Starting phenix.real_space_refine on Thu Feb 5 03:44:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lzw_63529/02_2026/9lzw_63529.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lzw_63529/02_2026/9lzw_63529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lzw_63529/02_2026/9lzw_63529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lzw_63529/02_2026/9lzw_63529.map" model { file = "/net/cci-nas-00/data/ceres_data/9lzw_63529/02_2026/9lzw_63529.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lzw_63529/02_2026/9lzw_63529.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.082 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: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 9335 2.51 5 N 2416 2.21 5 O 2837 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14654 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2381 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 288} Chain breaks: 1 Chain: "D" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 107 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "B" Number of atoms: 2292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2292 Classifications: {'peptide': 306} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 279} Chain: "E" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 107 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "C" Number of atoms: 2312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2312 Classifications: {'peptide': 309} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 282} Chain: "F" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 130 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "G" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2364 Classifications: {'peptide': 315} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 286} Chain breaks: 1 Chain: "J" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 115 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "H" Number of atoms: 2284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2284 Classifications: {'peptide': 305} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 278} Chain: "K" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 115 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "I" Number of atoms: 2312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2312 Classifications: {'peptide': 309} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 282} Chain: "L" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 135 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Time building chain proxies: 3.67, per 1000 atoms: 0.25 Number of scatterers: 14654 At special positions: 0 Unit cell: (115.5, 145.2, 107.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 2837 8.00 N 2416 7.00 C 9335 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS A 318 " distance=2.04 Simple disulfide: pdb=" SG CYS B 69 " - pdb=" SG CYS B 318 " distance=2.04 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 318 " distance=2.04 Simple disulfide: pdb=" SG CYS G 69 " - pdb=" SG CYS G 318 " distance=2.03 Simple disulfide: pdb=" SG CYS H 69 " - pdb=" SG CYS H 318 " distance=2.04 Simple disulfide: pdb=" SG CYS I 69 " - pdb=" SG CYS I 318 " distance=2.03 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: 0.90 Conformation dependent library (CDL) restraints added in 506.5 milliseconds 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3614 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 0 sheets defined 17.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 61 through 71 Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 220 through 224 removed outlier: 4.650A pdb=" N LEU A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 220 through 224' Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 269 through 272 No H-bonds generated for 'chain 'A' and resid 269 through 272' Processing helix chain 'A' and resid 329 through 332 No H-bonds generated for 'chain 'A' and resid 329 through 332' Processing helix chain 'A' and resid 341 through 353 Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'B' and resid 61 through 71 Processing helix chain 'B' and resid 148 through 152 Processing helix chain 'B' and resid 220 through 224 removed outlier: 4.909A pdb=" N LEU B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 220 through 224' Processing helix chain 'B' and resid 235 through 237 No H-bonds generated for 'chain 'B' and resid 235 through 237' Processing helix chain 'B' and resid 269 through 272 No H-bonds generated for 'chain 'B' and resid 269 through 272' Processing helix chain 'B' and resid 328 through 332 removed outlier: 5.168A pdb=" N PHE B 332 " --> pdb=" O MET B 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 328 through 332' Processing helix chain 'B' and resid 341 through 353 Processing helix chain 'E' and resid 366 through 377 Processing helix chain 'C' and resid 61 through 71 Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 148 through 152 Processing helix chain 'C' and resid 220 through 224 removed outlier: 4.935A pdb=" N LEU C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 220 through 224' Processing helix chain 'C' and resid 235 through 237 No H-bonds generated for 'chain 'C' and resid 235 through 237' Processing helix chain 'C' and resid 328 through 332 removed outlier: 4.977A pdb=" N PHE C 332 " --> pdb=" O MET C 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 328 through 332' Processing helix chain 'C' and resid 341 through 353 removed outlier: 3.643A pdb=" N ARG C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 362 No H-bonds generated for 'chain 'C' and resid 360 through 362' Processing helix chain 'F' and resid 366 through 380 removed outlier: 3.793A pdb=" N ALA F 380 " --> pdb=" O SER F 376 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 71 Processing helix chain 'G' and resid 148 through 152 Processing helix chain 'G' and resid 220 through 224 removed outlier: 4.570A pdb=" N LEU G 224 " --> pdb=" O LEU G 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 220 through 224' Processing helix chain 'G' and resid 235 through 237 No H-bonds generated for 'chain 'G' and resid 235 through 237' Processing helix chain 'G' and resid 269 through 272 No H-bonds generated for 'chain 'G' and resid 269 through 272' Processing helix chain 'G' and resid 329 through 332 No H-bonds generated for 'chain 'G' and resid 329 through 332' Processing helix chain 'G' and resid 341 through 353 Processing helix chain 'G' and resid 360 through 362 No H-bonds generated for 'chain 'G' and resid 360 through 362' Processing helix chain 'H' and resid 61 through 71 Processing helix chain 'H' and resid 148 through 152 Processing helix chain 'H' and resid 220 through 224 removed outlier: 4.466A pdb=" N LEU H 224 " --> pdb=" O LEU H 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 220 through 224' Processing helix chain 'H' and resid 235 through 237 No H-bonds generated for 'chain 'H' and resid 235 through 237' Processing helix chain 'H' and resid 269 through 272 No H-bonds generated for 'chain 'H' and resid 269 through 272' Processing helix chain 'H' and resid 328 through 332 removed outlier: 5.427A pdb=" N PHE H 332 " --> pdb=" O MET H 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 328 through 332' Processing helix chain 'H' and resid 341 through 353 Processing helix chain 'K' and resid 366 through 377 Processing helix chain 'I' and resid 61 through 71 Processing helix chain 'I' and resid 73 through 75 No H-bonds generated for 'chain 'I' and resid 73 through 75' Processing helix chain 'I' and resid 148 through 152 Processing helix chain 'I' and resid 220 through 224 removed outlier: 4.740A pdb=" N LEU I 224 " --> pdb=" O LEU I 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 220 through 224' Processing helix chain 'I' and resid 235 through 237 No H-bonds generated for 'chain 'I' and resid 235 through 237' Processing helix chain 'I' and resid 328 through 332 removed outlier: 4.860A pdb=" N PHE I 332 " --> pdb=" O MET I 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 328 through 332' Processing helix chain 'I' and resid 341 through 353 Processing helix chain 'I' and resid 360 through 362 No H-bonds generated for 'chain 'I' and resid 360 through 362' Processing helix chain 'L' and resid 366 through 380 138 hydrogen bonds defined for protein. 414 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.54 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4738 1.35 - 1.47: 3679 1.47 - 1.59: 6511 1.59 - 1.71: 0 1.71 - 1.84: 108 Bond restraints: 15036 Sorted by residual: bond pdb=" C PRO G 73 " pdb=" N PRO G 74 " ideal model delta sigma weight residual 1.334 1.361 -0.028 8.40e-03 1.42e+04 1.09e+01 bond pdb=" C PRO B 73 " pdb=" N PRO B 74 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.28e+00 bond pdb=" CB ASP G 75 " pdb=" CG ASP G 75 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.14e+00 bond pdb=" CA ASP G 75 " pdb=" CB ASP G 75 " ideal model delta sigma weight residual 1.528 1.541 -0.014 1.35e-02 5.49e+03 1.01e+00 bond pdb=" CB PRO B 80 " pdb=" CG PRO B 80 " ideal model delta sigma weight residual 1.492 1.536 -0.044 5.00e-02 4.00e+02 7.87e-01 ... (remaining 15031 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 20298 1.74 - 3.49: 228 3.49 - 5.23: 17 5.23 - 6.97: 6 6.97 - 8.71: 1 Bond angle restraints: 20550 Sorted by residual: angle pdb=" C PRO A 323 " pdb=" N ASN A 324 " pdb=" CA ASN A 324 " ideal model delta sigma weight residual 121.27 129.98 -8.71 3.40e+00 8.65e-02 6.57e+00 angle pdb=" CA ASP G 75 " pdb=" CB ASP G 75 " pdb=" CG ASP G 75 " ideal model delta sigma weight residual 112.60 114.74 -2.14 1.00e+00 1.00e+00 4.59e+00 angle pdb=" N ILE C 236 " pdb=" CA ILE C 236 " pdb=" C ILE C 236 " ideal model delta sigma weight residual 109.34 113.47 -4.13 2.08e+00 2.31e-01 3.94e+00 angle pdb=" CB MET A 328 " pdb=" CG MET A 328 " pdb=" SD MET A 328 " ideal model delta sigma weight residual 112.70 118.59 -5.89 3.00e+00 1.11e-01 3.85e+00 angle pdb=" CA PRO A 74 " pdb=" N PRO A 74 " pdb=" CD PRO A 74 " ideal model delta sigma weight residual 112.00 109.27 2.73 1.40e+00 5.10e-01 3.80e+00 ... (remaining 20545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 7895 17.98 - 35.96: 807 35.96 - 53.93: 200 53.93 - 71.91: 48 71.91 - 89.89: 9 Dihedral angle restraints: 8959 sinusoidal: 3366 harmonic: 5593 Sorted by residual: dihedral pdb=" CA PRO G 73 " pdb=" C PRO G 73 " pdb=" N PRO G 74 " pdb=" CA PRO G 74 " ideal model delta harmonic sigma weight residual 180.00 -159.04 -20.96 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA ASP B 221 " pdb=" CB ASP B 221 " pdb=" CG ASP B 221 " pdb=" OD1 ASP B 221 " ideal model delta sinusoidal sigma weight residual -30.00 -88.96 58.96 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CB CYS C 69 " pdb=" SG CYS C 69 " pdb=" SG CYS C 318 " pdb=" CB CYS C 318 " ideal model delta sinusoidal sigma weight residual 93.00 121.43 -28.43 1 1.00e+01 1.00e-02 1.16e+01 ... (remaining 8956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1450 0.029 - 0.058: 526 0.058 - 0.087: 156 0.087 - 0.116: 176 0.116 - 0.146: 35 Chirality restraints: 2343 Sorted by residual: chirality pdb=" CA VAL C 128 " pdb=" N VAL C 128 " pdb=" C VAL C 128 " pdb=" CB VAL C 128 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CA ILE A 84 " pdb=" N ILE A 84 " pdb=" C ILE A 84 " pdb=" CB ILE A 84 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE G 312 " pdb=" N ILE G 312 " pdb=" C ILE G 312 " pdb=" CB ILE G 312 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.07e-01 ... (remaining 2340 not shown) Planarity restraints: 2687 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 72 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.76e+00 pdb=" N PRO C 73 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 73 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 73 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA I 72 " 0.035 5.00e-02 4.00e+02 5.31e-02 4.52e+00 pdb=" N PRO I 73 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO I 73 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO I 73 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA H 72 " -0.035 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PRO H 73 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO H 73 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 73 " -0.029 5.00e-02 4.00e+02 ... (remaining 2684 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2472 2.77 - 3.30: 12791 3.30 - 3.83: 22889 3.83 - 4.37: 27251 4.37 - 4.90: 49172 Nonbonded interactions: 114575 Sorted by model distance: nonbonded pdb=" O GLN H 260 " pdb=" OG SER H 280 " model vdw 2.237 3.040 nonbonded pdb=" O GLN I 260 " pdb=" OG SER I 280 " model vdw 2.251 3.040 nonbonded pdb=" O GLN B 260 " pdb=" OG SER B 280 " model vdw 2.256 3.040 nonbonded pdb=" O GLN C 260 " pdb=" OG SER C 280 " model vdw 2.262 3.040 nonbonded pdb=" O PRO I 129 " pdb=" OG1 THR I 132 " model vdw 2.292 3.040 ... (remaining 114570 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 58 through 362) selection = (chain 'B' and resid 58 through 362) selection = (chain 'C' and resid 58 through 362) selection = (chain 'G' and resid 58 through 362) selection = chain 'H' selection = (chain 'I' and resid 58 through 362) } ncs_group { reference = chain 'D' selection = chain 'E' selection = (chain 'J' and resid 365 through 377) selection = (chain 'K' and resid 365 through 377) } ncs_group { reference = chain 'F' selection = (chain 'L' and resid 365 through 381) } 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: 7.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.810 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.020 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 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 : 0.002 0.044 15042 Z= 0.096 Angle : 0.467 8.715 20562 Z= 0.240 Chirality : 0.043 0.146 2343 Planarity : 0.005 0.055 2687 Dihedral : 15.823 89.890 5327 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.35 % Allowed : 20.44 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.20), residues: 1923 helix: 0.38 (0.31), residues: 335 sheet: 0.46 (0.21), residues: 648 loop : -0.18 (0.22), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 352 TYR 0.010 0.001 TYR C 321 PHE 0.010 0.001 PHE I 231 TRP 0.011 0.001 TRP L 367 HIS 0.001 0.000 HIS I 215 Details of bonding type rmsd covalent geometry : bond 0.00213 (15036) covalent geometry : angle 0.46525 (20550) SS BOND : bond 0.00618 ( 6) SS BOND : angle 1.87402 ( 12) hydrogen bonds : bond 0.03092 ( 138) hydrogen bonds : angle 3.42402 ( 414) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 GLU cc_start: 0.8929 (tp30) cc_final: 0.8724 (tp30) REVERT: G 75 ASP cc_start: 0.8094 (t70) cc_final: 0.7419 (m-30) REVERT: G 196 LYS cc_start: 0.8589 (mttp) cc_final: 0.8294 (mttp) REVERT: H 352 ARG cc_start: 0.8725 (ttp80) cc_final: 0.8305 (ttp-170) outliers start: 22 outliers final: 17 residues processed: 147 average time/residue: 0.1147 time to fit residues: 25.0402 Evaluate side-chains 141 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 318 CYS Chi-restraints excluded: chain H residue 318 CYS Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 318 CYS Chi-restraints excluded: chain I residue 363 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.0060 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 20.0000 overall best weight: 5.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN B 61 GLN G 183 GLN G 363 ASN I 334 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.093819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.081074 restraints weight = 23152.974| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 1.62 r_work: 0.2756 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 15042 Z= 0.215 Angle : 0.569 7.108 20562 Z= 0.294 Chirality : 0.048 0.167 2343 Planarity : 0.006 0.052 2687 Dihedral : 5.298 58.143 2063 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.11 % Allowed : 18.35 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.20), residues: 1923 helix: 0.28 (0.31), residues: 324 sheet: 0.50 (0.23), residues: 549 loop : -0.61 (0.20), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 167 TYR 0.010 0.002 TYR C 123 PHE 0.012 0.001 PHE I 231 TRP 0.011 0.002 TRP C 191 HIS 0.003 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00556 (15036) covalent geometry : angle 0.56051 (20550) SS BOND : bond 0.01496 ( 6) SS BOND : angle 4.02037 ( 12) hydrogen bonds : bond 0.05840 ( 138) hydrogen bonds : angle 3.63630 ( 414) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 131 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 233 GLU cc_start: 0.8928 (tp30) cc_final: 0.8573 (mm-30) REVERT: B 101 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8532 (tt0) REVERT: C 242 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8159 (pt0) REVERT: C 256 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9027 (mt) REVERT: G 64 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8229 (tt) REVERT: H 82 LYS cc_start: 0.6901 (OUTLIER) cc_final: 0.6427 (ptpt) REVERT: H 352 ARG cc_start: 0.8785 (ttp80) cc_final: 0.8343 (ttp-170) REVERT: I 182 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.6899 (mmm) REVERT: I 318 CYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7854 (m) outliers start: 67 outliers final: 44 residues processed: 190 average time/residue: 0.1010 time to fit residues: 28.8256 Evaluate side-chains 179 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 128 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 310 SER Chi-restraints excluded: chain G residue 318 CYS Chi-restraints excluded: chain G residue 363 ASN Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 318 CYS Chi-restraints excluded: chain K residue 376 SER Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain I residue 182 MET Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 278 MET Chi-restraints excluded: chain I residue 286 SER Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 295 ASP Chi-restraints excluded: chain I residue 318 CYS Chi-restraints excluded: chain I residue 362 GLN Chi-restraints excluded: chain I residue 363 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 0.2980 chunk 158 optimal weight: 0.9990 chunk 143 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 43 optimal weight: 20.0000 chunk 122 optimal weight: 4.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 GLN G 183 GLN G 363 ASN H 293 ASN I 334 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.096394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.083598 restraints weight = 23282.530| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.63 r_work: 0.2848 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.0594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15042 Z= 0.104 Angle : 0.477 6.114 20562 Z= 0.244 Chirality : 0.045 0.154 2343 Planarity : 0.005 0.053 2687 Dihedral : 4.831 59.177 2053 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.95 % Allowed : 19.09 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.20), residues: 1923 helix: 0.25 (0.31), residues: 337 sheet: 0.40 (0.21), residues: 641 loop : -0.32 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 352 TYR 0.008 0.001 TYR I 321 PHE 0.008 0.001 PHE G 231 TRP 0.007 0.001 TRP I 191 HIS 0.001 0.001 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00267 (15036) covalent geometry : angle 0.47256 (20550) SS BOND : bond 0.00941 ( 6) SS BOND : angle 2.77677 ( 12) hydrogen bonds : bond 0.04032 ( 138) hydrogen bonds : angle 3.44040 ( 414) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 131 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 345 GLN cc_start: 0.8048 (tp40) cc_final: 0.7671 (mm-40) REVERT: B 101 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8477 (tt0) REVERT: C 256 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8987 (mt) REVERT: G 75 ASP cc_start: 0.8083 (t70) cc_final: 0.7349 (m-30) REVERT: H 82 LYS cc_start: 0.6882 (OUTLIER) cc_final: 0.6417 (ptpt) REVERT: H 352 ARG cc_start: 0.8741 (ttp80) cc_final: 0.8313 (ttp-170) REVERT: I 182 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.6883 (mmm) REVERT: I 318 CYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7372 (m) outliers start: 48 outliers final: 34 residues processed: 174 average time/residue: 0.1123 time to fit residues: 28.8369 Evaluate side-chains 163 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 124 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 310 SER Chi-restraints excluded: chain G residue 318 CYS Chi-restraints excluded: chain G residue 329 LEU Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 318 CYS Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain I residue 182 MET Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 295 ASP Chi-restraints excluded: chain I residue 318 CYS Chi-restraints excluded: chain I residue 362 GLN Chi-restraints excluded: chain I residue 363 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 104 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 179 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 138 optimal weight: 0.5980 chunk 19 optimal weight: 10.0000 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 GLN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.092122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.079300 restraints weight = 23605.588| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 1.65 r_work: 0.2715 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 15042 Z= 0.204 Angle : 0.561 7.073 20562 Z= 0.290 Chirality : 0.048 0.167 2343 Planarity : 0.006 0.050 2687 Dihedral : 5.137 57.807 2052 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.17 % Allowed : 18.05 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.20), residues: 1923 helix: 0.19 (0.31), residues: 325 sheet: 0.30 (0.22), residues: 572 loop : -0.72 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 352 TYR 0.011 0.002 TYR B 168 PHE 0.011 0.001 PHE I 231 TRP 0.010 0.001 TRP I 191 HIS 0.003 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00529 (15036) covalent geometry : angle 0.55263 (20550) SS BOND : bond 0.01460 ( 6) SS BOND : angle 3.99337 ( 12) hydrogen bonds : bond 0.05707 ( 138) hydrogen bonds : angle 3.62538 ( 414) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 132 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6824 (OUTLIER) cc_final: 0.6426 (ttp-110) REVERT: A 345 GLN cc_start: 0.8019 (tp40) cc_final: 0.7603 (mm-40) REVERT: B 101 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8502 (tt0) REVERT: E 366 MET cc_start: 0.6837 (tpt) cc_final: 0.6354 (tpt) REVERT: C 242 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8158 (pt0) REVERT: C 256 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9043 (mt) REVERT: H 82 LYS cc_start: 0.6920 (OUTLIER) cc_final: 0.6483 (ptpt) REVERT: H 352 ARG cc_start: 0.8763 (ttp80) cc_final: 0.8306 (ttp-170) REVERT: I 61 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.7781 (mt0) REVERT: I 182 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.6949 (mmm) REVERT: I 318 CYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7917 (m) outliers start: 68 outliers final: 52 residues processed: 194 average time/residue: 0.1091 time to fit residues: 31.5317 Evaluate side-chains 188 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 128 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 310 SER Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 318 CYS Chi-restraints excluded: chain G residue 329 LEU Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 318 CYS Chi-restraints excluded: chain K residue 376 SER Chi-restraints excluded: chain I residue 61 GLN Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain I residue 182 MET Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 295 ASP Chi-restraints excluded: chain I residue 318 CYS Chi-restraints excluded: chain I residue 362 GLN Chi-restraints excluded: chain I residue 363 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 157 optimal weight: 8.9990 chunk 142 optimal weight: 9.9990 chunk 147 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 187 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.091655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.079062 restraints weight = 23560.463| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 1.62 r_work: 0.2676 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 15042 Z= 0.235 Angle : 0.596 7.368 20562 Z= 0.310 Chirality : 0.049 0.173 2343 Planarity : 0.006 0.052 2687 Dihedral : 5.324 56.397 2052 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.73 % Allowed : 17.50 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.19), residues: 1923 helix: -0.05 (0.30), residues: 325 sheet: -0.05 (0.22), residues: 608 loop : -0.79 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 352 TYR 0.011 0.002 TYR C 123 PHE 0.013 0.002 PHE I 231 TRP 0.011 0.002 TRP C 191 HIS 0.003 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00610 (15036) covalent geometry : angle 0.58662 (20550) SS BOND : bond 0.01613 ( 6) SS BOND : angle 4.39738 ( 12) hydrogen bonds : bond 0.06249 ( 138) hydrogen bonds : angle 3.78509 ( 414) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 136 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6953 (OUTLIER) cc_final: 0.6456 (ttp-110) REVERT: A 345 GLN cc_start: 0.7967 (tp40) cc_final: 0.7485 (mm-40) REVERT: B 101 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8490 (tt0) REVERT: E 366 MET cc_start: 0.7375 (tpt) cc_final: 0.6902 (tpt) REVERT: C 242 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8258 (pt0) REVERT: C 256 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9072 (mt) REVERT: F 366 MET cc_start: 0.8933 (tpp) cc_final: 0.8635 (tpp) REVERT: H 82 LYS cc_start: 0.6974 (OUTLIER) cc_final: 0.6503 (ptpt) REVERT: H 99 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8406 (tp) REVERT: H 352 ARG cc_start: 0.8758 (ttp80) cc_final: 0.8292 (ttp-170) REVERT: I 61 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.7775 (mt0) REVERT: I 182 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.6944 (mmm) outliers start: 77 outliers final: 60 residues processed: 206 average time/residue: 0.0998 time to fit residues: 31.0105 Evaluate side-chains 201 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 133 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 310 SER Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 318 CYS Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 183 GLN Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 318 CYS Chi-restraints excluded: chain K residue 376 SER Chi-restraints excluded: chain I residue 61 GLN Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain I residue 182 MET Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 278 MET Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 295 ASP Chi-restraints excluded: chain I residue 363 ASN Chi-restraints excluded: chain L residue 372 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 9 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 37 optimal weight: 0.0470 chunk 40 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 overall best weight: 2.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.094617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.082029 restraints weight = 23178.040| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 1.62 r_work: 0.2724 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15042 Z= 0.125 Angle : 0.502 6.259 20562 Z= 0.257 Chirality : 0.046 0.143 2343 Planarity : 0.005 0.053 2687 Dihedral : 4.908 58.762 2051 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.99 % Allowed : 18.35 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.20), residues: 1923 helix: 0.21 (0.31), residues: 325 sheet: 0.23 (0.22), residues: 589 loop : -0.53 (0.20), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 352 TYR 0.009 0.001 TYR A 145 PHE 0.010 0.001 PHE G 231 TRP 0.008 0.001 TRP C 191 HIS 0.002 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00325 (15036) covalent geometry : angle 0.49595 (20550) SS BOND : bond 0.00989 ( 6) SS BOND : angle 3.12022 ( 12) hydrogen bonds : bond 0.04508 ( 138) hydrogen bonds : angle 3.54720 ( 414) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 138 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6862 (OUTLIER) cc_final: 0.6459 (ttp-110) REVERT: A 345 GLN cc_start: 0.7962 (tp40) cc_final: 0.7541 (mm-40) REVERT: B 101 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8463 (tt0) REVERT: E 366 MET cc_start: 0.7295 (tpt) cc_final: 0.6883 (tpt) REVERT: C 242 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8285 (pt0) REVERT: C 256 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9012 (mt) REVERT: H 82 LYS cc_start: 0.6913 (OUTLIER) cc_final: 0.6478 (ptpt) REVERT: H 352 ARG cc_start: 0.8694 (ttp80) cc_final: 0.8227 (ttp-170) REVERT: I 182 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.6889 (mmm) REVERT: I 318 CYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7639 (m) outliers start: 65 outliers final: 50 residues processed: 196 average time/residue: 0.1104 time to fit residues: 31.9453 Evaluate side-chains 191 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 134 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 310 SER Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 318 CYS Chi-restraints excluded: chain G residue 329 LEU Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 183 GLN Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 318 CYS Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain I residue 182 MET Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 295 ASP Chi-restraints excluded: chain I residue 318 CYS Chi-restraints excluded: chain I residue 362 GLN Chi-restraints excluded: chain I residue 363 ASN Chi-restraints excluded: chain L residue 372 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 56 optimal weight: 10.0000 chunk 129 optimal weight: 0.7980 chunk 91 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 162 optimal weight: 0.9980 chunk 174 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A 242 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.093368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.080686 restraints weight = 23241.442| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 1.63 r_work: 0.2705 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15042 Z= 0.155 Angle : 0.526 6.363 20562 Z= 0.271 Chirality : 0.047 0.151 2343 Planarity : 0.006 0.050 2687 Dihedral : 4.949 59.039 2051 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.17 % Allowed : 18.23 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.20), residues: 1923 helix: 0.20 (0.31), residues: 325 sheet: 0.22 (0.22), residues: 589 loop : -0.57 (0.20), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 352 TYR 0.011 0.002 TYR C 321 PHE 0.008 0.001 PHE I 231 TRP 0.010 0.001 TRP I 191 HIS 0.002 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00402 (15036) covalent geometry : angle 0.51924 (20550) SS BOND : bond 0.01186 ( 6) SS BOND : angle 3.45282 ( 12) hydrogen bonds : bond 0.05048 ( 138) hydrogen bonds : angle 3.50363 ( 414) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 135 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6871 (OUTLIER) cc_final: 0.6250 (ttp-110) REVERT: A 345 GLN cc_start: 0.7989 (tp40) cc_final: 0.7530 (mm-40) REVERT: B 101 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8482 (tt0) REVERT: B 171 MET cc_start: 0.9101 (ptt) cc_final: 0.8874 (ptt) REVERT: E 366 MET cc_start: 0.7478 (tpt) cc_final: 0.7095 (tpt) REVERT: C 242 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8316 (pt0) REVERT: C 256 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9026 (mt) REVERT: H 82 LYS cc_start: 0.6933 (OUTLIER) cc_final: 0.6484 (ptpt) REVERT: H 352 ARG cc_start: 0.8692 (ttp80) cc_final: 0.8207 (ttp-170) REVERT: I 182 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.6888 (mmm) outliers start: 68 outliers final: 58 residues processed: 198 average time/residue: 0.1080 time to fit residues: 31.5073 Evaluate side-chains 197 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 133 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 310 SER Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 318 CYS Chi-restraints excluded: chain G residue 329 LEU Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 183 GLN Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 318 CYS Chi-restraints excluded: chain K residue 376 SER Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain I residue 182 MET Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 278 MET Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 295 ASP Chi-restraints excluded: chain I residue 362 GLN Chi-restraints excluded: chain I residue 363 ASN Chi-restraints excluded: chain L residue 372 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 39 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 62 optimal weight: 20.0000 chunk 102 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 chunk 85 optimal weight: 10.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.092069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.079314 restraints weight = 23629.202| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 1.66 r_work: 0.2712 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15042 Z= 0.143 Angle : 0.518 6.327 20562 Z= 0.266 Chirality : 0.046 0.151 2343 Planarity : 0.005 0.051 2687 Dihedral : 4.929 59.350 2051 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.11 % Allowed : 18.42 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.20), residues: 1923 helix: 0.22 (0.31), residues: 325 sheet: 0.24 (0.22), residues: 589 loop : -0.55 (0.20), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 352 TYR 0.010 0.001 TYR C 321 PHE 0.008 0.001 PHE G 231 TRP 0.009 0.001 TRP I 191 HIS 0.002 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00372 (15036) covalent geometry : angle 0.51216 (20550) SS BOND : bond 0.01130 ( 6) SS BOND : angle 3.32285 ( 12) hydrogen bonds : bond 0.04844 ( 138) hydrogen bonds : angle 3.48481 ( 414) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 137 time to evaluate : 0.583 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6876 (OUTLIER) cc_final: 0.6261 (ttp-110) REVERT: A 345 GLN cc_start: 0.8001 (tp40) cc_final: 0.7557 (mm-40) REVERT: B 101 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8488 (tt0) REVERT: E 366 MET cc_start: 0.7488 (tpt) cc_final: 0.7117 (tpt) REVERT: C 182 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8498 (mtt) REVERT: C 242 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8299 (pt0) REVERT: C 256 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9021 (mt) REVERT: H 82 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6504 (ptpt) REVERT: H 352 ARG cc_start: 0.8712 (ttp80) cc_final: 0.8240 (ttp-170) REVERT: K 368 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7165 (mp0) REVERT: I 182 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.6914 (mmm) REVERT: I 318 CYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7850 (m) outliers start: 67 outliers final: 58 residues processed: 199 average time/residue: 0.1143 time to fit residues: 33.4405 Evaluate side-chains 201 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 135 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 310 SER Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 318 CYS Chi-restraints excluded: chain G residue 329 LEU Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 183 GLN Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 318 CYS Chi-restraints excluded: chain K residue 376 SER Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain I residue 182 MET Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 295 ASP Chi-restraints excluded: chain I residue 318 CYS Chi-restraints excluded: chain I residue 362 GLN Chi-restraints excluded: chain I residue 363 ASN Chi-restraints excluded: chain L residue 372 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 114 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 150 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 chunk 147 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.093779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.081202 restraints weight = 23417.788| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 1.62 r_work: 0.2707 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15042 Z= 0.163 Angle : 0.535 6.358 20562 Z= 0.276 Chirality : 0.047 0.155 2343 Planarity : 0.006 0.051 2687 Dihedral : 4.982 59.121 2051 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.36 % Allowed : 18.35 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.20), residues: 1923 helix: 0.18 (0.31), residues: 325 sheet: 0.10 (0.21), residues: 609 loop : -0.66 (0.20), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 352 TYR 0.010 0.002 TYR C 321 PHE 0.009 0.001 PHE I 231 TRP 0.010 0.001 TRP I 191 HIS 0.002 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00422 (15036) covalent geometry : angle 0.52839 (20550) SS BOND : bond 0.01252 ( 6) SS BOND : angle 3.56360 ( 12) hydrogen bonds : bond 0.05173 ( 138) hydrogen bonds : angle 3.51517 ( 414) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 137 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6790 (OUTLIER) cc_final: 0.6183 (ttp-110) REVERT: A 345 GLN cc_start: 0.7908 (tp40) cc_final: 0.7500 (mm-40) REVERT: A 362 GLN cc_start: 0.7938 (mt0) cc_final: 0.7568 (mt0) REVERT: B 101 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8469 (tt0) REVERT: E 366 MET cc_start: 0.7564 (tpt) cc_final: 0.7183 (tpt) REVERT: C 182 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8511 (mtt) REVERT: C 242 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8296 (pt0) REVERT: C 256 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9032 (mt) REVERT: H 82 LYS cc_start: 0.6970 (OUTLIER) cc_final: 0.6504 (ptpt) REVERT: H 352 ARG cc_start: 0.8695 (ttp80) cc_final: 0.8209 (ttp-170) REVERT: I 182 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.6897 (mmm) REVERT: I 318 CYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7860 (m) outliers start: 71 outliers final: 61 residues processed: 203 average time/residue: 0.1153 time to fit residues: 34.8862 Evaluate side-chains 202 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 133 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 310 SER Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 318 CYS Chi-restraints excluded: chain G residue 329 LEU Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain G residue 363 ASN Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 183 GLN Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 318 CYS Chi-restraints excluded: chain K residue 376 SER Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain I residue 182 MET Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 295 ASP Chi-restraints excluded: chain I residue 318 CYS Chi-restraints excluded: chain I residue 362 GLN Chi-restraints excluded: chain I residue 363 ASN Chi-restraints excluded: chain L residue 372 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 20 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 121 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 1 optimal weight: 0.0970 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.095015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.082388 restraints weight = 23193.467| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 1.62 r_work: 0.2727 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15042 Z= 0.126 Angle : 0.504 7.106 20562 Z= 0.259 Chirality : 0.046 0.142 2343 Planarity : 0.005 0.052 2687 Dihedral : 4.859 59.857 2051 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.17 % Allowed : 18.54 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.20), residues: 1923 helix: 0.29 (0.31), residues: 325 sheet: 0.21 (0.22), residues: 609 loop : -0.47 (0.21), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 352 TYR 0.011 0.001 TYR C 321 PHE 0.009 0.001 PHE G 231 TRP 0.009 0.001 TRP I 191 HIS 0.002 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00328 (15036) covalent geometry : angle 0.49904 (20550) SS BOND : bond 0.00982 ( 6) SS BOND : angle 3.02910 ( 12) hydrogen bonds : bond 0.04451 ( 138) hydrogen bonds : angle 3.42549 ( 414) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 133 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6807 (OUTLIER) cc_final: 0.6204 (ttp-110) REVERT: A 345 GLN cc_start: 0.7875 (tp40) cc_final: 0.7480 (mm-40) REVERT: A 362 GLN cc_start: 0.7933 (mt0) cc_final: 0.7570 (mt0) REVERT: B 101 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8449 (tt0) REVERT: E 366 MET cc_start: 0.7576 (tpt) cc_final: 0.7225 (tpt) REVERT: C 182 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8466 (mtt) REVERT: C 242 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8296 (pt0) REVERT: C 256 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8980 (mt) REVERT: H 82 LYS cc_start: 0.7011 (OUTLIER) cc_final: 0.6524 (ptpt) REVERT: H 352 ARG cc_start: 0.8687 (ttp80) cc_final: 0.8211 (ttp-170) REVERT: I 182 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.6891 (mmm) outliers start: 68 outliers final: 60 residues processed: 195 average time/residue: 0.1163 time to fit residues: 33.5394 Evaluate side-chains 198 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 131 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 310 SER Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 318 CYS Chi-restraints excluded: chain G residue 329 LEU Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain G residue 363 ASN Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 183 GLN Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 318 CYS Chi-restraints excluded: chain K residue 376 SER Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain I residue 182 MET Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 242 GLN Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 295 ASP Chi-restraints excluded: chain I residue 363 ASN Chi-restraints excluded: chain L residue 372 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 169 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 162 optimal weight: 9.9990 chunk 141 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.092041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.079593 restraints weight = 23338.657| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 1.60 r_work: 0.2679 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 15042 Z= 0.249 Angle : 0.615 7.572 20562 Z= 0.319 Chirality : 0.050 0.177 2343 Planarity : 0.006 0.049 2687 Dihedral : 5.265 57.738 2051 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.30 % Allowed : 18.23 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.19), residues: 1923 helix: 0.02 (0.30), residues: 325 sheet: 0.06 (0.22), residues: 568 loop : -0.88 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 352 TYR 0.013 0.002 TYR B 168 PHE 0.015 0.002 PHE I 231 TRP 0.011 0.002 TRP C 191 HIS 0.003 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00644 (15036) covalent geometry : angle 0.60467 (20550) SS BOND : bond 0.01667 ( 6) SS BOND : angle 4.58142 ( 12) hydrogen bonds : bond 0.06466 ( 138) hydrogen bonds : angle 3.69027 ( 414) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2903.83 seconds wall clock time: 50 minutes 32.70 seconds (3032.70 seconds total)