Starting phenix.real_space_refine on Fri Jun 13 05:54:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8onz_17003/06_2025/8onz_17003.cif Found real_map, /net/cci-nas-00/data/ceres_data/8onz_17003/06_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_17003/06_2025/8onz_17003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8onz_17003/06_2025/8onz_17003.map" model { file = "/net/cci-nas-00/data/ceres_data/8onz_17003/06_2025/8onz_17003.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8onz_17003/06_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 15.42, per 1000 atoms: 1.03 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: 3.44 Conformation dependent library (CDL) restraints added in 1.2 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: 6.93 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: 6.84 Time building geometry restraints manager: 3.96 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: 346.460 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: 0.020 Extract box with map and model: 0.720 Check model and map are aligned: 0.090 Set scattering table: 0.160 Process input model: 47.340 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 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:15.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 410.040 ------------------------------------------------------------------------------- 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 : 1.130 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: 1.2235 time to fit residues: 107.3519 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 : 1.759 ------------------------------------------------------------------------------- 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 = 51368.031| |-----------------------------------------------------------------------------| 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 : 1.251 Fit side-chains REVERT: LR 144 ARG cc_start: 0.3410 (mtm-85) cc_final: 0.2250 (mtp-110) REVERT: LX 138 ARG cc_start: 0.4290 (OUTLIER) cc_final: 0.1806 (mmp-170) REVERT: LY 74 ARG cc_start: 0.1386 (mtt180) cc_final: 0.0896 (mmt90) REVERT: Lh 33 GLN cc_start: 0.1019 (OUTLIER) cc_final: 0.0630 (tt0) REVERT: Lh 83 LEU cc_start: 0.2551 (OUTLIER) cc_final: 0.1728 (tp) REVERT: A 233 MET cc_start: 0.1590 (ptm) cc_final: 0.1127 (tpp) REVERT: A 323 GLU cc_start: 0.3185 (OUTLIER) cc_final: 0.2802 (pt0) outliers start: 25 outliers final: 9 residues processed: 77 average time/residue: 1.1148 time to fit residues: 97.0396 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 : 1.143 ------------------------------------------------------------------------------- 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: 3.9990 chunk 82 optimal weight: 30.0000 chunk 74 optimal weight: 30.0000 chunk 70 optimal weight: 30.0000 chunk 15 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5363 r_free = 0.5363 target = 0.294813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.5303 r_free = 0.5303 target = 0.288326 restraints weight = 51536.158| |-----------------------------------------------------------------------------| r_work (start): 0.5296 rms_B_bonded: 1.03 r_work: 0.5236 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.5236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1247 moved from start: 0.5717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15947 Z= 0.130 Angle : 0.622 8.848 23084 Z= 0.318 Chirality : 0.037 0.197 2851 Planarity : 0.005 0.043 1715 Dihedral : 23.004 150.736 6221 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.77 % Allowed : 11.21 % Favored : 86.01 % 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: -0.37 (0.26), residues: 979 helix: 0.14 (0.24), residues: 425 sheet: -0.10 (0.51), residues: 104 loop : -0.53 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 235 HIS 0.010 0.002 HIS A 221 PHE 0.017 0.002 PHELY 19 TYR 0.030 0.002 TYRLY 73 ARG 0.005 0.001 ARG A 361 Details of bonding type rmsd hydrogen bonds : bond 0.07161 ( 600) hydrogen bonds : angle 4.54916 ( 1462) covalent geometry : bond 0.00255 (15947) covalent geometry : angle 0.62151 (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 56 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 32 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: LR 144 ARG cc_start: 0.3321 (mtm-85) cc_final: 0.1853 (mtp-110) REVERT: LX 124 ASN cc_start: 0.5466 (p0) cc_final: 0.4848 (t0) REVERT: LX 126 LEU cc_start: 0.3549 (OUTLIER) cc_final: 0.3242 (tt) REVERT: LY 11 ARG cc_start: 0.4974 (ttt90) cc_final: 0.2567 (pmm-80) REVERT: A 114 GLU cc_start: -0.0423 (OUTLIER) cc_final: -0.0623 (tt0) REVERT: A 312 ILE cc_start: -0.1003 (OUTLIER) cc_final: -0.1415 (mm) outliers start: 24 outliers final: 11 residues processed: 51 average time/residue: 1.0365 time to fit residues: 60.7265 Evaluate side-chains 42 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 28 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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 73 HIS Chi-restraints excluded: chain LX residue 101 VAL Chi-restraints excluded: chain LX residue 126 LEU Chi-restraints excluded: chain LY residue 8 SER 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 208 LEU 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: 6.9990 chunk 35 optimal weight: 6.9990 chunk 18 optimal weight: 0.0870 chunk 54 optimal weight: 5.9990 chunk 116 optimal weight: 0.0980 chunk 65 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 88 optimal weight: 20.0000 chunk 128 optimal weight: 5.9990 overall best weight: 1.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LR 7 GLN ** LX 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 11 GLN ** Lh 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 HIS A 170 HIS ** A 197 HIS ** 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 = 0.5366 r_free = 0.5366 target = 0.294830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.5304 r_free = 0.5304 target = 0.288697 restraints weight = 51534.733| |-----------------------------------------------------------------------------| r_work (start): 0.5298 rms_B_bonded: 0.95 r_work: 0.5252 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.5209 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.5209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1344 moved from start: 0.6566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 15947 Z= 0.121 Angle : 0.591 9.946 23084 Z= 0.298 Chirality : 0.035 0.203 2851 Planarity : 0.005 0.038 1715 Dihedral : 22.770 157.301 6221 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.24 % Allowed : 13.41 % Favored : 83.35 % 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: -0.06 (0.26), residues: 979 helix: 0.59 (0.25), residues: 423 sheet: -0.23 (0.50), residues: 107 loop : -0.50 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPLR 95 HIS 0.007 0.001 HIS A 136 PHE 0.013 0.002 PHELY 19 TYR 0.019 0.001 TYRLY 73 ARG 0.015 0.001 ARGLY 74 Details of bonding type rmsd hydrogen bonds : bond 0.06881 ( 600) hydrogen bonds : angle 4.18872 ( 1462) covalent geometry : bond 0.00244 (15947) covalent geometry : angle 0.59062 (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 67 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 39 time to evaluate : 1.215 Fit side-chains REVERT: LR 7 GLN cc_start: 0.2502 (OUTLIER) cc_final: 0.2301 (tp40) REVERT: LR 89 MET cc_start: 0.1918 (tpp) cc_final: 0.0857 (ppp) REVERT: LR 144 ARG cc_start: 0.3120 (mtm-85) cc_final: 0.1424 (mtp-110) REVERT: LX 124 ASN cc_start: 0.5428 (p0) cc_final: 0.4439 (t0) REVERT: LY 11 ARG cc_start: 0.4939 (ttt90) cc_final: 0.2450 (ptt180) REVERT: LY 86 ARG cc_start: 0.0880 (ttm-80) cc_final: -0.0261 (ttp-170) REVERT: Lh 83 LEU cc_start: 0.2271 (OUTLIER) cc_final: 0.1452 (tp) REVERT: A 114 GLU cc_start: -0.0665 (OUTLIER) cc_final: -0.1116 (mm-30) REVERT: A 312 ILE cc_start: -0.1520 (OUTLIER) cc_final: -0.1946 (tt) outliers start: 28 outliers final: 11 residues processed: 61 average time/residue: 1.1281 time to fit residues: 77.9013 Evaluate side-chains 49 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 34 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LR residue 7 GLN 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 LY residue 78 VAL Chi-restraints excluded: chain Lh residue 83 LEU 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 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: 0.0470 chunk 103 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 81 optimal weight: 30.0000 chunk 104 optimal weight: 9.9990 chunk 75 optimal weight: 30.0000 chunk 44 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 79 optimal weight: 40.0000 overall best weight: 0.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LR 7 GLN ** LX 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.5368 r_free = 0.5368 target = 0.295186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.5309 r_free = 0.5309 target = 0.289063 restraints weight = 52324.057| |-----------------------------------------------------------------------------| r_work (start): 0.5302 rms_B_bonded: 0.97 r_work: 0.5256 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.5211 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.5211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1293 moved from start: 0.6816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15947 Z= 0.099 Angle : 0.535 12.254 23084 Z= 0.268 Chirality : 0.033 0.192 2851 Planarity : 0.004 0.041 1715 Dihedral : 22.624 156.637 6221 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.89 % Allowed : 14.45 % Favored : 82.66 % 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: 0.26 (0.27), residues: 979 helix: 0.85 (0.25), residues: 430 sheet: -0.14 (0.51), residues: 107 loop : -0.31 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPLR 95 HIS 0.010 0.001 HIS A 221 PHE 0.011 0.001 PHE A 424 TYR 0.015 0.001 TYRLY 73 ARG 0.004 0.000 ARGLR 42 Details of bonding type rmsd hydrogen bonds : bond 0.06168 ( 600) hydrogen bonds : angle 3.89569 ( 1462) covalent geometry : bond 0.00193 (15947) covalent geometry : angle 0.53488 (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 60 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 35 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: LR 89 MET cc_start: 0.1650 (tpp) cc_final: 0.0620 (ppp) REVERT: LR 144 ARG cc_start: 0.3018 (mtm-85) cc_final: 0.1378 (mtp-110) REVERT: LX 124 ASN cc_start: 0.5346 (p0) cc_final: 0.4357 (t0) REVERT: LX 126 LEU cc_start: 0.3599 (OUTLIER) cc_final: 0.3367 (tt) REVERT: LY 11 ARG cc_start: 0.4769 (ttt90) cc_final: 0.2341 (pmm150) REVERT: LY 86 ARG cc_start: 0.0862 (ttm-80) cc_final: -0.0130 (ttp-170) REVERT: Lh 83 LEU cc_start: 0.2177 (OUTLIER) cc_final: 0.1248 (tp) REVERT: A 114 GLU cc_start: -0.1046 (OUTLIER) cc_final: -0.1310 (mm-30) REVERT: A 312 ILE cc_start: -0.1767 (OUTLIER) cc_final: -0.2129 (tt) outliers start: 25 outliers final: 13 residues processed: 56 average time/residue: 0.9611 time to fit residues: 61.6930 Evaluate side-chains 49 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 32 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LR residue 17 CYS 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 71 SER Chi-restraints excluded: chain LY residue 77 TYR Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain Lh residue 83 LEU 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 275 GLU 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: 0.3980 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** LX 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 33 GLN ** Lh 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 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 = 0.5362 r_free = 0.5362 target = 0.294480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.5300 r_free = 0.5300 target = 0.288023 restraints weight = 52292.147| |-----------------------------------------------------------------------------| r_work (start): 0.5291 rms_B_bonded: 1.01 r_work: 0.5258 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.5212 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.5212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1410 moved from start: 0.7481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15947 Z= 0.109 Angle : 0.560 9.700 23084 Z= 0.281 Chirality : 0.034 0.189 2851 Planarity : 0.004 0.040 1715 Dihedral : 22.602 159.589 6221 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.35 % Allowed : 14.68 % Favored : 81.97 % 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: 0.32 (0.27), residues: 979 helix: 0.96 (0.25), residues: 429 sheet: -0.20 (0.51), residues: 107 loop : -0.32 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRPLR 95 HIS 0.007 0.001 HIS A 348 PHE 0.019 0.002 PHE A 332 TYR 0.016 0.001 TYRLY 73 ARG 0.004 0.000 ARGLY 74 Details of bonding type rmsd hydrogen bonds : bond 0.06384 ( 600) hydrogen bonds : angle 3.90823 ( 1462) covalent geometry : bond 0.00216 (15947) covalent geometry : angle 0.55976 (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 61 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 32 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: LR 89 MET cc_start: 0.1678 (tpp) cc_final: 0.0636 (ppp) REVERT: LR 144 ARG cc_start: 0.3141 (mtm-85) cc_final: 0.1570 (mtp-110) REVERT: LX 90 GLU cc_start: 0.2218 (OUTLIER) cc_final: 0.1640 (tm-30) REVERT: LX 126 LEU cc_start: 0.3620 (OUTLIER) cc_final: 0.3390 (tt) REVERT: LY 11 ARG cc_start: 0.4619 (ttt90) cc_final: 0.2296 (mtt90) REVERT: Lh 83 LEU cc_start: 0.2425 (OUTLIER) cc_final: 0.1483 (tp) REVERT: Lk 18 LYS cc_start: 0.0768 (OUTLIER) cc_final: 0.0331 (tptt) REVERT: Lk 31 THR cc_start: 0.0645 (OUTLIER) cc_final: 0.0175 (p) REVERT: A 114 GLU cc_start: -0.0820 (OUTLIER) cc_final: -0.1183 (mm-30) REVERT: A 312 ILE cc_start: -0.1828 (OUTLIER) cc_final: -0.2138 (tt) outliers start: 29 outliers final: 12 residues processed: 57 average time/residue: 1.3161 time to fit residues: 87.5805 Evaluate side-chains 49 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 30 time to evaluate : 1.907 ------------------------------------------------------------------------------- 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 90 GLU Chi-restraints excluded: chain LX residue 126 LEU Chi-restraints excluded: chain LY residue 49 ILE Chi-restraints excluded: chain LY residue 77 TYR Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain Lh residue 83 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 75 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 275 GLU 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=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: 5.9990 chunk 26 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 4 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 70 optimal weight: 20.0000 chunk 1 optimal weight: 0.6980 chunk 113 optimal weight: 40.0000 chunk 118 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LX 93 ASN ** LX 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** A 221 HIS A 236 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5357 r_free = 0.5357 target = 0.293646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5305 r_free = 0.5305 target = 0.288256 restraints weight = 52806.443| |-----------------------------------------------------------------------------| r_work (start): 0.5298 rms_B_bonded: 0.87 r_work: 0.5264 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.5222 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.5222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1603 moved from start: 0.8752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15947 Z= 0.126 Angle : 0.609 9.408 23084 Z= 0.306 Chirality : 0.036 0.185 2851 Planarity : 0.005 0.047 1715 Dihedral : 22.757 159.803 6221 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.47 % Allowed : 14.68 % Favored : 81.85 % 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: 0.07 (0.27), residues: 979 helix: 0.85 (0.26), residues: 418 sheet: -0.21 (0.55), residues: 97 loop : -0.56 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRPLR 95 HIS 0.011 0.002 HIS A 348 PHE 0.016 0.002 PHE A 332 TYR 0.018 0.002 TYRLY 73 ARG 0.007 0.001 ARGLX 128 Details of bonding type rmsd hydrogen bonds : bond 0.06728 ( 600) hydrogen bonds : angle 4.13431 ( 1462) covalent geometry : bond 0.00247 (15947) covalent geometry : angle 0.60891 (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 64 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 34 time to evaluate : 2.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: LR 23 TRP cc_start: 0.1376 (t-100) cc_final: 0.0172 (t-100) REVERT: LR 144 ARG cc_start: 0.3643 (mtm-85) cc_final: 0.1708 (mtp-110) REVERT: LX 90 GLU cc_start: 0.2199 (OUTLIER) cc_final: 0.1796 (tm-30) REVERT: LX 126 LEU cc_start: 0.3803 (OUTLIER) cc_final: 0.3494 (tt) REVERT: LY 11 ARG cc_start: 0.4584 (ttt90) cc_final: 0.2120 (pmm150) REVERT: Lh 83 LEU cc_start: 0.3511 (OUTLIER) cc_final: 0.2440 (tp) REVERT: Lk 18 LYS cc_start: 0.0853 (OUTLIER) cc_final: 0.0198 (tptt) REVERT: A 75 THR cc_start: 0.2299 (OUTLIER) cc_final: 0.1965 (m) REVERT: A 114 GLU cc_start: -0.0733 (OUTLIER) cc_final: -0.1250 (mm-30) REVERT: A 121 MET cc_start: 0.3695 (ppp) cc_final: 0.3371 (ptm) REVERT: A 304 ILE cc_start: 0.3425 (tt) cc_final: 0.3211 (tt) REVERT: A 316 HIS cc_start: 0.4609 (OUTLIER) cc_final: 0.4299 (t-90) outliers start: 30 outliers final: 13 residues processed: 59 average time/residue: 1.4617 time to fit residues: 98.2903 Evaluate side-chains 51 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 31 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LR residue 17 CYS Chi-restraints excluded: chain LX residue 90 GLU Chi-restraints excluded: chain LX residue 126 LEU Chi-restraints excluded: chain LY residue 19 PHE Chi-restraints excluded: chain LY residue 71 SER Chi-restraints excluded: chain LY residue 77 TYR Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain Lh residue 83 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 75 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 369 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 26 optimal weight: 5.9990 chunk 117 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 40.0000 chunk 37 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 1 optimal weight: 0.0980 chunk 97 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LR 3 ASN LX 93 ASN ** LX 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lh 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5366 r_free = 0.5366 target = 0.294862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.5315 r_free = 0.5315 target = 0.289528 restraints weight = 52026.087| |-----------------------------------------------------------------------------| r_work (start): 0.5308 rms_B_bonded: 0.90 r_work: 0.5273 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.5231 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.5231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1372 moved from start: 0.8787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15947 Z= 0.092 Angle : 0.517 10.175 23084 Z= 0.255 Chirality : 0.032 0.187 2851 Planarity : 0.004 0.040 1715 Dihedral : 22.455 158.150 6221 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.31 % Allowed : 15.95 % Favored : 81.73 % 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: 0.43 (0.27), residues: 979 helix: 1.21 (0.26), residues: 430 sheet: -0.06 (0.56), residues: 97 loop : -0.48 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPLR 23 HIS 0.005 0.001 HISLh 50 PHE 0.018 0.001 PHE A 332 TYR 0.010 0.001 TYRLY 73 ARG 0.004 0.000 ARGLX 128 Details of bonding type rmsd hydrogen bonds : bond 0.05854 ( 600) hydrogen bonds : angle 3.69594 ( 1462) covalent geometry : bond 0.00181 (15947) covalent geometry : angle 0.51707 (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 56 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 36 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: LR 144 ARG cc_start: 0.2995 (mtm-85) cc_final: 0.1452 (mtp-110) REVERT: LX 126 LEU cc_start: 0.3697 (OUTLIER) cc_final: 0.3436 (tt) REVERT: LY 11 ARG cc_start: 0.4559 (ttt90) cc_final: 0.2077 (mtp-110) REVERT: Lk 18 LYS cc_start: 0.0609 (OUTLIER) cc_final: 0.0003 (tptt) REVERT: Lk 31 THR cc_start: 0.0467 (OUTLIER) cc_final: 0.0044 (p) REVERT: A 75 THR cc_start: 0.2106 (OUTLIER) cc_final: 0.1744 (m) REVERT: A 121 MET cc_start: 0.3761 (ppp) cc_final: 0.3509 (ptm) REVERT: A 304 ILE cc_start: 0.3553 (tt) cc_final: 0.3296 (tt) outliers start: 20 outliers final: 8 residues processed: 54 average time/residue: 1.2061 time to fit residues: 74.6336 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 : 1.203 ------------------------------------------------------------------------------- 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 126 LEU Chi-restraints excluded: chain LY residue 71 SER Chi-restraints excluded: chain LY residue 73 TYR Chi-restraints excluded: chain LY residue 77 TYR Chi-restraints excluded: chain Lk residue 18 LYS Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 339 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 105 optimal weight: 4.9990 chunk 52 optimal weight: 0.0470 chunk 103 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 93 optimal weight: 0.0030 chunk 9 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 128 optimal weight: 20.0000 chunk 25 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 overall best weight: 2.1692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** LX 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.5357 r_free = 0.5357 target = 0.293496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5311 r_free = 0.5311 target = 0.288565 restraints weight = 52418.408| |-----------------------------------------------------------------------------| r_work (start): 0.5306 rms_B_bonded: 0.79 r_work: 0.5271 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.5232 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.5232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1638 moved from start: 0.9409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 15947 Z= 0.123 Angle : 0.599 10.381 23084 Z= 0.299 Chirality : 0.035 0.189 2851 Planarity : 0.005 0.042 1715 Dihedral : 22.695 161.790 6221 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.97 % Allowed : 16.18 % Favored : 81.85 % 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: 0.17 (0.27), residues: 979 helix: 0.97 (0.26), residues: 429 sheet: -0.30 (0.54), residues: 97 loop : -0.55 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPLR 95 HIS 0.011 0.002 HIS A 221 PHE 0.016 0.002 PHELY 19 TYR 0.014 0.001 TYRLY 73 ARG 0.005 0.001 ARG A 225 Details of bonding type rmsd hydrogen bonds : bond 0.06710 ( 600) hydrogen bonds : angle 4.01085 ( 1462) covalent geometry : bond 0.00243 (15947) covalent geometry : angle 0.59916 (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 51 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 34 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: LR 23 TRP cc_start: 0.1554 (t-100) cc_final: 0.0342 (t-100) REVERT: LR 144 ARG cc_start: 0.4049 (mtm-85) cc_final: 0.2132 (mtp-110) REVERT: LX 126 LEU cc_start: 0.3691 (OUTLIER) cc_final: 0.3328 (tt) REVERT: LY 11 ARG cc_start: 0.4296 (ttt90) cc_final: 0.2488 (mmt90) REVERT: Lh 83 LEU cc_start: 0.3637 (OUTLIER) cc_final: 0.2575 (tp) REVERT: Lk 18 LYS cc_start: 0.0873 (OUTLIER) cc_final: 0.0082 (tptt) REVERT: A 121 MET cc_start: 0.3638 (ppp) cc_final: 0.3359 (ptm) REVERT: A 330 GLU cc_start: -0.1328 (OUTLIER) cc_final: -0.1566 (mt-10) outliers start: 17 outliers final: 10 residues processed: 48 average time/residue: 1.3760 time to fit residues: 75.1468 Evaluate side-chains 45 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 31 time to evaluate : 1.396 ------------------------------------------------------------------------------- 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 126 LEU Chi-restraints excluded: chain LY residue 73 TYR Chi-restraints excluded: chain LY residue 77 TYR Chi-restraints excluded: chain LY residue 98 ILE Chi-restraints excluded: chain Lh residue 83 LEU Chi-restraints excluded: chain Lk residue 18 LYS Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 339 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 127 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 116 optimal weight: 0.0570 chunk 1 optimal weight: 0.2980 chunk 32 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 102 optimal weight: 0.0970 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 overall best weight: 1.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** LX 124 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 = 0.5357 r_free = 0.5357 target = 0.293583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.5309 r_free = 0.5309 target = 0.288260 restraints weight = 52500.082| |-----------------------------------------------------------------------------| r_work (start): 0.5304 rms_B_bonded: 0.95 r_work: 0.5266 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.5222 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.5222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1631 moved from start: 0.9758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15947 Z= 0.117 Angle : 0.582 11.406 23084 Z= 0.289 Chirality : 0.034 0.248 2851 Planarity : 0.005 0.051 1715 Dihedral : 22.652 159.614 6221 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.97 % Allowed : 16.30 % Favored : 81.73 % 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: 0.19 (0.27), residues: 979 helix: 0.98 (0.26), residues: 428 sheet: -0.26 (0.54), residues: 97 loop : -0.55 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRPLR 95 HIS 0.012 0.002 HISLY 80 PHE 0.016 0.002 PHELY 19 TYR 0.012 0.001 TYRLY 73 ARG 0.006 0.000 ARGLX 128 Details of bonding type rmsd hydrogen bonds : bond 0.06393 ( 600) hydrogen bonds : angle 3.92882 ( 1462) covalent geometry : bond 0.00234 (15947) covalent geometry : angle 0.58210 (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 48 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 31 time to evaluate : 2.685 Fit side-chains revert: symmetry clash REVERT: LX 126 LEU cc_start: 0.3769 (OUTLIER) cc_final: 0.3349 (tt) REVERT: LY 11 ARG cc_start: 0.4283 (ttt90) cc_final: 0.2070 (mtp-110) REVERT: Lh 83 LEU cc_start: 0.3657 (OUTLIER) cc_final: 0.2366 (tp) REVERT: Lk 18 LYS cc_start: 0.1244 (OUTLIER) cc_final: 0.0261 (tptt) REVERT: A 121 MET cc_start: 0.4104 (ppp) cc_final: 0.3825 (ptm) REVERT: A 316 HIS cc_start: 0.4624 (OUTLIER) cc_final: 0.4403 (t-90) REVERT: A 330 GLU cc_start: -0.1272 (OUTLIER) cc_final: -0.1523 (mt-10) outliers start: 17 outliers final: 8 residues processed: 45 average time/residue: 1.3253 time to fit residues: 67.9274 Evaluate side-chains 43 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 30 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 126 LEU Chi-restraints excluded: chain LY residue 73 TYR Chi-restraints excluded: chain LY residue 77 TYR Chi-restraints excluded: chain Lh residue 83 LEU Chi-restraints excluded: chain Lk residue 18 LYS Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 330 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 8 optimal weight: 0.0770 chunk 28 optimal weight: 0.8980 chunk 120 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 89 optimal weight: 20.0000 chunk 86 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 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: 3.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** LR 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 124 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 = 0.5344 r_free = 0.5344 target = 0.291780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5303 r_free = 0.5303 target = 0.286618 restraints weight = 52449.883| |-----------------------------------------------------------------------------| r_work (start): 0.5295 rms_B_bonded: 0.87 r_work: 0.5258 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.5217 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.5217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1980 moved from start: 1.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15947 Z= 0.179 Angle : 0.778 11.497 23084 Z= 0.392 Chirality : 0.042 0.236 2851 Planarity : 0.006 0.081 1715 Dihedral : 23.306 161.726 6221 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.31 % Allowed : 16.42 % Favored : 81.27 % 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: -0.47 (0.27), residues: 979 helix: 0.39 (0.25), residues: 421 sheet: -0.63 (0.53), residues: 95 loop : -0.81 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRPLR 95 HIS 0.010 0.002 HIS A 221 PHE 0.028 0.002 PHELY 19 TYR 0.020 0.002 TYRLh 121 ARG 0.016 0.001 ARGLR 38 Details of bonding type rmsd hydrogen bonds : bond 0.08337 ( 600) hydrogen bonds : angle 4.67058 ( 1462) covalent geometry : bond 0.00352 (15947) covalent geometry : angle 0.77843 (23084) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12319.25 seconds wall clock time: 218 minutes 58.42 seconds (13138.42 seconds total)