m-30) REVERT: E 120 MET cc_start: 0.9165 (mmp) cc_final: 0.8779 (mmm) REVERT: F 59 LYS cc_start: 0.9511 (mmmm) cc_final: 0.9195 (tppp) REVERT: G 51 LEU cc_start: 0.9592 (tp) cc_final: 0.9320 (pp) REVERT: G 78 ILE cc_start: 0.9501 (pt) cc_final: 0.9018 (mm) REVERT: G 99 LYS cc_start: 0.9071 (mtmm) cc_final: 0.8539 (mmmt) REVERT: H 71 GLU cc_start: 0.9337 (tm-30) cc_final: 0.8895 (tm-30) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1255 time to fit residues: 25.0113 Evaluate side-chains 98 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 24 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** K 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.052842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.032943 restraints weight = 140856.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.033501 restraints weight = 80760.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.033838 restraints weight = 58799.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.033990 restraints weight = 49670.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 67)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.034112 restraints weight = 46180.462| |-----------------------------------------------------------------------------| r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.5407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15830 Z= 0.135 Angle : 0.643 7.371 22591 Z= 0.361 Chirality : 0.044 0.328 2540 Planarity : 0.005 0.059 1858 Dihedral : 30.423 179.651 4405 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.79 (0.26), residues: 1105 helix: 1.64 (0.20), residues: 686 sheet: -0.77 (0.81), residues: 51 loop : -1.47 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 299 TYR 0.026 0.001 TYR C 50 PHE 0.012 0.001 PHE E 104 TRP 0.008 0.001 TRP K 431 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.14 (15829) covalent geometry : angle 0.64278 / 0.36 (22591) hydrogen bonds : bond 0.04776 / 3.32 ( 889) hydrogen bonds : angle 3.58891 / 2.60 ( 2267) metal coordination : bond 0.00043 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2959.56 seconds wall clock time: 51 minutes 48.31 seconds (3108.31 seconds total)