Starting phenix.real_space_refine on Fri May 16 18:11:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8onz_17003/05_2025/8onz_17003.cif Found real_map, /net/cci-nas-00/data/ceres_data/8onz_17003/05_2025/8onz_17003.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8onz_17003/05_2025/8onz_17003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8onz_17003/05_2025/8onz_17003.map" model { file = "/net/cci-nas-00/data/ceres_data/8onz_17003/05_2025/8onz_17003.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8onz_17003/05_2025/8onz_17003.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.106 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: 5 Type Number sf(0) Gaussians P 329 5.49 5 S 15 5.16 5 C 8151 2.51 5 N 2794 2.21 5 O 3701 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14990 Number of models: 1 Model: "" Number of chains: 8 Chain: "LR" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1251 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 3, 'TRANS': 149} Chain: "LX" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 965 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 8, 'TRANS': 112} Chain: "LY" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1065 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 6, 'TRANS': 127} Chain: "Lh" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1003 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "Lk" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 632 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 4, 'TRANS': 71} Chain: "1" Number of atoms: 5777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 5777 Classifications: {'RNA': 270} Modifications used: {'rna2p_pur': 19, 'rna2p_pyr': 17, 'rna3p_pur': 126, 'rna3p_pyr': 108} Link IDs: {'rna2p': 35, 'rna3p': 234} Chain breaks: 7 Chain: "2" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1261 Classifications: {'RNA': 59} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 1, 'rna3p_pur': 24, 'rna3p_pyr': 24} Link IDs: {'rna2p': 11, 'rna3p': 47} Chain: "A" Number of atoms: 3036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3036 Classifications: {'peptide': 385} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 365} Time building chain proxies: 15.19, per 1000 atoms: 1.01 Number of scatterers: 14990 At special positions: 0 Unit cell: (134.54, 151.032, 190.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 329 15.00 O 3701 8.00 N 2794 7.00 C 8151 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: 3.47 Conformation dependent library (CDL) restraints added in 1.1 seconds 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1866 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 12 sheets defined 46.4% alpha, 15.7% beta 91 base pairs and 150 stacking pairs defined. Time for finding SS restraints: 6.66 Creating SS restraints... Processing helix chain 'LR' and resid 4 through 16 Processing helix chain 'LR' and resid 18 through 20 No H-bonds generated for 'chain 'LR' and resid 18 through 20' Processing helix chain 'LR' and resid 28 through 34 removed outlier: 3.578A pdb=" N ASNLR 34 " --> pdb=" O SERLR 30 " (cutoff:3.500A) Processing helix chain 'LR' and resid 37 through 47 Processing helix chain 'LR' and resid 60 through 72 removed outlier: 3.539A pdb=" N ILELR 72 " --> pdb=" O LEULR 68 " (cutoff:3.500A) Processing helix chain 'LR' and resid 77 through 81 Processing helix chain 'LR' and resid 84 through 89 Processing helix chain 'LR' and resid 90 through 112 Processing helix chain 'LR' and resid 116 through 129 Processing helix chain 'LR' and resid 134 through 152 Processing helix chain 'LX' and resid 71 through 75 Processing helix chain 'LX' and resid 82 through 91 Processing helix chain 'LX' and resid 104 through 117 Processing helix chain 'LX' and resid 144 through 152 Processing helix chain 'LY' and resid 10 through 20 Processing helix chain 'LY' and resid 22 through 30 removed outlier: 3.944A pdb=" N VALLY 28 " --> pdb=" O SERLY 24 " (cutoff:3.500A) Processing helix chain 'LY' and resid 35 through 43 Processing helix chain 'LY' and resid 74 through 77 Processing helix chain 'LY' and resid 99 through 101 No H-bonds generated for 'chain 'LY' and resid 99 through 101' Processing helix chain 'LY' and resid 111 through 133 removed outlier: 3.571A pdb=" N ASNLY 116 " --> pdb=" O LYSLY 112 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 8 through 13 removed outlier: 3.555A pdb=" N LEULh 12 " --> pdb=" O LYSLh 8 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRPLh 13 " --> pdb=" O ALALh 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'Lh' and resid 8 through 13' Processing helix chain 'Lh' and resid 16 through 37 removed outlier: 3.566A pdb=" N GLNLh 37 " --> pdb=" O GLNLh 33 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 45 through 75 removed outlier: 4.173A pdb=" N ILELh 49 " --> pdb=" O LYSLh 45 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 90 through 96 Processing helix chain 'Lh' and resid 98 through 103 Processing helix chain 'Lh' and resid 106 through 116 Processing helix chain 'Lk' and resid 7 through 17 removed outlier: 3.652A pdb=" N PHELk 11 " --> pdb=" O ASPLk 7 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLULk 13 " --> pdb=" O LYSLk 9 " (cutoff:3.500A) Processing helix chain 'Lk' and resid 51 through 60 removed outlier: 3.816A pdb=" N LYSLk 57 " --> pdb=" O ASPLk 53 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLNLk 60 " --> pdb=" O GLULk 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 89 removed outlier: 3.638A pdb=" N LEU A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 111 removed outlier: 4.906A pdb=" N TYR A 108 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 122 removed outlier: 3.974A pdb=" N GLN A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 147 Processing helix chain 'A' and resid 152 through 169 Processing helix chain 'A' and resid 176 through 180 Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 239 through 257 removed outlier: 4.329A pdb=" N LEU A 243 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU A 244 " --> pdb=" O ASN A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 276 removed outlier: 3.680A pdb=" N ILE A 266 " --> pdb=" O ARG A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 376 removed outlier: 4.068A pdb=" N ASN A 370 " --> pdb=" O LYS A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 394 through 405 Processing sheet with id=AA1, first strand: chain 'LR' and resid 22 through 24 Processing sheet with id=AA2, first strand: chain 'LX' and resid 76 through 79 removed outlier: 6.994A pdb=" N ILELX 98 " --> pdb=" O ILELX 77 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VALLX 96 " --> pdb=" O PROLX 79 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYSLX 133 " --> pdb=" O VALLX 99 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYSLX 122 " --> pdb=" O ARGLX 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'LY' and resid 31 through 33 Processing sheet with id=AA4, first strand: chain 'LY' and resid 78 through 81 removed outlier: 7.056A pdb=" N VALLY 78 " --> pdb=" O VALLY 72 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N VALLY 72 " --> pdb=" O VALLY 78 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N HISLY 80 " --> pdb=" O THRLY 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'LY' and resid 85 through 87 Processing sheet with id=AA6, first strand: chain 'Lk' and resid 3 through 4 removed outlier: 6.670A pdb=" N GLNLk 3 " --> pdb=" O THRLk 46 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N VALLk 48 " --> pdb=" O GLNLk 3 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SERLk 22 " --> pdb=" O ARGLk 39 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.627A pdb=" N PHE A 424 " --> pdb=" O THR A 331 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.627A pdb=" N PHE A 424 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS A 297 " --> pdb=" O ALA A 328 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 181 through 191 removed outlier: 6.910A pdb=" N GLY A 219 " --> pdb=" O GLY A 184 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASP A 217 " --> pdb=" O PRO A 186 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N GLY A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LYS A 215 " --> pdb=" O GLY A 188 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 194 through 196 removed outlier: 6.661A pdb=" N LEU A 413 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 278 through 281 Processing sheet with id=AB3, first strand: chain 'A' and resid 381 through 382 removed outlier: 3.928A pdb=" N HIS A 348 " --> pdb=" O TYR A 410 " (cutoff:3.500A) 380 hydrogen bonds defined for protein. 1080 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 233 hydrogen bonds 382 hydrogen bond angles 0 basepair planarities 91 basepair parallelities 150 stacking parallelities Total time for adding SS restraints: 6.46 Time building geometry restraints manager: 4.01 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: 2903 1.33 - 1.45: 5122 1.45 - 1.57: 7248 1.57 - 1.69: 649 1.69 - 1.81: 25 Bond restraints: 15947 Sorted by residual: bond pdb=" CB GLU A 275 " pdb=" CG GLU A 275 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.96e+00 bond pdb=" N1 C 11958 " pdb=" C2 C 11958 " ideal model delta sigma weight residual 1.397 1.370 0.027 2.00e-02 2.50e+03 1.87e+00 bond pdb=" C3' G 12030 " pdb=" O3' G 12030 " ideal model delta sigma weight residual 1.417 1.437 -0.020 1.50e-02 4.44e+03 1.86e+00 bond pdb=" N1 C 11957 " pdb=" C2 C 11957 " ideal model delta sigma weight residual 1.397 1.424 -0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" CA GLU A 392 " pdb=" CB GLU A 392 " ideal model delta sigma weight residual 1.523 1.549 -0.026 1.94e-02 2.66e+03 1.75e+00 ... (remaining 15942 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 22819 2.74 - 5.48: 236 5.48 - 8.22: 23 8.22 - 10.96: 5 10.96 - 13.70: 1 Bond angle restraints: 23084 Sorted by residual: angle pdb=" C3' U 12024 " pdb=" O3' U 12024 " pdb=" P U 12025 " ideal model delta sigma weight residual 120.20 129.74 -9.54 1.50e+00 4.44e-01 4.05e+01 angle pdb=" C3' C 12028 " pdb=" O3' C 12028 " pdb=" P A 12029 " ideal model delta sigma weight residual 120.20 128.89 -8.69 1.50e+00 4.44e-01 3.36e+01 angle pdb=" O3' U 12024 " pdb=" P U 12025 " pdb=" O5' U 12025 " ideal model delta sigma weight residual 104.00 112.02 -8.02 1.50e+00 4.44e-01 2.86e+01 angle pdb=" C4' A 12029 " pdb=" C3' A 12029 " pdb=" O3' A 12029 " ideal model delta sigma weight residual 113.00 120.76 -7.76 1.50e+00 4.44e-01 2.67e+01 angle pdb=" C4' C 12028 " pdb=" C3' C 12028 " pdb=" O3' C 12028 " ideal model delta sigma weight residual 109.40 116.85 -7.45 1.50e+00 4.44e-01 2.46e+01 ... (remaining 23079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.74: 8990 27.74 - 55.49: 708 55.49 - 83.23: 478 83.23 - 110.98: 18 110.98 - 138.72: 5 Dihedral angle restraints: 10199 sinusoidal: 7321 harmonic: 2878 Sorted by residual: dihedral pdb=" O4' U 12041 " pdb=" C1' U 12041 " pdb=" N1 U 12041 " pdb=" C2 U 12041 " ideal model delta sinusoidal sigma weight residual 200.00 61.54 138.46 1 1.50e+01 4.44e-03 7.46e+01 dihedral pdb=" O4' U 11478 " pdb=" C1' U 11478 " pdb=" N1 U 11478 " pdb=" C2 U 11478 " ideal model delta sinusoidal sigma weight residual 200.00 67.06 132.94 1 1.50e+01 4.44e-03 7.17e+01 dihedral pdb=" O4' C 11955 " pdb=" C1' C 11955 " pdb=" N1 C 11955 " pdb=" C2 C 11955 " ideal model delta sinusoidal sigma weight residual -160.00 -77.80 -82.20 1 1.50e+01 4.44e-03 3.69e+01 ... (remaining 10196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 2762 0.104 - 0.209: 80 0.209 - 0.313: 6 0.313 - 0.417: 1 0.417 - 0.522: 2 Chirality restraints: 2851 Sorted by residual: chirality pdb=" C3' A 12029 " pdb=" C4' A 12029 " pdb=" O3' A 12029 " pdb=" C2' A 12029 " both_signs ideal model delta sigma weight residual False -2.48 -1.96 -0.52 2.00e-01 2.50e+01 6.81e+00 chirality pdb=" C3' C 12028 " pdb=" C4' C 12028 " pdb=" O3' C 12028 " pdb=" C2' C 12028 " both_signs ideal model delta sigma weight residual False -2.74 -2.32 -0.43 2.00e-01 2.50e+01 4.53e+00 chirality pdb=" C4' A 12029 " pdb=" C5' A 12029 " pdb=" O4' A 12029 " pdb=" C3' A 12029 " both_signs ideal model delta sigma weight residual False -2.50 -2.13 -0.37 2.00e-01 2.50e+01 3.41e+00 ... (remaining 2848 not shown) Planarity restraints: 1715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C 11958 " -0.028 2.00e-02 2.50e+03 4.00e-02 3.60e+01 pdb=" N1 C 11958 " 0.072 2.00e-02 2.50e+03 pdb=" C2 C 11958 " -0.083 2.00e-02 2.50e+03 pdb=" O2 C 11958 " 0.037 2.00e-02 2.50e+03 pdb=" N3 C 11958 " 0.008 2.00e-02 2.50e+03 pdb=" C4 C 11958 " -0.007 2.00e-02 2.50e+03 pdb=" N4 C 11958 " 0.007 2.00e-02 2.50e+03 pdb=" C5 C 11958 " -0.004 2.00e-02 2.50e+03 pdb=" C6 C 11958 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 11488 " -0.038 2.00e-02 2.50e+03 3.46e-02 2.69e+01 pdb=" N1 C 11488 " 0.082 2.00e-02 2.50e+03 pdb=" C2 C 11488 " -0.046 2.00e-02 2.50e+03 pdb=" O2 C 11488 " 0.015 2.00e-02 2.50e+03 pdb=" N3 C 11488 " 0.005 2.00e-02 2.50e+03 pdb=" C4 C 11488 " -0.001 2.00e-02 2.50e+03 pdb=" N4 C 11488 " -0.005 2.00e-02 2.50e+03 pdb=" C5 C 11488 " -0.003 2.00e-02 2.50e+03 pdb=" C6 C 11488 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 11487 " -0.028 2.00e-02 2.50e+03 2.60e-02 1.86e+01 pdb=" N9 A 11487 " 0.068 2.00e-02 2.50e+03 pdb=" C8 A 11487 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A 11487 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A 11487 " -0.007 2.00e-02 2.50e+03 pdb=" C6 A 11487 " -0.001 2.00e-02 2.50e+03 pdb=" N6 A 11487 " -0.002 2.00e-02 2.50e+03 pdb=" N1 A 11487 " 0.005 2.00e-02 2.50e+03 pdb=" C2 A 11487 " 0.007 2.00e-02 2.50e+03 pdb=" N3 A 11487 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A 11487 " -0.043 2.00e-02 2.50e+03 ... (remaining 1712 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 130 2.57 - 3.15: 11378 3.15 - 3.73: 26811 3.73 - 4.32: 36405 4.32 - 4.90: 50996 Nonbonded interactions: 125720 Sorted by model distance: nonbonded pdb=" O2' G 12030 " pdb=" OP1 G 12031 " model vdw 1.983 3.040 nonbonded pdb=" OD2 ASP A 128 " pdb=" NH2 ARG A 225 " model vdw 2.058 3.120 nonbonded pdb=" N2 G 11963 " pdb=" O2 C 12008 " model vdw 2.074 2.496 nonbonded pdb=" N2 G 11968 " pdb=" O2 C 12003 " model vdw 2.085 2.496 nonbonded pdb=" N2 G 11962 " pdb=" O2 C 12009 " model vdw 2.093 2.496 ... (remaining 125715 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 37.960 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: 0.000 Extract box with map and model: 0.750 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 46.840 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:10.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0316 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 15947 Z= 0.189 Angle : 0.743 13.703 23084 Z= 0.413 Chirality : 0.045 0.522 2851 Planarity : 0.007 0.110 1715 Dihedral : 21.845 138.723 8333 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.25), residues: 979 helix: 0.58 (0.25), residues: 413 sheet: 0.62 (0.43), residues: 114 loop : -0.09 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 142 HIS 0.004 0.001 HISLR 58 PHE 0.016 0.002 PHE A 185 TYR 0.020 0.002 TYR A 339 ARG 0.029 0.001 ARG A 384 Details of bonding type rmsd hydrogen bonds : bond 0.17864 ( 600) hydrogen bonds : angle 6.27643 ( 1462) covalent geometry : bond 0.00377 (15947) covalent geometry : angle 0.74287 (23084) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 1.162 Fit side-chains revert: symmetry clash REVERT: LX 94 THR cc_start: 0.2165 (p) cc_final: 0.1853 (p) REVERT: LY 11 ARG cc_start: 0.3418 (ttt90) cc_final: 0.2125 (mmt-90) REVERT: A 302 TYR cc_start: 0.1015 (m-80) cc_final: 0.0422 (m-80) REVERT: A 321 MET cc_start: 0.0862 (ttm) cc_final: 0.0070 (mpt) REVERT: A 346 VAL cc_start: 0.3921 (p) cc_final: 0.2749 (p) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 1.1717 time to fit residues: 102.5588 Evaluate side-chains 36 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 75 optimal weight: 40.0000 chunk 117 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LX 73 HIS ** LY 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LY 109 HIS Lh 64 ASN Lk 28 ASN Lk 33 GLN ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN A 305 HIS A 400 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5353 r_free = 0.5353 target = 0.293958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.5297 r_free = 0.5297 target = 0.287802 restraints weight = 51368.020| |-----------------------------------------------------------------------------| r_work (start): 0.5291 rms_B_bonded: 0.99 r_work: 0.5220 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.5220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1448 moved from start: 0.5653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 15947 Z= 0.298 Angle : 1.112 12.873 23084 Z= 0.561 Chirality : 0.054 0.283 2851 Planarity : 0.011 0.169 1715 Dihedral : 23.947 154.506 6221 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.89 % Allowed : 8.21 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.25), residues: 979 helix: -0.85 (0.22), residues: 414 sheet: -0.02 (0.50), residues: 104 loop : -0.71 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 235 HIS 0.020 0.003 HISLR 75 PHE 0.050 0.005 PHELY 19 TYR 0.062 0.004 TYRLY 73 ARG 0.020 0.002 ARGLX 138 Details of bonding type rmsd hydrogen bonds : bond 0.12886 ( 600) hydrogen bonds : angle 5.83235 ( 1462) covalent geometry : bond 0.00603 (15947) covalent geometry : angle 1.11207 (23084) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 55 time to evaluate : 0.989 Fit side-chains REVERT: LR 144 ARG cc_start: 0.3414 (mtm-85) cc_final: 0.2249 (mtp-110) REVERT: LX 138 ARG cc_start: 0.4288 (OUTLIER) cc_final: 0.1803 (mmp-170) REVERT: LY 74 ARG cc_start: 0.1380 (mtt180) cc_final: 0.0888 (mmt90) REVERT: Lh 33 GLN cc_start: 0.1013 (OUTLIER) cc_final: 0.0625 (tt0) REVERT: Lh 83 LEU cc_start: 0.2558 (OUTLIER) cc_final: 0.1735 (tp) REVERT: A 233 MET cc_start: 0.1583 (ptm) cc_final: 0.1120 (tpp) REVERT: A 323 GLU cc_start: 0.3187 (OUTLIER) cc_final: 0.2801 (pt0) outliers start: 25 outliers final: 9 residues processed: 77 average time/residue: 1.0754 time to fit residues: 93.6687 Evaluate side-chains 51 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LR residue 17 CYS Chi-restraints excluded: chain LR residue 56 THR Chi-restraints excluded: chain LR residue 146 LYS Chi-restraints excluded: chain LX residue 124 ASN Chi-restraints excluded: chain LX residue 138 ARG Chi-restraints excluded: chain LY residue 8 SER Chi-restraints excluded: chain LY residue 19 PHE Chi-restraints excluded: chain LY residue 98 ILE Chi-restraints excluded: chain Lh residue 33 GLN Chi-restraints excluded: chain Lh residue 83 LEU Chi-restraints excluded: chain Lh residue 113 LEU Chi-restraints excluded: chain Lk residue 51 ASP Chi-restraints excluded: chain A residue 323 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 42 optimal weight: 2.9990 chunk 82 optimal weight: 30.0000 chunk 74 optimal weight: 30.0000 chunk 70 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 20 optimal weight: 0.0980 chunk 97 optimal weight: 10.0000 chunk 109 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** LR 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LY 80 HIS ** Lh 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lk 28 ASN A 87 HIS A 170 HIS ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5367 r_free = 0.5367 target = 0.295320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.5309 r_free = 0.5309 target = 0.288930 restraints weight = 51594.298| |-----------------------------------------------------------------------------| r_work (start): 0.5301 rms_B_bonded: 0.99 r_work: 0.5248 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.5200 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.5200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1180 moved from start: 0.5511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15947 Z= 0.122 Angle : 0.591 9.208 23084 Z= 0.304 Chirality : 0.036 0.199 2851 Planarity : 0.005 0.040 1715 Dihedral : 22.878 149.994 6221 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.54 % Allowed : 11.33 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.26), residues: 979 helix: 0.34 (0.24), residues: 425 sheet: 0.09 (0.51), residues: 104 loop : -0.43 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 235 HIS 0.010 0.001 HIS A 221 PHE 0.012 0.001 PHE A 185 TYR 0.022 0.001 TYRLY 73 ARG 0.005 0.001 ARG A 361 Details of bonding type rmsd hydrogen bonds : bond 0.06854 ( 600) hydrogen bonds : angle 4.37831 ( 1462) covalent geometry : bond 0.00231 (15947) covalent geometry : angle 0.59118 (23084) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 31 time to evaluate : 1.024 Fit side-chains REVERT: LR 89 MET cc_start: 0.1416 (tpp) cc_final: 0.0454 (ppp) REVERT: LR 144 ARG cc_start: 0.2581 (mtm-85) cc_final: 0.1175 (mtp-110) REVERT: LX 124 ASN cc_start: 0.5298 (p0) cc_final: 0.5047 (t0) REVERT: LY 11 ARG cc_start: 0.4960 (ttt90) cc_final: 0.2632 (pmm-80) REVERT: A 114 GLU cc_start: -0.0753 (OUTLIER) cc_final: -0.1011 (tt0) REVERT: A 312 ILE cc_start: -0.1180 (OUTLIER) cc_final: -0.1754 (tt) REVERT: A 339 TYR cc_start: -0.0138 (OUTLIER) cc_final: -0.1878 (p90) outliers start: 22 outliers final: 7 residues processed: 48 average time/residue: 1.0287 time to fit residues: 56.4631 Evaluate side-chains 39 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LR residue 17 CYS Chi-restraints excluded: chain LR residue 146 LYS Chi-restraints excluded: chain LX residue 101 VAL Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain Lk residue 51 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 369 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 36 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 116 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 88 optimal weight: 20.0000 chunk 128 optimal weight: 30.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Lh 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5348 r_free = 0.5348 target = 0.292540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.5285 r_free = 0.5285 target = 0.286057 restraints weight = 51071.993| |-----------------------------------------------------------------------------| r_work (start): 0.5277 rms_B_bonded: 0.99 r_work: 0.5244 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.5201 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.5201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1729 moved from start: 0.7490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 15947 Z= 0.236 Angle : 0.876 12.134 23084 Z= 0.441 Chirality : 0.047 0.385 2851 Planarity : 0.007 0.089 1715 Dihedral : 23.534 158.209 6221 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.47 % Allowed : 13.18 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.26), residues: 979 helix: -0.21 (0.24), residues: 411 sheet: -0.44 (0.55), residues: 90 loop : -0.82 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 235 HIS 0.011 0.003 HISLR 75 PHE 0.027 0.003 PHELY 19 TYR 0.036 0.003 TYRLY 73 ARG 0.009 0.001 ARG A 361 Details of bonding type rmsd hydrogen bonds : bond 0.09277 ( 600) hydrogen bonds : angle 5.12777 ( 1462) covalent geometry : bond 0.00472 (15947) covalent geometry : angle 0.87648 (23084) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 42 time to evaluate : 1.147 Fit side-chains REVERT: LX 126 LEU cc_start: 0.3668 (OUTLIER) cc_final: 0.3218 (tt) REVERT: A 75 THR cc_start: 0.2460 (OUTLIER) cc_final: 0.2104 (m) REVERT: A 114 GLU cc_start: 0.0536 (OUTLIER) cc_final: -0.0237 (tt0) REVERT: A 312 ILE cc_start: -0.1230 (OUTLIER) cc_final: -0.1630 (tt) REVERT: A 373 LYS cc_start: -0.1446 (mtmt) cc_final: -0.2309 (tppt) outliers start: 30 outliers final: 11 residues processed: 65 average time/residue: 1.1763 time to fit residues: 85.8999 Evaluate side-chains 51 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LR residue 17 CYS Chi-restraints excluded: chain LR residue 56 THR Chi-restraints excluded: chain LX residue 73 HIS Chi-restraints excluded: chain LX residue 101 VAL Chi-restraints excluded: chain LX residue 126 LEU Chi-restraints excluded: chain LY residue 77 TYR Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 369 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 92 optimal weight: 0.0970 chunk 103 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 41 optimal weight: 0.4980 chunk 81 optimal weight: 30.0000 chunk 104 optimal weight: 0.0570 chunk 75 optimal weight: 30.0000 chunk 44 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 79 optimal weight: 40.0000 overall best weight: 2.3300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LX 93 ASN Lh 11 GLN ** Lh 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5360 r_free = 0.5360 target = 0.293716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5308 r_free = 0.5308 target = 0.287946 restraints weight = 52335.912| |-----------------------------------------------------------------------------| r_work (start): 0.5299 rms_B_bonded: 0.92 r_work: 0.5261 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.5220 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.5220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1571 moved from start: 0.7881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15947 Z= 0.133 Angle : 0.635 9.097 23084 Z= 0.324 Chirality : 0.037 0.240 2851 Planarity : 0.005 0.041 1715 Dihedral : 23.017 154.586 6221 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.31 % Allowed : 16.18 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.26), residues: 979 helix: 0.12 (0.25), residues: 423 sheet: -0.48 (0.53), residues: 96 loop : -0.74 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPLR 95 HIS 0.007 0.001 HIS A 221 PHE 0.016 0.002 PHELY 19 TYR 0.017 0.002 TYRLY 73 ARG 0.009 0.000 ARGLR 144 Details of bonding type rmsd hydrogen bonds : bond 0.06904 ( 600) hydrogen bonds : angle 4.54683 ( 1462) covalent geometry : bond 0.00261 (15947) covalent geometry : angle 0.63451 (23084) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 38 time to evaluate : 1.076 Fit side-chains REVERT: LY 11 ARG cc_start: 0.4774 (ttt90) cc_final: 0.2303 (pmm-80) REVERT: Lk 18 LYS cc_start: 0.0929 (OUTLIER) cc_final: 0.0254 (tptt) REVERT: A 75 THR cc_start: 0.2739 (OUTLIER) cc_final: 0.2443 (m) REVERT: A 114 GLU cc_start: -0.0078 (OUTLIER) cc_final: -0.0562 (mm-30) REVERT: A 312 ILE cc_start: -0.1272 (OUTLIER) cc_final: -0.1601 (tt) REVERT: A 373 LYS cc_start: -0.1389 (mtmt) cc_final: -0.2404 (tppt) outliers start: 20 outliers final: 11 residues processed: 52 average time/residue: 1.0881 time to fit residues: 64.7548 Evaluate side-chains 47 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 32 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LR residue 17 CYS Chi-restraints excluded: chain LX residue 146 LEU Chi-restraints excluded: chain LY residue 19 PHE Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain LY residue 98 ILE Chi-restraints excluded: chain Lk residue 18 LYS Chi-restraints excluded: chain Lk residue 51 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 369 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 90 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 1 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 39 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LR 99 GLN ** Lh 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5343 r_free = 0.5343 target = 0.291930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.5288 r_free = 0.5288 target = 0.285697 restraints weight = 52481.798| |-----------------------------------------------------------------------------| r_work (start): 0.5280 rms_B_bonded: 0.98 r_work: 0.5246 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.5204 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.5204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1905 moved from start: 0.9211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15947 Z= 0.183 Angle : 0.788 9.307 23084 Z= 0.400 Chirality : 0.043 0.281 2851 Planarity : 0.007 0.079 1715 Dihedral : 23.420 160.655 6221 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.58 % Allowed : 16.07 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.26), residues: 979 helix: -0.12 (0.24), residues: 421 sheet: -0.74 (0.52), residues: 97 loop : -1.02 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRPLR 95 HIS 0.020 0.002 HIS A 348 PHE 0.021 0.003 PHELY 19 TYR 0.026 0.003 TYR A 349 ARG 0.008 0.001 ARGLR 97 Details of bonding type rmsd hydrogen bonds : bond 0.08541 ( 600) hydrogen bonds : angle 4.95968 ( 1462) covalent geometry : bond 0.00359 (15947) covalent geometry : angle 0.78809 (23084) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 38 time to evaluate : 1.035 Fit side-chains REVERT: LR 23 TRP cc_start: 0.1571 (t-100) cc_final: 0.0428 (t-100) REVERT: Lk 18 LYS cc_start: 0.1178 (OUTLIER) cc_final: 0.0262 (tptt) REVERT: A 114 GLU cc_start: -0.0119 (OUTLIER) cc_final: -0.0811 (mt-10) REVERT: A 312 ILE cc_start: -0.1391 (OUTLIER) cc_final: -0.1675 (tt) REVERT: A 373 LYS cc_start: -0.1425 (mtmt) cc_final: -0.2104 (mmmt) outliers start: 31 outliers final: 16 residues processed: 65 average time/residue: 1.2632 time to fit residues: 91.4495 Evaluate side-chains 53 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 34 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LR residue 56 THR Chi-restraints excluded: chain LR residue 120 TYR Chi-restraints excluded: chain LX residue 90 GLU Chi-restraints excluded: chain LY residue 19 PHE Chi-restraints excluded: chain LY residue 77 TYR Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain LY residue 98 ILE Chi-restraints excluded: chain Lk residue 18 LYS Chi-restraints excluded: chain Lk residue 51 ASP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 428 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 79 optimal weight: 40.0000 chunk 66 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 4 optimal weight: 0.0030 chunk 53 optimal weight: 30.0000 chunk 70 optimal weight: 20.0000 chunk 1 optimal weight: 0.2980 chunk 113 optimal weight: 8.9990 chunk 118 optimal weight: 20.0000 overall best weight: 4.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LX 110 GLN A 122 GLN A 144 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5344 r_free = 0.5344 target = 0.291728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.5300 r_free = 0.5300 target = 0.286619 restraints weight = 53062.930| |-----------------------------------------------------------------------------| r_work (start): 0.5294 rms_B_bonded: 0.79 r_work: 0.5263 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.5228 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.5228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1980 moved from start: 1.0396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15947 Z= 0.185 Angle : 0.778 9.760 23084 Z= 0.395 Chirality : 0.043 0.359 2851 Planarity : 0.007 0.077 1715 Dihedral : 23.559 156.875 6221 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.51 % Allowed : 16.76 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.26), residues: 979 helix: -0.27 (0.25), residues: 420 sheet: -0.81 (0.53), residues: 95 loop : -1.24 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRPLR 95 HIS 0.008 0.002 HISLY 62 PHE 0.023 0.003 PHELY 19 TYR 0.023 0.002 TYRLY 77 ARG 0.010 0.001 ARGLR 97 Details of bonding type rmsd hydrogen bonds : bond 0.08079 ( 600) hydrogen bonds : angle 4.98645 ( 1462) covalent geometry : bond 0.00370 (15947) covalent geometry : angle 0.77773 (23084) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 36 time to evaluate : 1.085 Fit side-chains REVERT: LR 21 LYS cc_start: 0.2900 (OUTLIER) cc_final: 0.1934 (mttm) REVERT: LX 87 LYS cc_start: 0.4958 (OUTLIER) cc_final: 0.4298 (ptmm) REVERT: LY 30 MET cc_start: 0.2837 (mtm) cc_final: 0.2262 (mtp) REVERT: Lh 84 ASP cc_start: 0.4361 (OUTLIER) cc_final: 0.1692 (t0) REVERT: Lk 18 LYS cc_start: 0.1208 (OUTLIER) cc_final: 0.0229 (tptt) REVERT: A 114 GLU cc_start: -0.0302 (OUTLIER) cc_final: -0.0808 (mt-10) REVERT: A 312 ILE cc_start: -0.1277 (OUTLIER) cc_final: -0.1493 (mm) outliers start: 39 outliers final: 20 residues processed: 70 average time/residue: 1.1555 time to fit residues: 90.7415 Evaluate side-chains 59 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 33 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LR residue 21 LYS Chi-restraints excluded: chain LR residue 56 THR Chi-restraints excluded: chain LR residue 120 TYR Chi-restraints excluded: chain LX residue 87 LYS Chi-restraints excluded: chain LX residue 124 ASN Chi-restraints excluded: chain LX residue 126 LEU Chi-restraints excluded: chain LY residue 19 PHE Chi-restraints excluded: chain LY residue 73 TYR Chi-restraints excluded: chain LY residue 77 TYR Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain LY residue 98 ILE Chi-restraints excluded: chain Lh residue 84 ASP Chi-restraints excluded: chain Lh residue 90 THR Chi-restraints excluded: chain Lk residue 18 LYS Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 51 ASP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 428 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 26 optimal weight: 0.3980 chunk 117 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 83 optimal weight: 30.0000 chunk 37 optimal weight: 7.9990 chunk 121 optimal weight: 0.4980 chunk 27 optimal weight: 0.1980 chunk 1 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Lh 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 ASN A 370 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5352 r_free = 0.5352 target = 0.292720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.5310 r_free = 0.5310 target = 0.287899 restraints weight = 52337.530| |-----------------------------------------------------------------------------| r_work (start): 0.5306 rms_B_bonded: 0.76 r_work: 0.5273 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.5236 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.5236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1814 moved from start: 1.0570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15947 Z= 0.129 Angle : 0.639 12.196 23084 Z= 0.325 Chirality : 0.037 0.259 2851 Planarity : 0.005 0.074 1715 Dihedral : 23.293 157.776 6221 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.01 % Allowed : 17.69 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.26), residues: 979 helix: 0.15 (0.26), residues: 420 sheet: -0.65 (0.53), residues: 95 loop : -1.12 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPLR 95 HIS 0.008 0.002 HIS A 221 PHE 0.025 0.002 PHE A 332 TYR 0.014 0.001 TYRLY 77 ARG 0.012 0.001 ARGLX 47 Details of bonding type rmsd hydrogen bonds : bond 0.07005 ( 600) hydrogen bonds : angle 4.49322 ( 1462) covalent geometry : bond 0.00253 (15947) covalent geometry : angle 0.63922 (23084) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 33 time to evaluate : 1.047 Fit side-chains REVERT: LR 21 LYS cc_start: 0.2203 (OUTLIER) cc_final: 0.1517 (mttp) REVERT: LY 30 MET cc_start: 0.2713 (mtm) cc_final: 0.2071 (mtt) REVERT: Lk 18 LYS cc_start: 0.1334 (OUTLIER) cc_final: 0.0272 (tptt) REVERT: A 114 GLU cc_start: -0.0712 (OUTLIER) cc_final: -0.1122 (mt-10) REVERT: A 121 MET cc_start: 0.4134 (ppp) cc_final: 0.3818 (ptm) REVERT: A 274 MET cc_start: -0.1664 (mtt) cc_final: -0.1984 (ttm) outliers start: 26 outliers final: 19 residues processed: 56 average time/residue: 1.0742 time to fit residues: 68.3425 Evaluate side-chains 53 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 31 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LR residue 21 LYS Chi-restraints excluded: chain LR residue 56 THR Chi-restraints excluded: chain LR residue 120 TYR Chi-restraints excluded: chain LR residue 146 LYS Chi-restraints excluded: chain LX residue 124 ASN Chi-restraints excluded: chain LY residue 19 PHE Chi-restraints excluded: chain LY residue 73 TYR Chi-restraints excluded: chain LY residue 77 TYR Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain Lh residue 60 LEU Chi-restraints excluded: chain Lh residue 90 THR Chi-restraints excluded: chain Lk residue 18 LYS Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 51 ASP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 369 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 105 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 103 optimal weight: 0.3980 chunk 97 optimal weight: 9.9990 chunk 93 optimal weight: 0.0570 chunk 9 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 124 optimal weight: 20.0000 overall best weight: 1.0700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** LR 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LX 107 GLN ** Lh 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5358 r_free = 0.5358 target = 0.293465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.5317 r_free = 0.5317 target = 0.288764 restraints weight = 52423.387| |-----------------------------------------------------------------------------| r_work (start): 0.5314 rms_B_bonded: 0.76 r_work: 0.5281 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.5243 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.5243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1664 moved from start: 1.0686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15947 Z= 0.109 Angle : 0.578 11.072 23084 Z= 0.291 Chirality : 0.034 0.207 2851 Planarity : 0.004 0.046 1715 Dihedral : 23.027 157.912 6221 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.85 % Allowed : 18.61 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.27), residues: 979 helix: 0.45 (0.26), residues: 423 sheet: -0.47 (0.54), residues: 95 loop : -0.98 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPLR 95 HIS 0.005 0.001 HISLh 50 PHE 0.018 0.002 PHE A 332 TYR 0.009 0.001 TYRLY 77 ARG 0.009 0.000 ARG A 431 Details of bonding type rmsd hydrogen bonds : bond 0.06400 ( 600) hydrogen bonds : angle 4.13160 ( 1462) covalent geometry : bond 0.00216 (15947) covalent geometry : angle 0.57782 (23084) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 31 time to evaluate : 1.036 Fit side-chains REVERT: LR 23 TRP cc_start: 0.1430 (t-100) cc_final: 0.0908 (t-100) REVERT: Lk 18 LYS cc_start: 0.1213 (OUTLIER) cc_final: 0.0249 (tptt) REVERT: A 330 GLU cc_start: -0.0728 (OUTLIER) cc_final: -0.1085 (mt-10) outliers start: 16 outliers final: 10 residues processed: 45 average time/residue: 1.2102 time to fit residues: 61.5653 Evaluate side-chains 43 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LR residue 146 LYS Chi-restraints excluded: chain LY residue 73 TYR Chi-restraints excluded: chain LY residue 77 TYR Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain Lh residue 60 LEU Chi-restraints excluded: chain Lk residue 18 LYS Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 51 ASP Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 369 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 127 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 46 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Lh 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5337 r_free = 0.5337 target = 0.291010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.5289 r_free = 0.5289 target = 0.285208 restraints weight = 53173.668| |-----------------------------------------------------------------------------| r_work (start): 0.5280 rms_B_bonded: 0.90 r_work: 0.5252 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.5214 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.5214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2021 moved from start: 1.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15947 Z= 0.165 Angle : 0.739 11.507 23084 Z= 0.371 Chirality : 0.040 0.227 2851 Planarity : 0.006 0.062 1715 Dihedral : 23.386 161.236 6221 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.66 % Allowed : 18.27 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.26), residues: 979 helix: 0.20 (0.25), residues: 419 sheet: -0.64 (0.53), residues: 95 loop : -1.13 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPLR 95 HIS 0.009 0.002 HISLX 46 PHE 0.021 0.002 PHE A 332 TYR 0.019 0.002 TYRLY 77 ARG 0.015 0.001 ARGLX 47 Details of bonding type rmsd hydrogen bonds : bond 0.08002 ( 600) hydrogen bonds : angle 4.63312 ( 1462) covalent geometry : bond 0.00326 (15947) covalent geometry : angle 0.73879 (23084) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 35 time to evaluate : 1.156 Fit side-chains REVERT: LR 78 PHE cc_start: 0.4346 (m-10) cc_final: 0.2185 (t80) REVERT: LY 30 MET cc_start: 0.2945 (mtm) cc_final: 0.2325 (mtt) REVERT: Lh 84 ASP cc_start: 0.4547 (OUTLIER) cc_final: 0.1904 (t0) REVERT: Lk 18 LYS cc_start: 0.1036 (OUTLIER) cc_final: -0.0092 (tptt) REVERT: A 121 MET cc_start: 0.3223 (ptm) cc_final: 0.2541 (ptm) REVERT: A 330 GLU cc_start: -0.0536 (OUTLIER) cc_final: -0.1042 (mt-10) outliers start: 23 outliers final: 15 residues processed: 56 average time/residue: 1.0895 time to fit residues: 69.3447 Evaluate side-chains 49 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 31 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LR residue 56 THR Chi-restraints excluded: chain LR residue 120 TYR Chi-restraints excluded: chain LR residue 146 LYS Chi-restraints excluded: chain LX residue 124 ASN Chi-restraints excluded: chain LY residue 19 PHE Chi-restraints excluded: chain LY residue 73 TYR Chi-restraints excluded: chain LY residue 77 TYR Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain Lh residue 60 LEU Chi-restraints excluded: chain Lh residue 84 ASP Chi-restraints excluded: chain Lh residue 90 THR Chi-restraints excluded: chain Lk residue 18 LYS Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 51 ASP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 369 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 8 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 119 optimal weight: 9.9990 chunk 89 optimal weight: 20.0000 chunk 86 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 73 optimal weight: 30.0000 chunk 75 optimal weight: 40.0000 chunk 84 optimal weight: 20.0000 chunk 128 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LX 66 HIS LX 73 HIS ** LY 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 37 GLN ** Lh 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5309 r_free = 0.5309 target = 0.287756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.5264 r_free = 0.5264 target = 0.282157 restraints weight = 52376.799| |-----------------------------------------------------------------------------| r_work (start): 0.5257 rms_B_bonded: 0.95 r_work: 0.5220 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.5175 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.5175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2440 moved from start: 1.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 15947 Z= 0.267 Angle : 1.040 10.971 23084 Z= 0.519 Chirality : 0.052 0.275 2851 Planarity : 0.009 0.117 1715 Dihedral : 24.339 161.055 6221 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 20.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.12 % Allowed : 18.27 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.25), residues: 979 helix: -0.83 (0.24), residues: 415 sheet: -1.03 (0.53), residues: 95 loop : -1.86 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRPLR 95 HIS 0.011 0.003 HISLR 75 PHE 0.041 0.003 PHELY 19 TYR 0.032 0.003 TYRLY 77 ARG 0.015 0.001 ARGLX 47 Details of bonding type rmsd hydrogen bonds : bond 0.11649 ( 600) hydrogen bonds : angle 5.73713 ( 1462) covalent geometry : bond 0.00529 (15947) covalent geometry : angle 1.04002 (23084) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10271.22 seconds wall clock time: 179 minutes 1.34 seconds (10741.34 seconds total)