Starting phenix.real_space_refine on Thu Oct 22 23:26:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/26la_80738/10_2026/26la_80738.cif Found real_map, /net/cci-nas-00/data/ceres_data/26la_80738/10_2026/26la_80738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/26la_80738/10_2026/26la_80738.cif" } default_model = "/net/cci-nas-00/data/ceres_data/26la_80738/10_2026/26la_80738.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/26la_80738/10_2026/26la_80738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/26la_80738/10_2026/26la_80738.map" } resolution = 3.33 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= -0.001 sd= 0.055 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 21 5.16 5 C 4147 2.51 5 N 1120 2.21 5 O 1296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6584 Number of models: 1 Model: "" Number of chains: 4 Chain: "Q" Number of atoms: 2161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2161 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 12, 'TRANS': 266} Chain breaks: 3 Chain: "U" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1029 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 9, 'TRANS': 126} Chain: "W" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1029 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 9, 'TRANS': 126} Chain: "X" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2365 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 14, 'TRANS': 289} Time building chain proxies: 1.45, per 1000 atoms: 0.22 Number of scatterers: 6584 At special positions: 0 Unit cell: (120.35, 93.79, 332, 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 21 16.00 O 1296 8.00 N 1120 7.00 C 4147 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 342.1 milliseconds 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1574 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 10 sheets defined 34.2% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'U' and resid 35 through 45 Processing helix chain 'U' and resid 46 through 48 No H-bonds generated for 'chain 'U' and resid 46 through 48' Processing helix chain 'U' and resid 72 through 76 removed outlier: 3.552A pdb=" N ASP U 75 " --> pdb=" O THR U 72 " (cutoff:3.500A) Processing helix chain 'W' and resid 35 through 45 Processing helix chain 'W' and resid 72 through 76 Processing helix chain 'X' and resid 4 through 31 removed outlier: 3.512A pdb=" N GLN X 29 " --> pdb=" O THR X 25 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN X 31 " --> pdb=" O ARG X 27 " (cutoff:3.500A) Processing helix chain 'X' and resid 55 through 60 removed outlier: 3.745A pdb=" N LEU X 60 " --> pdb=" O GLY X 57 " (cutoff:3.500A) Processing helix chain 'X' and resid 64 through 84 Processing helix chain 'X' and resid 87 through 103 Proline residue: X 95 - end of helix Processing helix chain 'X' and resid 104 through 106 No H-bonds generated for 'chain 'X' and resid 104 through 106' Processing helix chain 'X' and resid 115 through 144 Processing helix chain 'X' and resid 150 through 215 removed outlier: 3.754A pdb=" N LEU X 154 " --> pdb=" O PRO X 150 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL X 155 " --> pdb=" O PRO X 151 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET X 188 " --> pdb=" O LYS X 184 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU X 193 " --> pdb=" O LYS X 189 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP X 208 " --> pdb=" O GLN X 204 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE X 209 " --> pdb=" O ALA X 205 " (cutoff:3.500A) Processing helix chain 'X' and resid 217 through 279 removed outlier: 4.467A pdb=" N LEU X 221 " --> pdb=" O PRO X 217 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU X 222 " --> pdb=" O ASN X 218 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR X 235 " --> pdb=" O TYR X 231 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL X 244 " --> pdb=" O ASN X 240 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU X 245 " --> pdb=" O TYR X 241 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET X 260 " --> pdb=" O ALA X 256 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER X 279 " --> pdb=" O ASN X 275 " (cutoff:3.500A) Processing helix chain 'X' and resid 279 through 301 removed outlier: 3.927A pdb=" N LEU X 283 " --> pdb=" O SER X 279 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN X 301 " --> pdb=" O ALA X 297 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'U' and resid 97 through 98 removed outlier: 3.524A pdb=" N ASP U 105 " --> pdb=" O ALA U 97 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY U 162 " --> pdb=" O MET Q 450 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR W 164 " --> pdb=" O TYR Q 457 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'U' and resid 111 through 114 removed outlier: 3.659A pdb=" N ALA U 111 " --> pdb=" O LEU U 159 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY U 162 " --> pdb=" O MET Q 450 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR W 164 " --> pdb=" O TYR Q 457 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Q' and resid 469 through 472 removed outlier: 3.567A pdb=" N GLN Q 469 " --> pdb=" O TYR Q 482 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Q' and resid 489 through 493 removed outlier: 3.804A pdb=" N GLY Q 489 " --> pdb=" O ILE Q 500 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Q' and resid 518 through 523 removed outlier: 6.182A pdb=" N LEU Q 518 " --> pdb=" O ASP Q 596 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Q' and resid 567 through 568 Processing sheet with id=AA7, first strand: chain 'Q' and resid 567 through 568 removed outlier: 5.636A pdb=" N LEU Q 537 " --> pdb=" O GLY Q 610 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY Q 610 " --> pdb=" O LEU Q 537 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SER Q 539 " --> pdb=" O GLU Q 608 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN Q 604 " --> pdb=" O GLY Q 543 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'U' and resid 81 through 82 removed outlier: 10.248A pdb=" N THR U 120 " --> pdb=" O SER U 147 " (cutoff:3.500A) removed outlier: 11.369A pdb=" N SER U 147 " --> pdb=" O THR U 120 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N TYR U 122 " --> pdb=" O PHE U 145 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER U 141 " --> pdb=" O LEU U 126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'W' and resid 57 through 60 removed outlier: 3.820A pdb=" N SER W 141 " --> pdb=" O LEU W 126 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'W' and resid 119 through 121 331 hydrogen bonds defined for protein. 927 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: 0.97 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2180 1.34 - 1.45: 932 1.45 - 1.57: 3564 1.57 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 6714 Sorted by residual: bond pdb=" N GLN U 117 " pdb=" CA GLN U 117 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.09e-02 8.42e+03 9.16e+00 bond pdb=" N GLU Q 343 " pdb=" CA GLU Q 343 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.25e-02 6.40e+03 7.97e+00 bond pdb=" N LEU X 103 " pdb=" CA LEU X 103 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.06e+00 bond pdb=" N LYS X 107 " pdb=" CA LYS X 107 " ideal model delta sigma weight residual 1.462 1.487 -0.025 1.05e-02 9.07e+03 5.68e+00 bond pdb=" N GLN X 106 " pdb=" CA GLN X 106 " ideal model delta sigma weight residual 1.460 1.488 -0.029 1.22e-02 6.72e+03 5.50e+00 ... (remaining 6709 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 8674 1.47 - 2.93: 372 2.93 - 4.40: 65 4.40 - 5.87: 22 5.87 - 7.34: 3 Bond angle restraints: 9136 Sorted by residual: angle pdb=" CB GLU Q 343 " pdb=" CG GLU Q 343 " pdb=" CD GLU Q 343 " ideal model delta sigma weight residual 112.60 119.94 -7.34 1.70e+00 3.46e-01 1.86e+01 angle pdb=" CA GLU Q 343 " pdb=" C GLU Q 343 " pdb=" O GLU Q 343 " ideal model delta sigma weight residual 121.45 117.49 3.96 1.07e+00 8.73e-01 1.37e+01 angle pdb=" N PHE Q 485 " pdb=" CA PHE Q 485 " pdb=" C PHE Q 485 " ideal model delta sigma weight residual 111.87 107.11 4.76 1.41e+00 5.03e-01 1.14e+01 angle pdb=" N GLN Q 355 " pdb=" CA GLN Q 355 " pdb=" C GLN Q 355 " ideal model delta sigma weight residual 109.31 113.92 -4.61 1.42e+00 4.96e-01 1.05e+01 angle pdb=" CA ASP U 118 " pdb=" CB ASP U 118 " pdb=" CG ASP U 118 " ideal model delta sigma weight residual 112.60 115.84 -3.24 1.00e+00 1.00e+00 1.05e+01 ... (remaining 9131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 3464 17.86 - 35.73: 435 35.73 - 53.59: 84 53.59 - 71.46: 14 71.46 - 89.32: 7 Dihedral angle restraints: 4004 sinusoidal: 1551 harmonic: 2453 Sorted by residual: dihedral pdb=" CA THR X 93 " pdb=" C THR X 93 " pdb=" N LYS X 94 " pdb=" CA LYS X 94 " ideal model delta harmonic sigma weight residual -180.00 -153.63 -26.37 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA ASN Q 604 " pdb=" C ASN Q 604 " pdb=" N ILE Q 605 " pdb=" CA ILE Q 605 " ideal model delta harmonic sigma weight residual 180.00 154.26 25.74 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA LEU Q 357 " pdb=" C LEU Q 357 " pdb=" N ILE Q 358 " pdb=" CA ILE Q 358 " ideal model delta harmonic sigma weight residual 180.00 160.56 19.44 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 4001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 709 0.039 - 0.077: 231 0.077 - 0.116: 86 0.116 - 0.155: 13 0.155 - 0.193: 2 Chirality restraints: 1041 Sorted by residual: chirality pdb=" CA LEU X 103 " pdb=" N LEU X 103 " pdb=" C LEU X 103 " pdb=" CB LEU X 103 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.33e-01 chirality pdb=" CA LYS X 94 " pdb=" N LYS X 94 " pdb=" C LYS X 94 " pdb=" CB LYS X 94 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.99e-01 chirality pdb=" CA LYS X 107 " pdb=" N LYS X 107 " pdb=" C LYS X 107 " pdb=" CB LYS X 107 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.29e-01 ... (remaining 1038 not shown) Planarity restraints: 1200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE W 76 " -0.033 5.00e-02 4.00e+02 5.05e-02 4.08e+00 pdb=" N PRO W 77 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO W 77 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO W 77 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER Q 336 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" C SER Q 336 " -0.032 2.00e-02 2.50e+03 pdb=" O SER Q 336 " 0.012 2.00e-02 2.50e+03 pdb=" N THR Q 337 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR X 88 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.26e+00 pdb=" C THR X 88 " -0.031 2.00e-02 2.50e+03 pdb=" O THR X 88 " 0.012 2.00e-02 2.50e+03 pdb=" N ALA X 89 " 0.011 2.00e-02 2.50e+03 ... (remaining 1197 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1396 2.78 - 3.31: 5634 3.31 - 3.84: 9535 3.84 - 4.37: 9741 4.37 - 4.90: 18232 Nonbonded interactions: 44538 Sorted by model distance: nonbonded pdb=" N GLU Q 511 " pdb=" OE1 GLU Q 511 " model vdw 2.252 3.120 nonbonded pdb=" N GLU Q 380 " pdb=" OE1 GLU Q 380 " model vdw 2.285 3.120 nonbonded pdb=" O GLU W 88 " pdb=" NZ LYS W 132 " model vdw 2.308 3.120 nonbonded pdb=" OH TYR U 98 " pdb=" OD1 ASP W 40 " model vdw 2.311 3.040 nonbonded pdb=" OD1 ASP X 5 " pdb=" N THR X 6 " model vdw 2.338 3.120 ... (remaining 44533 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 'U' selection = chain 'W' } 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: 11.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.020 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 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 : 0.005 0.049 6714 Z= 0.251 Angle : 0.725 7.336 9136 Z= 0.413 Chirality : 0.044 0.193 1041 Planarity : 0.005 0.051 1200 Dihedral : 16.142 89.322 2430 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.76 % Favored : 95.01 % Rotamer: Outliers : 0.28 % Allowed : 20.71 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.28), residues: 841 helix: 2.95 (0.31), residues: 277 sheet: 1.40 (0.52), residues: 98 loop : -2.05 (0.23), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG U 96 TYR 0.019 0.002 TYR W 122 PHE 0.016 0.002 PHE Q 485 TRP 0.014 0.002 TRP Q 379 HIS 0.001 0.001 HIS X 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.25 ( 6714) covalent geometry : angle 0.72476 / 0.41 ( 9136) hydrogen bonds : bond 0.18422 / 12.51 ( 310) hydrogen bonds : angle 6.21132 / 4.26 ( 927) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: X 81 GLU cc_start: 0.7757 (tp30) cc_final: 0.7385 (tp30) outliers start: 2 outliers final: 2 residues processed: 103 average time/residue: 0.0970 time to fit residues: 12.8295 Evaluate side-chains 101 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 337 THR Chi-restraints excluded: chain Q residue 338 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... W 155 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.122916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.108830 restraints weight = 10484.702| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.94 r_work: 0.3120 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.0788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6714 Z= 0.148 Angle : 0.576 9.684 9136 Z= 0.296 Chirality : 0.041 0.164 1041 Planarity : 0.004 0.036 1200 Dihedral : 4.220 26.425 933 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.97 % Favored : 96.91 % Rotamer: Outliers : 2.27 % Allowed : 19.72 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.65 (0.29), residues: 841 helix: 3.30 (0.31), residues: 278 sheet: 1.58 (0.54), residues: 95 loop : -1.79 (0.24), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 96 TYR 0.013 0.001 TYR U 86 PHE 0.014 0.001 PHE W 61 TRP 0.009 0.001 TRP Q 379 HIS 0.002 0.001 HIS X 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 6714) covalent geometry : angle 0.57577 / 0.30 ( 9136) hydrogen bonds : bond 0.07974 / 5.50 ( 310) hydrogen bonds : angle 4.46100 / 3.02 ( 927) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.231 Fit side-chains REVERT: U 110 ARG cc_start: 0.8962 (mpp80) cc_final: 0.8340 (mtp85) REVERT: W 86 TYR cc_start: 0.9168 (p90) cc_final: 0.8809 (p90) REVERT: X 81 GLU cc_start: 0.8655 (tp30) cc_final: 0.8379 (tp30) outliers start: 16 outliers final: 9 residues processed: 129 average time/residue: 0.0909 time to fit residues: 15.0147 Evaluate side-chains 111 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 350 THR Chi-restraints excluded: chain Q residue 613 SER Chi-restraints excluded: chain U residue 159 LEU Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 126 LEU Chi-restraints excluded: chain W residue 127 VAL Chi-restraints excluded: chain W residue 152 THR Chi-restraints excluded: chain W residue 160 ILE Chi-restraints excluded: chain X residue 64 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: [45, 80, 32, 64, 1, 66, 8, 53, 14, 73, 58] chunk 45 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 32 optimal weight: 0.0370 chunk 64 optimal weight: 0.9980 chunk 1 optimal weight: 20.0000 chunk 66 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 112 GLN U 158 GLN X 136 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.120985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.106950 restraints weight = 10468.924| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.89 r_work: 0.3125 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6714 Z= 0.142 Angle : 0.555 11.449 9136 Z= 0.282 Chirality : 0.041 0.160 1041 Planarity : 0.004 0.030 1200 Dihedral : 4.002 24.824 931 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.92 % Favored : 95.96 % Rotamer: Outliers : 2.98 % Allowed : 20.14 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.75 (0.29), residues: 841 helix: 3.40 (0.31), residues: 278 sheet: 1.63 (0.51), residues: 99 loop : -1.76 (0.25), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 288 TYR 0.011 0.001 TYR U 86 PHE 0.013 0.001 PHE Q 485 TRP 0.009 0.001 TRP Q 379 HIS 0.002 0.001 HIS X 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 6714) covalent geometry : angle 0.55528 / 0.28 ( 9136) hydrogen bonds : bond 0.07438 / 5.15 ( 310) hydrogen bonds : angle 4.12359 / 2.79 ( 927) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: W 45 SER cc_start: 0.9280 (t) cc_final: 0.8914 (m) REVERT: W 86 TYR cc_start: 0.9139 (p90) cc_final: 0.8755 (p90) REVERT: X 81 GLU cc_start: 0.8680 (tp30) cc_final: 0.8428 (tp30) outliers start: 21 outliers final: 18 residues processed: 128 average time/residue: 0.0893 time to fit residues: 14.6278 Evaluate side-chains 125 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 350 THR Chi-restraints excluded: chain Q residue 406 VAL Chi-restraints excluded: chain Q residue 408 LEU Chi-restraints excluded: chain Q residue 428 LEU Chi-restraints excluded: chain Q residue 452 ASP Chi-restraints excluded: chain Q residue 552 PHE Chi-restraints excluded: chain Q residue 613 SER Chi-restraints excluded: chain U residue 66 ILE Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 159 LEU Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 104 MET Chi-restraints excluded: chain W residue 127 VAL Chi-restraints excluded: chain W residue 155 GLN Chi-restraints excluded: chain W residue 160 ILE Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain X residue 274 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: [26, 70, 81, 23, 16, 73, 37, 18, 36, 78, 7] chunk 26 optimal weight: 0.0000 chunk 70 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 18 optimal weight: 0.0060 chunk 36 optimal weight: 0.7980 chunk 78 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 overall best weight: 0.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 137 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.124831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.110873 restraints weight = 10380.054| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.89 r_work: 0.3176 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6714 Z= 0.118 Angle : 0.513 9.816 9136 Z= 0.258 Chirality : 0.039 0.142 1041 Planarity : 0.003 0.034 1200 Dihedral : 3.717 22.529 931 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.21 % Favored : 96.67 % Rotamer: Outliers : 2.13 % Allowed : 21.28 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.98 (0.29), residues: 841 helix: 3.60 (0.31), residues: 278 sheet: 1.60 (0.45), residues: 124 loop : -1.79 (0.26), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 110 TYR 0.010 0.001 TYR W 86 PHE 0.009 0.001 PHE W 61 TRP 0.008 0.001 TRP X 98 HIS 0.002 0.001 HIS X 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 ( 6714) covalent geometry : angle 0.51276 / 0.26 ( 9136) hydrogen bonds : bond 0.06272 / 4.35 ( 310) hydrogen bonds : angle 3.82104 / 2.56 ( 927) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.176 Fit side-chains REVERT: U 169 ASN cc_start: 0.6375 (m-40) cc_final: 0.6122 (m-40) REVERT: W 45 SER cc_start: 0.9250 (t) cc_final: 0.8876 (m) REVERT: W 86 TYR cc_start: 0.9068 (p90) cc_final: 0.8732 (p90) outliers start: 15 outliers final: 10 residues processed: 127 average time/residue: 0.0911 time to fit residues: 14.9032 Evaluate side-chains 118 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 350 THR Chi-restraints excluded: chain Q residue 408 LEU Chi-restraints excluded: chain Q residue 552 PHE Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 104 MET Chi-restraints excluded: chain W residue 127 VAL Chi-restraints excluded: chain W residue 160 ILE Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 64 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: [2, 59, 81, 33, 60, 31, 38, 36, 22, 6, 20] chunk 2 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 533 ASN U 158 GLN W 117 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.116582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.102540 restraints weight = 10731.033| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.92 r_work: 0.3075 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6714 Z= 0.209 Angle : 0.612 10.847 9136 Z= 0.313 Chirality : 0.043 0.167 1041 Planarity : 0.004 0.054 1200 Dihedral : 4.108 24.121 931 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.92 % Favored : 95.96 % Rotamer: Outliers : 3.69 % Allowed : 21.13 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.29), residues: 841 helix: 3.30 (0.31), residues: 279 sheet: 1.00 (0.54), residues: 99 loop : -1.63 (0.25), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG W 110 TYR 0.011 0.001 TYR W 165 PHE 0.018 0.002 PHE X 147 TRP 0.009 0.001 TRP X 79 HIS 0.002 0.001 HIS Q 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.21 ( 6714) covalent geometry : angle 0.61249 / 0.31 ( 9136) hydrogen bonds : bond 0.08188 / 5.64 ( 310) hydrogen bonds : angle 4.17270 / 2.84 ( 927) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.171 Fit side-chains REVERT: Q 459 ASN cc_start: 0.8935 (OUTLIER) cc_final: 0.8591 (m-40) REVERT: W 45 SER cc_start: 0.9368 (t) cc_final: 0.9006 (m) outliers start: 26 outliers final: 22 residues processed: 128 average time/residue: 0.0845 time to fit residues: 14.0350 Evaluate side-chains 130 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 338 THR Chi-restraints excluded: chain Q residue 350 THR Chi-restraints excluded: chain Q residue 406 VAL Chi-restraints excluded: chain Q residue 407 LEU Chi-restraints excluded: chain Q residue 459 ASN Chi-restraints excluded: chain Q residue 480 THR Chi-restraints excluded: chain Q residue 552 PHE Chi-restraints excluded: chain Q residue 613 SER Chi-restraints excluded: chain U residue 66 ILE Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain W residue 54 SER Chi-restraints excluded: chain W residue 104 MET Chi-restraints excluded: chain W residue 127 VAL Chi-restraints excluded: chain W residue 152 THR Chi-restraints excluded: chain W residue 155 GLN Chi-restraints excluded: chain W residue 160 ILE Chi-restraints excluded: chain X residue 3 ILE Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain X residue 138 ILE Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain X residue 270 VAL Chi-restraints excluded: chain X residue 274 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: [81, 47, 75, 2, 63, 30, 64, 12, 76, 46, 69] chunk 81 optimal weight: 3.9990 chunk 47 optimal weight: 0.3980 chunk 75 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 12 optimal weight: 0.0070 chunk 76 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 overall best weight: 0.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.123500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.109462 restraints weight = 10501.772| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.91 r_work: 0.3160 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6714 Z= 0.122 Angle : 0.524 9.475 9136 Z= 0.265 Chirality : 0.039 0.146 1041 Planarity : 0.003 0.035 1200 Dihedral : 3.708 22.178 931 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.69 % Favored : 96.20 % Rotamer: Outliers : 2.55 % Allowed : 22.27 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.94 (0.30), residues: 841 helix: 3.63 (0.31), residues: 278 sheet: 0.59 (0.47), residues: 136 loop : -1.56 (0.26), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG W 110 TYR 0.011 0.001 TYR U 86 PHE 0.009 0.001 PHE X 190 TRP 0.010 0.001 TRP X 98 HIS 0.003 0.001 HIS X 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 ( 6714) covalent geometry : angle 0.52398 / 0.27 ( 9136) hydrogen bonds : bond 0.06389 / 4.42 ( 310) hydrogen bonds : angle 3.81478 / 2.56 ( 927) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.259 Fit side-chains REVERT: Q 459 ASN cc_start: 0.8905 (OUTLIER) cc_final: 0.8601 (m-40) REVERT: W 45 SER cc_start: 0.9273 (t) cc_final: 0.8886 (m) REVERT: W 86 TYR cc_start: 0.9124 (p90) cc_final: 0.8766 (p90) outliers start: 18 outliers final: 14 residues processed: 128 average time/residue: 0.0847 time to fit residues: 14.2294 Evaluate side-chains 121 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 406 VAL Chi-restraints excluded: chain Q residue 452 ASP Chi-restraints excluded: chain Q residue 459 ASN Chi-restraints excluded: chain Q residue 552 PHE Chi-restraints excluded: chain Q residue 613 SER Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 104 MET Chi-restraints excluded: chain W residue 127 VAL Chi-restraints excluded: chain W residue 152 THR Chi-restraints excluded: chain W residue 160 ILE Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain X residue 138 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: [35, 76, 4, 61, 28, 42, 46, 25, 51, 48, 18] chunk 35 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 42 optimal weight: 0.2980 chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.121363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.107299 restraints weight = 10465.432| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.91 r_work: 0.3126 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6714 Z= 0.140 Angle : 0.545 10.156 9136 Z= 0.274 Chirality : 0.040 0.152 1041 Planarity : 0.003 0.033 1200 Dihedral : 3.736 22.919 931 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.80 % Favored : 96.08 % Rotamer: Outliers : 3.12 % Allowed : 21.99 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.92 (0.29), residues: 841 helix: 3.59 (0.31), residues: 278 sheet: 0.64 (0.47), residues: 134 loop : -1.57 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG W 110 TYR 0.010 0.001 TYR W 165 PHE 0.012 0.001 PHE U 61 TRP 0.006 0.001 TRP X 98 HIS 0.002 0.001 HIS X 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 6714) covalent geometry : angle 0.54485 / 0.27 ( 9136) hydrogen bonds : bond 0.06833 / 4.72 ( 310) hydrogen bonds : angle 3.83282 / 2.59 ( 927) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.229 Fit side-chains REVERT: Q 365 GLU cc_start: 0.4665 (mm-30) cc_final: 0.4460 (mm-30) REVERT: W 45 SER cc_start: 0.9317 (t) cc_final: 0.8947 (m) REVERT: W 86 TYR cc_start: 0.9148 (p90) cc_final: 0.8780 (p90) outliers start: 22 outliers final: 20 residues processed: 125 average time/residue: 0.0846 time to fit residues: 13.8068 Evaluate side-chains 126 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 338 THR Chi-restraints excluded: chain Q residue 350 THR Chi-restraints excluded: chain Q residue 396 VAL Chi-restraints excluded: chain Q residue 406 VAL Chi-restraints excluded: chain Q residue 445 THR Chi-restraints excluded: chain Q residue 452 ASP Chi-restraints excluded: chain Q residue 552 PHE Chi-restraints excluded: chain Q residue 613 SER Chi-restraints excluded: chain U residue 66 ILE Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain W residue 54 SER Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 104 MET Chi-restraints excluded: chain W residue 127 VAL Chi-restraints excluded: chain W residue 152 THR Chi-restraints excluded: chain W residue 160 ILE Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain X residue 138 ILE Chi-restraints excluded: chain X residue 274 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: [27, 77, 60, 50, 65, 73, 55, 24, 61, 16, 44] chunk 27 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.115675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.101656 restraints weight = 10584.096| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.91 r_work: 0.3060 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6714 Z= 0.214 Angle : 0.627 10.109 9136 Z= 0.320 Chirality : 0.044 0.169 1041 Planarity : 0.004 0.053 1200 Dihedral : 4.140 24.165 931 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.16 % Favored : 95.72 % Rotamer: Outliers : 2.70 % Allowed : 22.55 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.56 (0.29), residues: 841 helix: 3.26 (0.31), residues: 279 sheet: 1.11 (0.54), residues: 97 loop : -1.79 (0.25), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG W 96 TYR 0.013 0.001 TYR W 165 PHE 0.017 0.002 PHE U 61 TRP 0.008 0.001 TRP X 79 HIS 0.001 0.001 HIS X 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.21 ( 6714) covalent geometry : angle 0.62696 / 0.32 ( 9136) hydrogen bonds : bond 0.08390 / 5.77 ( 310) hydrogen bonds : angle 4.18777 / 2.84 ( 927) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.269 Fit side-chains REVERT: Q 365 GLU cc_start: 0.4907 (mm-30) cc_final: 0.4664 (mm-30) REVERT: W 45 SER cc_start: 0.9372 (t) cc_final: 0.8997 (m) outliers start: 19 outliers final: 18 residues processed: 119 average time/residue: 0.0907 time to fit residues: 14.0134 Evaluate side-chains 123 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 338 THR Chi-restraints excluded: chain Q residue 350 THR Chi-restraints excluded: chain Q residue 396 VAL Chi-restraints excluded: chain Q residue 406 VAL Chi-restraints excluded: chain Q residue 445 THR Chi-restraints excluded: chain Q residue 452 ASP Chi-restraints excluded: chain Q residue 552 PHE Chi-restraints excluded: chain Q residue 613 SER Chi-restraints excluded: chain U residue 66 ILE Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain W residue 54 SER Chi-restraints excluded: chain W residue 104 MET Chi-restraints excluded: chain W residue 152 THR Chi-restraints excluded: chain W residue 160 ILE Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain X residue 138 ILE Chi-restraints excluded: chain X residue 274 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: [16, 12, 7, 59, 55, 1, 26, 75, 72, 68, 56] chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.118466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.104399 restraints weight = 10640.094| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.96 r_work: 0.3053 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6714 Z= 0.207 Angle : 0.622 11.534 9136 Z= 0.317 Chirality : 0.043 0.165 1041 Planarity : 0.004 0.049 1200 Dihedral : 4.176 24.322 931 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.40 % Favored : 95.48 % Rotamer: Outliers : 2.70 % Allowed : 23.40 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.49 (0.29), residues: 841 helix: 3.21 (0.31), residues: 279 sheet: 0.71 (0.52), residues: 107 loop : -1.80 (0.25), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG W 91 TYR 0.013 0.001 TYR W 165 PHE 0.016 0.002 PHE U 61 TRP 0.008 0.001 TRP X 79 HIS 0.001 0.000 HIS X 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.21 ( 6714) covalent geometry : angle 0.62204 / 0.32 ( 9136) hydrogen bonds : bond 0.08325 / 5.74 ( 310) hydrogen bonds : angle 4.19628 / 2.84 ( 927) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.254 Fit side-chains REVERT: Q 365 GLU cc_start: 0.4915 (mm-30) cc_final: 0.4570 (tp30) REVERT: W 45 SER cc_start: 0.9373 (t) cc_final: 0.8997 (m) outliers start: 19 outliers final: 16 residues processed: 120 average time/residue: 0.0895 time to fit residues: 13.9654 Evaluate side-chains 121 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 350 THR Chi-restraints excluded: chain Q residue 396 VAL Chi-restraints excluded: chain Q residue 406 VAL Chi-restraints excluded: chain Q residue 445 THR Chi-restraints excluded: chain Q residue 452 ASP Chi-restraints excluded: chain Q residue 552 PHE Chi-restraints excluded: chain Q residue 613 SER Chi-restraints excluded: chain U residue 66 ILE Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain W residue 54 SER Chi-restraints excluded: chain W residue 104 MET Chi-restraints excluded: chain W residue 152 THR Chi-restraints excluded: chain W residue 160 ILE Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain X residue 274 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: [30, 13, 73, 21, 14, 76, 57, 32, 39, 48, 75] chunk 30 optimal weight: 0.0770 chunk 13 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.118853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.104866 restraints weight = 10563.881| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.91 r_work: 0.3094 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6714 Z= 0.150 Angle : 0.577 11.958 9136 Z= 0.290 Chirality : 0.041 0.158 1041 Planarity : 0.003 0.035 1200 Dihedral : 3.968 23.703 931 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.16 % Favored : 95.72 % Rotamer: Outliers : 2.70 % Allowed : 23.40 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.29), residues: 841 helix: 3.39 (0.31), residues: 279 sheet: 0.85 (0.52), residues: 111 loop : -1.72 (0.25), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG W 110 TYR 0.012 0.001 TYR W 165 PHE 0.012 0.001 PHE U 61 TRP 0.008 0.001 TRP X 98 HIS 0.002 0.001 HIS X 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 6714) covalent geometry : angle 0.57656 / 0.29 ( 9136) hydrogen bonds : bond 0.07463 / 5.16 ( 310) hydrogen bonds : angle 4.01967 / 2.71 ( 927) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.255 Fit side-chains REVERT: Q 365 GLU cc_start: 0.5032 (mm-30) cc_final: 0.4752 (mm-30) REVERT: Q 459 ASN cc_start: 0.8923 (OUTLIER) cc_final: 0.8576 (m-40) REVERT: W 45 SER cc_start: 0.9323 (t) cc_final: 0.8948 (m) REVERT: W 86 TYR cc_start: 0.9238 (p90) cc_final: 0.8817 (p90) REVERT: X 38 LYS cc_start: 0.5654 (tptt) cc_final: 0.5407 (tptt) outliers start: 19 outliers final: 16 residues processed: 126 average time/residue: 0.0874 time to fit residues: 14.3803 Evaluate side-chains 127 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 350 THR Chi-restraints excluded: chain Q residue 396 VAL Chi-restraints excluded: chain Q residue 406 VAL Chi-restraints excluded: chain Q residue 452 ASP Chi-restraints excluded: chain Q residue 459 ASN Chi-restraints excluded: chain Q residue 552 PHE Chi-restraints excluded: chain Q residue 613 SER Chi-restraints excluded: chain U residue 66 ILE Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain W residue 54 SER Chi-restraints excluded: chain W residue 104 MET Chi-restraints excluded: chain W residue 152 THR Chi-restraints excluded: chain W residue 160 ILE Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain X residue 270 VAL Chi-restraints excluded: chain X residue 274 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: [20, 31, 68, 40, 73, 75, 39, 82, 23, 29, 5] chunk 20 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.116268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.102316 restraints weight = 10611.533| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.91 r_work: 0.3056 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6714 Z= 0.207 Angle : 0.627 12.580 9136 Z= 0.317 Chirality : 0.043 0.164 1041 Planarity : 0.004 0.048 1200 Dihedral : 4.150 24.688 931 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.52 % Favored : 95.36 % Rotamer: Outliers : 3.12 % Allowed : 22.84 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.47 (0.29), residues: 841 helix: 3.24 (0.31), residues: 279 sheet: 0.67 (0.52), residues: 107 loop : -1.83 (0.25), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG W 91 TYR 0.011 0.001 TYR U 86 PHE 0.016 0.002 PHE U 61 TRP 0.008 0.001 TRP X 79 HIS 0.002 0.001 HIS X 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.21 ( 6714) covalent geometry : angle 0.62727 / 0.32 ( 9136) hydrogen bonds : bond 0.08254 / 5.69 ( 310) hydrogen bonds : angle 4.17340 / 2.83 ( 927) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2535.97 seconds wall clock time: 43 minutes 49.89 seconds (2629.89 seconds total)