Starting phenix.real_space_refine on Wed Mar 4 15:14:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x59_22046/03_2026/6x59_22046.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x59_22046/03_2026/6x59_22046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6x59_22046/03_2026/6x59_22046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x59_22046/03_2026/6x59_22046.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x59_22046/03_2026/6x59_22046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x59_22046/03_2026/6x59_22046.map" } resolution = 2.98 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= 0.004 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 61 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13921 SG CYS K 384 111.467 51.256 37.583 1.00189.24 S Time building chain proxies: 2.96, per 1000 atoms: 0.20 Number of scatterers: 14963 At special positions: 0 Unit cell: (130.54, 115.56, 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: 1.20 Conformation dependent library (CDL) restraints added in 460.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 601 " pdb="ZN ZN K 601 " - pdb=" NE2 HIS K 378 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 384 " 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 14 sheets defined 62.9% alpha, 8.1% beta 142 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.618A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.690A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.964A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.598A 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: 3.833A 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 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.757A 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: 3.618A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.688A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.553A pdb=" N ARG F 36 " --> pdb=" O PRO F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.910A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.576A 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 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.712A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (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 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 57 through 84 removed outlier: 3.544A 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: 3.906A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 185 removed outlier: 4.188A pdb=" N GLU K 166 " --> pdb=" O LYS K 162 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS K 184 " --> pdb=" O ARG K 180 " (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: 3.597A 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: 4.348A 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: 3.682A 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 501 through 506 removed outlier: 3.738A 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: 6.703A 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 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.197A 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 removed outlier: 6.610A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.814A 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: 7.192A 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 Processing sheet with id=AB2, first strand: chain 'K' and resid 192 through 195 removed outlier: 4.301A pdb=" N MET K 215 " --> pdb=" O LEU K 195 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N PHE K 212 " --> pdb=" O ASP K 307 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ILE K 309 " --> pdb=" O PHE K 212 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL K 214 " --> pdb=" O ILE K 309 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ALA K 311 " --> pdb=" O VAL K 214 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N PHE K 216 " --> pdb=" O ALA K 311 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLU K 313 " --> pdb=" O PHE K 216 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU K 218 " --> pdb=" O GLU K 313 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL K 294 " --> pdb=" O ILE K 308 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR K 295 " --> pdb=" O GLU K 285 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 192 through 195 removed outlier: 4.301A pdb=" N MET K 215 " --> pdb=" O LEU K 195 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N PHE K 212 " --> pdb=" O ASP K 307 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ILE K 309 " --> pdb=" O PHE K 212 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL K 214 " --> pdb=" O ILE K 309 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ALA K 311 " --> pdb=" O VAL K 214 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N PHE K 216 " --> pdb=" O ALA K 311 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLU K 313 " --> pdb=" O PHE K 216 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU K 218 " --> pdb=" O GLU K 313 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU K 310 " --> pdb=" O PRO K 349 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 223 through 227 Processing sheet with id=AB5, first strand: chain 'K' and resid 252 through 253 531 hydrogen bonds defined for protein. 1551 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 363 hydrogen bonds 722 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 3.66 Time building geometry restraints manager: 1.62 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: 2820 1.33 - 1.45: 4792 1.45 - 1.57: 7600 1.57 - 1.69: 579 1.69 - 1.81: 38 Bond restraints: 15829 Sorted by residual: bond pdb=" C PHE K 501 " pdb=" O PHE K 501 " ideal model delta sigma weight residual 1.233 1.255 -0.022 4.80e-03 4.34e+04 2.18e+01 bond pdb=" CB LYS K 173 " pdb=" CG LYS K 173 " ideal model delta sigma weight residual 1.520 1.585 -0.065 3.00e-02 1.11e+03 4.76e+00 bond pdb=" CG LYS K 484 " pdb=" CD LYS K 484 " ideal model delta sigma weight residual 1.520 1.577 -0.057 3.00e-02 1.11e+03 3.64e+00 bond pdb=" CG LYS K 162 " pdb=" CD LYS K 162 " ideal model delta sigma weight residual 1.520 1.570 -0.050 3.00e-02 1.11e+03 2.79e+00 bond pdb=" CG LYS K 173 " pdb=" CD LYS K 173 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.47e+00 ... (remaining 15824 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.84: 22478 3.84 - 7.68: 89 7.68 - 11.52: 17 11.52 - 15.37: 5 15.37 - 19.21: 2 Bond angle restraints: 22591 Sorted by residual: angle pdb=" N LYS K 160 " pdb=" CA LYS K 160 " pdb=" C LYS K 160 " ideal model delta sigma weight residual 111.02 97.86 13.16 1.22e+00 6.72e-01 1.16e+02 angle pdb=" CA TYR K 495 " pdb=" CB TYR K 495 " pdb=" CG TYR K 495 " ideal model delta sigma weight residual 113.90 125.36 -11.46 1.80e+00 3.09e-01 4.06e+01 angle pdb=" CA LEU K 159 " pdb=" CB LEU K 159 " pdb=" CG LEU K 159 " ideal model delta sigma weight residual 116.30 135.51 -19.21 3.50e+00 8.16e-02 3.01e+01 angle pdb=" CB LYS K 484 " pdb=" CG LYS K 484 " pdb=" CD LYS K 484 " ideal model delta sigma weight residual 111.30 122.94 -11.64 2.30e+00 1.89e-01 2.56e+01 angle pdb=" C LYS K 160 " pdb=" CA LYS K 160 " pdb=" CB LYS K 160 " ideal model delta sigma weight residual 110.92 118.74 -7.82 1.59e+00 3.96e-01 2.42e+01 ... (remaining 22586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.50: 7173 35.50 - 71.00: 1625 71.00 - 106.50: 23 106.50 - 142.00: 1 142.00 - 177.49: 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 -134.92 -45.08 0 5.00e+00 4.00e-02 8.13e+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 -152.81 -27.19 0 5.00e+00 4.00e-02 2.96e+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 -152.86 -27.14 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 8821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 2439 0.096 - 0.192: 94 0.192 - 0.288: 5 0.288 - 0.384: 1 0.384 - 0.481: 1 Chirality restraints: 2540 Sorted by residual: chirality pdb=" CG LEU K 150 " pdb=" CB LEU K 150 " pdb=" CD1 LEU K 150 " pdb=" CD2 LEU K 150 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.77e+00 chirality pdb=" CB VAL K 153 " pdb=" CA VAL K 153 " pdb=" CG1 VAL K 153 " pdb=" CG2 VAL K 153 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CG LEU K 157 " pdb=" CB LEU K 157 " pdb=" CD1 LEU K 157 " pdb=" CD2 LEU K 157 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 2537 not shown) Planarity restraints: 1858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP K 450 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.15e+00 pdb=" CG ASP K 450 " 0.043 2.00e-02 2.50e+03 pdb=" OD1 ASP K 450 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP K 450 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG K 158 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.55e+00 pdb=" C ARG K 158 " 0.041 2.00e-02 2.50e+03 pdb=" O ARG K 158 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU K 159 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP K 318 " -0.038 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO K 319 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO K 319 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO K 319 " -0.032 5.00e-02 4.00e+02 ... (remaining 1855 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 449 2.66 - 3.22: 12609 3.22 - 3.78: 26037 3.78 - 4.34: 36307 4.34 - 4.90: 51819 Nonbonded interactions: 127221 Sorted by model distance: nonbonded pdb=" O GLU K 487 " pdb=" OG SER K 490 " model vdw 2.103 3.040 nonbonded pdb=" O2 DC I 94 " pdb=" N2 DG J 52 " model vdw 2.147 2.496 nonbonded pdb=" ND2 ASN K 356 " pdb=" O PHE K 358 " model vdw 2.206 3.120 nonbonded pdb=" NH2 ARG E 69 " pdb=" OP2 DA I 90 " model vdw 2.239 3.120 nonbonded pdb=" O LEU K 297 " pdb=" NH2 ARG K 299 " model vdw 2.247 3.120 ... (remaining 127216 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.560 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 25.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 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 : 0.006 0.135 15831 Z= 0.262 Angle : 0.843 19.207 22591 Z= 0.482 Chirality : 0.045 0.481 2540 Planarity : 0.006 0.058 1858 Dihedral : 27.582 177.494 6712 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.15 % Favored : 93.67 % Rotamer: Outliers : 7.57 % Allowed : 20.12 % Favored : 72.30 % 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: -2.07 (0.22), residues: 1105 helix: -0.61 (0.17), residues: 680 sheet: -1.51 (0.63), residues: 54 loop : -2.69 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 394 TYR 0.037 0.002 TYR K 403 PHE 0.013 0.002 PHE K 455 TRP 0.019 0.002 TRP K 363 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00579 (15829) covalent geometry : angle 0.84283 (22591) hydrogen bonds : bond 0.12991 ( 891) hydrogen bonds : angle 4.73090 ( 2273) metal coordination : bond 0.11583 ( 2) *********************** 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 277 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 204 time to evaluate : 0.374 Fit side-chains REVERT: A 37 LYS cc_start: 0.6955 (OUTLIER) cc_final: 0.5671 (tppt) REVERT: D 76 GLU cc_start: 0.8355 (tp30) cc_final: 0.8094 (tp30) REVERT: F 79 LYS cc_start: 0.8851 (mttt) cc_final: 0.8640 (mttm) REVERT: G 95 LYS cc_start: 0.8998 (ttmt) cc_final: 0.8794 (tttm) REVERT: H 76 GLU cc_start: 0.8177 (tp30) cc_final: 0.7820 (tp30) REVERT: K 152 LYS cc_start: 0.8604 (pmtt) cc_final: 0.8314 (pmtt) REVERT: K 155 ASP cc_start: 0.8187 (t70) cc_final: 0.7945 (m-30) REVERT: K 194 GLN cc_start: 0.7657 (pp30) cc_final: 0.7231 (pp30) REVERT: K 226 GLN cc_start: 0.7337 (mp10) cc_final: 0.7070 (mm-40) REVERT: K 251 PHE cc_start: 0.7995 (m-10) cc_final: 0.7583 (m-10) REVERT: K 262 MET cc_start: 0.7834 (ptm) cc_final: 0.7400 (ptm) REVERT: K 326 LEU cc_start: 0.8897 (tp) cc_final: 0.8672 (tt) REVERT: K 335 LYS cc_start: 0.8533 (mmtm) cc_final: 0.8301 (mppt) REVERT: K 339 ASN cc_start: 0.8327 (m110) cc_final: 0.8046 (m-40) REVERT: K 346 TYR cc_start: 0.8635 (m-80) cc_final: 0.8322 (m-80) REVERT: K 385 CYS cc_start: 0.4065 (OUTLIER) cc_final: 0.3219 (p) REVERT: K 403 TYR cc_start: 0.6831 (m-10) cc_final: 0.6116 (m-80) REVERT: K 427 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7980 (tp) REVERT: K 430 MET cc_start: 0.7777 (tmm) cc_final: 0.7453 (tmm) REVERT: K 432 THR cc_start: 0.6990 (t) cc_final: 0.6444 (m) REVERT: K 461 ARG cc_start: 0.8185 (tpp-160) cc_final: 0.7838 (tpm170) REVERT: K 468 TYR cc_start: 0.8432 (t80) cc_final: 0.8115 (t80) REVERT: K 482 ASP cc_start: 0.5477 (OUTLIER) cc_final: 0.5189 (p0) REVERT: K 484 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8485 (tmmt) outliers start: 73 outliers final: 27 residues processed: 261 average time/residue: 0.7677 time to fit residues: 215.0455 Evaluate side-chains 197 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 159 LEU Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 249 SER Chi-restraints excluded: chain K residue 357 SER Chi-restraints excluded: chain K residue 385 CYS Chi-restraints excluded: chain K residue 387 SER Chi-restraints excluded: chain K residue 395 LYS Chi-restraints excluded: chain K residue 404 LEU Chi-restraints excluded: chain K residue 427 ILE Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain K residue 482 ASP Chi-restraints excluded: chain K residue 483 ARG Chi-restraints excluded: chain K residue 484 LYS Chi-restraints excluded: chain K residue 501 PHE Chi-restraints excluded: chain K residue 507 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN B 75 HIS C 24 GLN C 31 HIS C 73 ASN D 95 GLN E 68 GLN F 75 HIS F 93 GLN G 24 GLN G 73 ASN G 89 ASN G 104 GLN H 49 HIS H 63 ASN K 183 GLN K 196 ASN ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 226 GLN K 246 ASN K 300 ASN K 339 ASN ** K 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.135162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.091173 restraints weight = 21572.865| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.52 r_work: 0.2961 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 15831 Z= 0.344 Angle : 0.740 10.450 22591 Z= 0.419 Chirality : 0.044 0.166 2540 Planarity : 0.006 0.056 1858 Dihedral : 30.203 179.694 4458 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.34 % Favored : 94.48 % Rotamer: Outliers : 5.91 % Allowed : 25.73 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 2.56 % 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: -0.84 (0.24), residues: 1105 helix: 0.44 (0.19), residues: 695 sheet: -1.06 (0.63), residues: 53 loop : -2.44 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 79 TYR 0.021 0.002 TYR K 403 PHE 0.016 0.002 PHE K 412 TRP 0.012 0.002 TRP K 363 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00799 (15829) covalent geometry : angle 0.73956 (22591) hydrogen bonds : bond 0.06638 ( 891) hydrogen bonds : angle 3.77261 ( 2273) metal coordination : bond 0.00527 ( 2) *********************** 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 239 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 182 time to evaluate : 0.404 Fit side-chains REVERT: A 131 ARG cc_start: 0.9155 (OUTLIER) cc_final: 0.7681 (mtp85) REVERT: B 49 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9052 (mt) REVERT: C 15 LYS cc_start: 0.8816 (ttmt) cc_final: 0.8381 (mtpp) REVERT: D 105 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7981 (mm-30) REVERT: E 59 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8620 (pm20) REVERT: F 95 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7312 (mtp-110) REVERT: G 15 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8948 (ttpt) REVERT: G 95 LYS cc_start: 0.9289 (ttmt) cc_final: 0.8987 (tttm) REVERT: H 76 GLU cc_start: 0.8889 (tp30) cc_final: 0.8472 (tp30) REVERT: K 152 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8375 (pptt) REVERT: K 155 ASP cc_start: 0.8194 (t70) cc_final: 0.7969 (m-30) REVERT: K 182 MET cc_start: 0.7005 (mmp) cc_final: 0.6695 (mtm) REVERT: K 205 LYS cc_start: -0.0205 (OUTLIER) cc_final: -0.0426 (ttmt) REVERT: K 226 GLN cc_start: 0.7477 (mp-120) cc_final: 0.7039 (mm-40) REVERT: K 251 PHE cc_start: 0.8281 (m-10) cc_final: 0.7737 (m-10) REVERT: K 262 MET cc_start: 0.7882 (ptm) cc_final: 0.7370 (ptm) REVERT: K 300 ASN cc_start: 0.4835 (OUTLIER) cc_final: 0.4372 (t0) REVERT: K 326 LEU cc_start: 0.9003 (tp) cc_final: 0.8756 (tt) REVERT: K 339 ASN cc_start: 0.8440 (m-40) cc_final: 0.8160 (m-40) REVERT: K 346 TYR cc_start: 0.8555 (m-80) cc_final: 0.8308 (m-80) REVERT: K 353 LYS cc_start: 0.6604 (OUTLIER) cc_final: 0.6336 (mmpt) REVERT: K 403 TYR cc_start: 0.7136 (m-10) cc_final: 0.6479 (m-80) REVERT: K 430 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7519 (tmm) REVERT: K 432 THR cc_start: 0.6826 (t) cc_final: 0.6276 (m) REVERT: K 461 ARG cc_start: 0.8335 (tpp-160) cc_final: 0.7755 (mmp-170) REVERT: K 464 LYS cc_start: 0.6953 (OUTLIER) cc_final: 0.6635 (pptt) REVERT: K 468 TYR cc_start: 0.8580 (t80) cc_final: 0.8326 (t80) REVERT: K 481 ILE cc_start: 0.5659 (OUTLIER) cc_final: 0.5217 (tp) REVERT: K 482 ASP cc_start: 0.5349 (OUTLIER) cc_final: 0.5067 (p0) REVERT: K 484 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8459 (tmtt) outliers start: 57 outliers final: 18 residues processed: 224 average time/residue: 0.8357 time to fit residues: 200.2088 Evaluate side-chains 202 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 152 LYS Chi-restraints excluded: chain K residue 205 LYS Chi-restraints excluded: chain K residue 277 ILE Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain K residue 300 ASN Chi-restraints excluded: chain K residue 353 LYS Chi-restraints excluded: chain K residue 357 SER Chi-restraints excluded: chain K residue 430 MET Chi-restraints excluded: chain K residue 438 SER Chi-restraints excluded: chain K residue 464 LYS Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain K residue 482 ASP Chi-restraints excluded: chain K residue 484 LYS Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 501 PHE Chi-restraints excluded: chain K residue 506 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 42 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 76 GLN C 73 ASN D 84 ASN G 24 GLN G 104 GLN H 84 ASN K 194 GLN K 300 ASN ** K 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 356 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.139362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.095650 restraints weight = 21839.076| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.50 r_work: 0.3042 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15831 Z= 0.170 Angle : 0.638 9.653 22591 Z= 0.364 Chirality : 0.037 0.151 2540 Planarity : 0.005 0.049 1858 Dihedral : 29.935 179.482 4422 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 5.19 % Allowed : 25.73 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 2.56 % 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: 0.13 (0.25), residues: 1105 helix: 1.18 (0.20), residues: 693 sheet: -0.82 (0.69), residues: 50 loop : -1.98 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 180 TYR 0.014 0.001 TYR K 403 PHE 0.015 0.001 PHE K 418 TRP 0.008 0.001 TRP K 363 HIS 0.007 0.001 HIS K 378 Details of bonding type rmsd covalent geometry : bond 0.00372 (15829) covalent geometry : angle 0.63789 (22591) hydrogen bonds : bond 0.04894 ( 891) hydrogen bonds : angle 3.36720 ( 2273) metal coordination : bond 0.00504 ( 2) *********************** 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 230 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 180 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 49 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9116 (mp) REVERT: C 92 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7679 (mt-10) REVERT: D 51 ASP cc_start: 0.8007 (p0) cc_final: 0.7646 (p0) REVERT: D 93 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.7976 (mp0) REVERT: E 59 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8548 (pm20) REVERT: F 95 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7286 (mtp-110) REVERT: G 73 ASN cc_start: 0.8189 (m-40) cc_final: 0.7962 (t160) REVERT: G 95 LYS cc_start: 0.9263 (ttmt) cc_final: 0.8994 (tttm) REVERT: H 105 GLU cc_start: 0.8519 (tp30) cc_final: 0.8309 (mm-30) REVERT: K 152 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8360 (pptt) REVERT: K 155 ASP cc_start: 0.8242 (t70) cc_final: 0.7916 (m-30) REVERT: K 201 TYR cc_start: 0.6356 (p90) cc_final: 0.6039 (p90) REVERT: K 226 GLN cc_start: 0.7254 (mp-120) cc_final: 0.7004 (mm-40) REVERT: K 251 PHE cc_start: 0.8229 (m-10) cc_final: 0.7602 (m-10) REVERT: K 262 MET cc_start: 0.7856 (ptm) cc_final: 0.7379 (ptm) REVERT: K 300 ASN cc_start: 0.4402 (OUTLIER) cc_final: 0.4161 (t0) REVERT: K 304 ILE cc_start: 0.3866 (mt) cc_final: 0.3328 (mm) REVERT: K 324 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7865 (tp30) REVERT: K 326 LEU cc_start: 0.8889 (tp) cc_final: 0.8611 (tt) REVERT: K 339 ASN cc_start: 0.8364 (m-40) cc_final: 0.8091 (m-40) REVERT: K 380 ILE cc_start: 0.2636 (OUTLIER) cc_final: 0.2311 (mp) REVERT: K 401 MET cc_start: 0.6838 (tpt) cc_final: 0.6398 (tpp) REVERT: K 430 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7618 (tmm) REVERT: K 461 ARG cc_start: 0.8440 (tpp-160) cc_final: 0.7951 (mmp-170) REVERT: K 464 LYS cc_start: 0.6950 (OUTLIER) cc_final: 0.6610 (pptt) REVERT: K 481 ILE cc_start: 0.5525 (OUTLIER) cc_final: 0.5120 (tp) REVERT: K 484 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8528 (tmtt) REVERT: K 506 LYS cc_start: 0.0567 (OUTLIER) cc_final: 0.0317 (pmtt) outliers start: 50 outliers final: 13 residues processed: 218 average time/residue: 0.7984 time to fit residues: 186.1789 Evaluate side-chains 192 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 152 LYS Chi-restraints excluded: chain K residue 277 ILE Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain K residue 300 ASN Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 357 SER Chi-restraints excluded: chain K residue 380 ILE Chi-restraints excluded: chain K residue 430 MET Chi-restraints excluded: chain K residue 464 LYS Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain K residue 484 LYS Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 506 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 92 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN E 68 GLN G 24 GLN G 104 GLN K 194 GLN K 300 ASN ** K 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.137487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.093759 restraints weight = 21737.227| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.49 r_work: 0.3004 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 15831 Z= 0.227 Angle : 0.643 9.471 22591 Z= 0.368 Chirality : 0.039 0.144 2540 Planarity : 0.005 0.051 1858 Dihedral : 29.905 179.384 4414 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 5.50 % Allowed : 26.14 % Favored : 68.36 % 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: 0.35 (0.25), residues: 1105 helix: 1.35 (0.20), residues: 693 sheet: -0.63 (0.72), residues: 50 loop : -1.90 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 180 TYR 0.022 0.002 TYR K 468 PHE 0.018 0.001 PHE K 358 TRP 0.006 0.001 TRP K 363 HIS 0.007 0.001 HIS K 378 Details of bonding type rmsd covalent geometry : bond 0.00521 (15829) covalent geometry : angle 0.64338 (22591) hydrogen bonds : bond 0.05297 ( 891) hydrogen bonds : angle 3.32368 ( 2273) metal coordination : bond 0.00554 ( 2) *********************** 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 230 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 177 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 49 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9128 (mp) REVERT: C 92 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7746 (mt-10) REVERT: D 51 ASP cc_start: 0.8183 (p0) cc_final: 0.7836 (p0) REVERT: D 93 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8456 (mp0) REVERT: E 59 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8589 (pm20) REVERT: F 95 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.7314 (mtp-110) REVERT: G 73 ASN cc_start: 0.8204 (m-40) cc_final: 0.7970 (t0) REVERT: G 95 LYS cc_start: 0.9239 (ttmt) cc_final: 0.8993 (tttm) REVERT: H 76 GLU cc_start: 0.8871 (tp30) cc_final: 0.8609 (tp30) REVERT: H 105 GLU cc_start: 0.8543 (tp30) cc_final: 0.8329 (mm-30) REVERT: K 152 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8324 (pptt) REVERT: K 155 ASP cc_start: 0.8289 (t70) cc_final: 0.7966 (m-30) REVERT: K 201 TYR cc_start: 0.6444 (p90) cc_final: 0.6175 (p90) REVERT: K 226 GLN cc_start: 0.7257 (mp-120) cc_final: 0.7008 (mm-40) REVERT: K 251 PHE cc_start: 0.8236 (m-10) cc_final: 0.7597 (m-10) REVERT: K 262 MET cc_start: 0.7923 (ptm) cc_final: 0.7488 (ptm) REVERT: K 300 ASN cc_start: 0.4666 (OUTLIER) cc_final: 0.4261 (t0) REVERT: K 304 ILE cc_start: 0.3788 (mt) cc_final: 0.3244 (mm) REVERT: K 324 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7908 (tp30) REVERT: K 326 LEU cc_start: 0.8818 (tp) cc_final: 0.8528 (tt) REVERT: K 339 ASN cc_start: 0.8360 (m-40) cc_final: 0.8077 (m-40) REVERT: K 353 LYS cc_start: 0.6639 (OUTLIER) cc_final: 0.6375 (mmpt) REVERT: K 380 ILE cc_start: 0.2718 (OUTLIER) cc_final: 0.2332 (mp) REVERT: K 401 MET cc_start: 0.6830 (tpt) cc_final: 0.6354 (tpp) REVERT: K 430 MET cc_start: 0.8123 (tmm) cc_final: 0.7691 (tmm) REVERT: K 461 ARG cc_start: 0.8454 (tpp-160) cc_final: 0.7938 (mmp-170) REVERT: K 464 LYS cc_start: 0.6632 (OUTLIER) cc_final: 0.6366 (pptt) REVERT: K 476 PHE cc_start: 0.5894 (OUTLIER) cc_final: 0.5687 (m-10) REVERT: K 481 ILE cc_start: 0.5501 (OUTLIER) cc_final: 0.5295 (tp) REVERT: K 506 LYS cc_start: 0.0813 (OUTLIER) cc_final: 0.0559 (pmtt) outliers start: 53 outliers final: 22 residues processed: 210 average time/residue: 0.8464 time to fit residues: 190.0470 Evaluate side-chains 199 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 152 LYS Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 215 MET Chi-restraints excluded: chain K residue 223 ILE Chi-restraints excluded: chain K residue 252 LEU Chi-restraints excluded: chain K residue 295 THR Chi-restraints excluded: chain K residue 300 ASN Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 353 LYS Chi-restraints excluded: chain K residue 380 ILE Chi-restraints excluded: chain K residue 464 LYS Chi-restraints excluded: chain K residue 476 PHE Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 501 PHE Chi-restraints excluded: chain K residue 506 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 66 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN F 25 ASN G 24 GLN G 104 GLN K 194 GLN K 300 ASN ** K 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.137175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.093429 restraints weight = 21617.590| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.47 r_work: 0.2998 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 15831 Z= 0.249 Angle : 0.646 9.752 22591 Z= 0.369 Chirality : 0.039 0.144 2540 Planarity : 0.005 0.059 1858 Dihedral : 29.921 178.504 4409 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 5.39 % Allowed : 27.49 % Favored : 67.12 % 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: 0.37 (0.25), residues: 1105 helix: 1.37 (0.20), residues: 692 sheet: -0.54 (0.71), residues: 53 loop : -1.91 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG K 180 TYR 0.022 0.002 TYR K 468 PHE 0.012 0.002 PHE K 455 TRP 0.007 0.002 TRP K 363 HIS 0.006 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00574 (15829) covalent geometry : angle 0.64550 (22591) hydrogen bonds : bond 0.05388 ( 891) hydrogen bonds : angle 3.32646 ( 2273) metal coordination : bond 0.00208 ( 2) *********************** 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 220 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 168 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 49 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9127 (mp) REVERT: C 92 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.7723 (mt-10) REVERT: D 51 ASP cc_start: 0.8182 (p0) cc_final: 0.7861 (p0) REVERT: D 93 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8453 (mp0) REVERT: E 59 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8606 (pm20) REVERT: F 95 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7331 (mtp-110) REVERT: G 73 ASN cc_start: 0.8218 (m-40) cc_final: 0.7989 (t0) REVERT: G 95 LYS cc_start: 0.9236 (ttmt) cc_final: 0.8998 (tttm) REVERT: H 76 GLU cc_start: 0.8843 (tp30) cc_final: 0.8576 (tp30) REVERT: H 105 GLU cc_start: 0.8597 (tp30) cc_final: 0.8397 (mm-30) REVERT: K 152 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8326 (pptt) REVERT: K 155 ASP cc_start: 0.8291 (t70) cc_final: 0.7992 (m-30) REVERT: K 160 LYS cc_start: 0.8060 (mmtm) cc_final: 0.7643 (mtpt) REVERT: K 226 GLN cc_start: 0.7269 (mp-120) cc_final: 0.7029 (mm-40) REVERT: K 251 PHE cc_start: 0.8231 (m-10) cc_final: 0.7563 (m-10) REVERT: K 262 MET cc_start: 0.7915 (ptm) cc_final: 0.7480 (ptm) REVERT: K 300 ASN cc_start: 0.4411 (OUTLIER) cc_final: 0.4054 (t0) REVERT: K 324 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7846 (tp30) REVERT: K 326 LEU cc_start: 0.8792 (tp) cc_final: 0.8522 (tt) REVERT: K 339 ASN cc_start: 0.8359 (m-40) cc_final: 0.8087 (m-40) REVERT: K 353 LYS cc_start: 0.6684 (OUTLIER) cc_final: 0.6465 (mmpt) REVERT: K 380 ILE cc_start: 0.2806 (OUTLIER) cc_final: 0.2418 (mp) REVERT: K 401 MET cc_start: 0.6832 (tpt) cc_final: 0.6400 (tpp) REVERT: K 403 TYR cc_start: 0.7136 (m-10) cc_final: 0.6528 (m-80) REVERT: K 430 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7824 (tmm) REVERT: K 461 ARG cc_start: 0.8421 (tpp-160) cc_final: 0.7861 (mmp-170) REVERT: K 464 LYS cc_start: 0.6708 (OUTLIER) cc_final: 0.6433 (pptt) REVERT: K 481 ILE cc_start: 0.5589 (OUTLIER) cc_final: 0.5206 (tp) REVERT: K 506 LYS cc_start: 0.0813 (OUTLIER) cc_final: 0.0588 (pmtt) outliers start: 52 outliers final: 23 residues processed: 203 average time/residue: 0.8958 time to fit residues: 194.2941 Evaluate side-chains 199 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 152 LYS Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 223 ILE Chi-restraints excluded: chain K residue 252 LEU Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain K residue 295 THR Chi-restraints excluded: chain K residue 300 ASN Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 353 LYS Chi-restraints excluded: chain K residue 380 ILE Chi-restraints excluded: chain K residue 381 GLU Chi-restraints excluded: chain K residue 414 GLU Chi-restraints excluded: chain K residue 430 MET Chi-restraints excluded: chain K residue 464 LYS Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain K residue 501 PHE Chi-restraints excluded: chain K residue 506 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 110 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 126 optimal weight: 30.0000 chunk 135 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN F 25 ASN G 24 GLN G 104 GLN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 GLN K 300 ASN ** K 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.137888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.094321 restraints weight = 21575.201| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.47 r_work: 0.3016 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15831 Z= 0.211 Angle : 0.628 9.717 22591 Z= 0.359 Chirality : 0.038 0.145 2540 Planarity : 0.005 0.064 1858 Dihedral : 29.871 178.097 4409 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 5.50 % Allowed : 27.90 % Favored : 66.60 % 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: 0.52 (0.25), residues: 1105 helix: 1.48 (0.20), residues: 692 sheet: -0.54 (0.71), residues: 53 loop : -1.81 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG K 180 TYR 0.011 0.001 TYR D 40 PHE 0.010 0.001 PHE K 455 TRP 0.006 0.001 TRP K 363 HIS 0.006 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00483 (15829) covalent geometry : angle 0.62784 (22591) hydrogen bonds : bond 0.05031 ( 891) hydrogen bonds : angle 3.25891 ( 2273) metal coordination : bond 0.00077 ( 2) *********************** 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 222 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 169 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 49 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9126 (mp) REVERT: D 51 ASP cc_start: 0.8207 (p0) cc_final: 0.7890 (p0) REVERT: D 93 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8014 (mp0) REVERT: E 59 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8610 (pm20) REVERT: F 95 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7365 (mtp-110) REVERT: G 11 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7158 (mmm-85) REVERT: G 73 ASN cc_start: 0.8200 (m-40) cc_final: 0.8000 (t0) REVERT: G 95 LYS cc_start: 0.9232 (ttmt) cc_final: 0.8997 (tttm) REVERT: H 76 GLU cc_start: 0.8827 (tp30) cc_final: 0.8566 (tp30) REVERT: H 105 GLU cc_start: 0.8586 (tp30) cc_final: 0.8374 (mm-30) REVERT: K 152 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8321 (pptt) REVERT: K 155 ASP cc_start: 0.8291 (t70) cc_final: 0.8005 (m-30) REVERT: K 160 LYS cc_start: 0.8046 (mmtm) cc_final: 0.7671 (mtpt) REVERT: K 226 GLN cc_start: 0.7334 (mp-120) cc_final: 0.7092 (mm-40) REVERT: K 251 PHE cc_start: 0.8235 (m-10) cc_final: 0.7573 (m-10) REVERT: K 262 MET cc_start: 0.7906 (ptm) cc_final: 0.7489 (ptm) REVERT: K 300 ASN cc_start: 0.4613 (OUTLIER) cc_final: 0.4398 (t0) REVERT: K 324 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7871 (tp30) REVERT: K 326 LEU cc_start: 0.8805 (tp) cc_final: 0.8579 (tt) REVERT: K 380 ILE cc_start: 0.2828 (OUTLIER) cc_final: 0.2442 (mp) REVERT: K 401 MET cc_start: 0.6992 (tpt) cc_final: 0.6603 (tpp) REVERT: K 403 TYR cc_start: 0.7121 (m-80) cc_final: 0.6534 (m-80) REVERT: K 430 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7867 (tmm) REVERT: K 461 ARG cc_start: 0.8451 (tpp-160) cc_final: 0.7804 (mmp-170) REVERT: K 464 LYS cc_start: 0.6663 (OUTLIER) cc_final: 0.6391 (pptt) REVERT: K 476 PHE cc_start: 0.5897 (OUTLIER) cc_final: 0.5593 (m-10) REVERT: K 481 ILE cc_start: 0.5759 (OUTLIER) cc_final: 0.5433 (tp) outliers start: 53 outliers final: 27 residues processed: 200 average time/residue: 0.8299 time to fit residues: 177.2073 Evaluate side-chains 202 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 152 LYS Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 215 MET Chi-restraints excluded: chain K residue 223 ILE Chi-restraints excluded: chain K residue 252 LEU Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain K residue 295 THR Chi-restraints excluded: chain K residue 300 ASN Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 369 HIS Chi-restraints excluded: chain K residue 380 ILE Chi-restraints excluded: chain K residue 381 GLU Chi-restraints excluded: chain K residue 414 GLU Chi-restraints excluded: chain K residue 430 MET Chi-restraints excluded: chain K residue 464 LYS Chi-restraints excluded: chain K residue 476 PHE Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain K residue 501 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 53 optimal weight: 10.0000 chunk 111 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 40 optimal weight: 0.0170 chunk 22 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 overall best weight: 2.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN F 25 ASN G 24 GLN G 104 GLN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 GLN K 300 ASN ** K 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.137580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.095777 restraints weight = 21516.275| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.50 r_work: 0.2995 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 15831 Z= 0.224 Angle : 0.630 10.897 22591 Z= 0.360 Chirality : 0.038 0.145 2540 Planarity : 0.005 0.065 1858 Dihedral : 29.849 177.615 4409 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 5.19 % Allowed : 28.32 % Favored : 66.49 % 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: 0.57 (0.25), residues: 1105 helix: 1.51 (0.20), residues: 692 sheet: -0.57 (0.73), residues: 53 loop : -1.76 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG K 180 TYR 0.011 0.002 TYR D 40 PHE 0.010 0.001 PHE K 358 TRP 0.006 0.001 TRP K 331 HIS 0.007 0.001 HIS K 369 Details of bonding type rmsd covalent geometry : bond 0.00515 (15829) covalent geometry : angle 0.63023 (22591) hydrogen bonds : bond 0.05102 ( 891) hydrogen bonds : angle 3.24699 ( 2273) metal coordination : bond 0.00099 ( 2) *********************** 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 218 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 168 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9132 (mp) REVERT: C 92 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.7662 (mt-10) REVERT: D 51 ASP cc_start: 0.8236 (p0) cc_final: 0.7918 (p0) REVERT: D 93 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8030 (mp0) REVERT: E 59 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8658 (pm20) REVERT: F 95 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7396 (mtp-110) REVERT: G 11 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7092 (mmm-85) REVERT: G 95 LYS cc_start: 0.9252 (ttmt) cc_final: 0.9005 (tttm) REVERT: H 76 GLU cc_start: 0.8883 (tp30) cc_final: 0.8640 (tp30) REVERT: H 105 GLU cc_start: 0.8614 (tp30) cc_final: 0.8399 (mm-30) REVERT: K 155 ASP cc_start: 0.8301 (t70) cc_final: 0.8053 (m-30) REVERT: K 226 GLN cc_start: 0.7323 (mp-120) cc_final: 0.7087 (mm-40) REVERT: K 251 PHE cc_start: 0.8214 (m-10) cc_final: 0.7577 (m-10) REVERT: K 262 MET cc_start: 0.7938 (ptm) cc_final: 0.7520 (ptm) REVERT: K 324 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7943 (tp30) REVERT: K 380 ILE cc_start: 0.2938 (OUTLIER) cc_final: 0.2553 (mt) REVERT: K 401 MET cc_start: 0.6968 (tpt) cc_final: 0.6544 (tpp) REVERT: K 403 TYR cc_start: 0.7162 (m-80) cc_final: 0.6584 (m-80) REVERT: K 430 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7881 (tmm) REVERT: K 461 ARG cc_start: 0.8455 (tpp-160) cc_final: 0.7800 (mmp-170) REVERT: K 464 LYS cc_start: 0.6661 (OUTLIER) cc_final: 0.6403 (pptt) REVERT: K 481 ILE cc_start: 0.5599 (OUTLIER) cc_final: 0.5089 (tp) outliers start: 50 outliers final: 29 residues processed: 198 average time/residue: 0.8864 time to fit residues: 187.2505 Evaluate side-chains 203 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 223 ILE Chi-restraints excluded: chain K residue 252 LEU Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain K residue 295 THR Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 369 HIS Chi-restraints excluded: chain K residue 380 ILE Chi-restraints excluded: chain K residue 381 GLU Chi-restraints excluded: chain K residue 414 GLU Chi-restraints excluded: chain K residue 428 PHE Chi-restraints excluded: chain K residue 430 MET Chi-restraints excluded: chain K residue 464 LYS Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 501 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 70 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 110 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN E 39 HIS F 25 ASN G 24 GLN G 73 ASN G 104 GLN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 GLN K 329 GLN ** K 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.137857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.095974 restraints weight = 21670.962| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.53 r_work: 0.3003 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 15831 Z= 0.212 Angle : 0.634 15.800 22591 Z= 0.359 Chirality : 0.038 0.157 2540 Planarity : 0.005 0.050 1858 Dihedral : 29.820 177.226 4409 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 5.19 % Allowed : 28.73 % Favored : 66.08 % 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: 0.64 (0.25), residues: 1105 helix: 1.57 (0.20), residues: 692 sheet: -0.72 (0.71), residues: 55 loop : -1.72 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG K 180 TYR 0.011 0.001 TYR D 40 PHE 0.011 0.001 PHE K 358 TRP 0.008 0.002 TRP K 431 HIS 0.006 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00484 (15829) covalent geometry : angle 0.63352 (22591) hydrogen bonds : bond 0.04947 ( 891) hydrogen bonds : angle 3.21702 ( 2273) metal coordination : bond 0.00088 ( 2) *********************** 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 214 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 164 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9151 (mp) REVERT: C 92 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.7650 (mt-10) REVERT: D 51 ASP cc_start: 0.8257 (p0) cc_final: 0.7965 (p0) REVERT: D 93 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8001 (mp0) REVERT: E 59 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8643 (pm20) REVERT: F 95 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7355 (mtp-110) REVERT: G 11 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7099 (mmm-85) REVERT: G 15 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8750 (ttpt) REVERT: G 95 LYS cc_start: 0.9260 (ttmt) cc_final: 0.9018 (tttm) REVERT: H 76 GLU cc_start: 0.8910 (tp30) cc_final: 0.8672 (tp30) REVERT: K 155 ASP cc_start: 0.8301 (t70) cc_final: 0.8018 (m-30) REVERT: K 226 GLN cc_start: 0.7303 (mp-120) cc_final: 0.7103 (mm-40) REVERT: K 251 PHE cc_start: 0.8196 (m-10) cc_final: 0.7545 (m-10) REVERT: K 262 MET cc_start: 0.7906 (ptm) cc_final: 0.7503 (ptm) REVERT: K 324 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7921 (tp30) REVERT: K 329 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.7335 (pm20) REVERT: K 339 ASN cc_start: 0.8349 (m-40) cc_final: 0.8073 (m-40) REVERT: K 380 ILE cc_start: 0.2894 (OUTLIER) cc_final: 0.2537 (mt) REVERT: K 403 TYR cc_start: 0.7230 (m-80) cc_final: 0.6679 (m-80) REVERT: K 430 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7799 (tmm) REVERT: K 461 ARG cc_start: 0.8467 (tpp-160) cc_final: 0.7822 (mmp-170) REVERT: K 464 LYS cc_start: 0.6657 (OUTLIER) cc_final: 0.6430 (pptt) REVERT: K 481 ILE cc_start: 0.5596 (OUTLIER) cc_final: 0.5141 (tp) outliers start: 50 outliers final: 27 residues processed: 197 average time/residue: 0.8283 time to fit residues: 174.7199 Evaluate side-chains 198 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 223 ILE Chi-restraints excluded: chain K residue 252 LEU Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain K residue 295 THR Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 329 GLN Chi-restraints excluded: chain K residue 369 HIS Chi-restraints excluded: chain K residue 380 ILE Chi-restraints excluded: chain K residue 381 GLU Chi-restraints excluded: chain K residue 414 GLU Chi-restraints excluded: chain K residue 430 MET Chi-restraints excluded: chain K residue 464 LYS Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 501 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 12 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 124 optimal weight: 40.0000 chunk 120 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN F 25 ASN G 104 GLN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3831 r_free = 0.3831 target = 0.138226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.096403 restraints weight = 21656.640| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.49 r_work: 0.3006 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15831 Z= 0.200 Angle : 0.629 11.109 22591 Z= 0.358 Chirality : 0.037 0.146 2540 Planarity : 0.005 0.075 1858 Dihedral : 29.797 177.213 4409 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.94 % Allowed : 30.08 % Favored : 65.98 % 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: 0.69 (0.25), residues: 1105 helix: 1.61 (0.20), residues: 692 sheet: -0.77 (0.70), residues: 55 loop : -1.68 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG K 180 TYR 0.012 0.001 TYR K 468 PHE 0.010 0.001 PHE K 358 TRP 0.010 0.001 TRP K 431 HIS 0.009 0.001 HIS K 203 Details of bonding type rmsd covalent geometry : bond 0.00455 (15829) covalent geometry : angle 0.62905 (22591) hydrogen bonds : bond 0.04829 ( 891) hydrogen bonds : angle 3.19312 ( 2273) metal coordination : bond 0.00083 ( 2) *********************** 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 202 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 164 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9157 (mp) REVERT: D 51 ASP cc_start: 0.8219 (p0) cc_final: 0.7922 (p0) REVERT: D 93 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.7989 (mp0) REVERT: E 59 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8629 (pm20) REVERT: F 95 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7339 (mtp-110) REVERT: G 11 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7161 (mmm-85) REVERT: G 15 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8744 (ttpt) REVERT: G 95 LYS cc_start: 0.9262 (ttmt) cc_final: 0.9016 (tttm) REVERT: H 76 GLU cc_start: 0.8924 (tp30) cc_final: 0.8695 (tp30) REVERT: K 155 ASP cc_start: 0.8262 (t70) cc_final: 0.7979 (m-30) REVERT: K 251 PHE cc_start: 0.8158 (m-10) cc_final: 0.7513 (m-10) REVERT: K 262 MET cc_start: 0.7930 (ptm) cc_final: 0.7529 (ptm) REVERT: K 324 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7860 (tp30) REVERT: K 339 ASN cc_start: 0.8347 (m-40) cc_final: 0.8081 (m-40) REVERT: K 380 ILE cc_start: 0.2916 (OUTLIER) cc_final: 0.2555 (mt) REVERT: K 403 TYR cc_start: 0.7218 (m-80) cc_final: 0.6688 (m-80) REVERT: K 430 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7897 (tmm) REVERT: K 461 ARG cc_start: 0.8451 (tpp-160) cc_final: 0.7832 (mmp-170) REVERT: K 464 LYS cc_start: 0.6650 (OUTLIER) cc_final: 0.6411 (pptt) REVERT: K 481 ILE cc_start: 0.5657 (OUTLIER) cc_final: 0.5251 (tp) outliers start: 38 outliers final: 22 residues processed: 188 average time/residue: 0.8591 time to fit residues: 172.5303 Evaluate side-chains 194 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain K residue 223 ILE Chi-restraints excluded: chain K residue 252 LEU Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain K residue 295 THR Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 369 HIS Chi-restraints excluded: chain K residue 380 ILE Chi-restraints excluded: chain K residue 381 GLU Chi-restraints excluded: chain K residue 414 GLU Chi-restraints excluded: chain K residue 430 MET Chi-restraints excluded: chain K residue 464 LYS Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 501 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 125 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 53 optimal weight: 0.0980 chunk 44 optimal weight: 0.0980 chunk 75 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN F 25 ASN G 73 ASN G 104 GLN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.139760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.098017 restraints weight = 21595.690| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.54 r_work: 0.3038 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15831 Z= 0.151 Angle : 0.629 13.524 22591 Z= 0.356 Chirality : 0.036 0.156 2540 Planarity : 0.004 0.045 1858 Dihedral : 29.784 177.568 4409 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.11 % Allowed : 31.02 % Favored : 65.87 % 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: 0.88 (0.26), residues: 1105 helix: 1.75 (0.20), residues: 692 sheet: -0.80 (0.71), residues: 55 loop : -1.56 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 244 TYR 0.013 0.001 TYR K 468 PHE 0.017 0.001 PHE K 428 TRP 0.012 0.001 TRP K 431 HIS 0.010 0.001 HIS K 203 Details of bonding type rmsd covalent geometry : bond 0.00328 (15829) covalent geometry : angle 0.62878 (22591) hydrogen bonds : bond 0.04451 ( 891) hydrogen bonds : angle 3.15674 ( 2273) metal coordination : bond 0.00019 ( 2) ********************** 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 200 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8322 (mtm110) cc_final: 0.7896 (mtp85) REVERT: D 51 ASP cc_start: 0.8177 (p0) cc_final: 0.7860 (p0) REVERT: E 59 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8626 (pm20) REVERT: F 95 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.7291 (mtp-110) REVERT: G 11 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7145 (mmm-85) REVERT: G 15 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8754 (ttpt) REVERT: G 95 LYS cc_start: 0.9239 (ttmt) cc_final: 0.9015 (tttm) REVERT: H 76 GLU cc_start: 0.8878 (tp30) cc_final: 0.8621 (tp30) REVERT: K 155 ASP cc_start: 0.8276 (t70) cc_final: 0.8004 (m-30) REVERT: K 160 LYS cc_start: 0.8003 (mmtm) cc_final: 0.7572 (mtpt) REVERT: K 185 ARG cc_start: 0.4044 (ttp80) cc_final: 0.3816 (ptt180) REVERT: K 251 PHE cc_start: 0.8185 (m-10) cc_final: 0.7568 (m-10) REVERT: K 262 MET cc_start: 0.7912 (ptm) cc_final: 0.7384 (ptm) REVERT: K 324 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7856 (tp30) REVERT: K 339 ASN cc_start: 0.8365 (m-40) cc_final: 0.8094 (m-40) REVERT: K 380 ILE cc_start: 0.2932 (OUTLIER) cc_final: 0.2599 (mm) REVERT: K 403 TYR cc_start: 0.7237 (m-80) cc_final: 0.6692 (m-80) REVERT: K 430 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7783 (tmm) REVERT: K 461 ARG cc_start: 0.8450 (tpp-160) cc_final: 0.7805 (mmp-170) REVERT: K 464 LYS cc_start: 0.6637 (OUTLIER) cc_final: 0.6403 (pptt) REVERT: K 481 ILE cc_start: 0.5665 (OUTLIER) cc_final: 0.5361 (tp) outliers start: 30 outliers final: 16 residues processed: 190 average time/residue: 0.8671 time to fit residues: 176.1927 Evaluate side-chains 191 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain K residue 223 ILE Chi-restraints excluded: chain K residue 252 LEU Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain K residue 295 THR Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 369 HIS Chi-restraints excluded: chain K residue 380 ILE Chi-restraints excluded: chain K residue 414 GLU Chi-restraints excluded: chain K residue 430 MET Chi-restraints excluded: chain K residue 464 LYS Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain K residue 501 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 128 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN E 68 GLN F 25 ASN G 104 GLN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 329 GLN ** K 369 HIS ** 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 = 0.3864 r_free = 0.3864 target = 0.140510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.097324 restraints weight = 21476.258| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.47 r_work: 0.3066 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15831 Z= 0.164 Angle : 0.617 11.425 22591 Z= 0.350 Chirality : 0.036 0.152 2540 Planarity : 0.005 0.070 1858 Dihedral : 29.648 176.907 4409 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.80 % Allowed : 31.43 % Favored : 65.77 % 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: 1.05 (0.26), residues: 1105 helix: 1.88 (0.20), residues: 692 sheet: -0.69 (0.74), residues: 55 loop : -1.50 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG K 180 TYR 0.014 0.001 TYR K 468 PHE 0.015 0.001 PHE K 428 TRP 0.012 0.001 TRP K 431 HIS 0.005 0.001 HIS K 203 Details of bonding type rmsd covalent geometry : bond 0.00365 (15829) covalent geometry : angle 0.61716 (22591) hydrogen bonds : bond 0.04320 ( 891) hydrogen bonds : angle 3.09202 ( 2273) metal coordination : bond 0.00477 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6046.66 seconds wall clock time: 103 minutes 10.89 seconds (6190.89 seconds total)