Starting phenix.real_space_refine on Thu Jul 2 03:46:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w9t_37381/07_2026/8w9t_37381.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w9t_37381/07_2026/8w9t_37381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w9t_37381/07_2026/8w9t_37381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w9t_37381/07_2026/8w9t_37381.map" model { file = "/net/cci-nas-00/data/ceres_data/8w9t_37381/07_2026/8w9t_37381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w9t_37381/07_2026/8w9t_37381.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 46 5.16 5 Na 2 4.78 5 C 4324 2.51 5 N 1054 2.21 5 O 1148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6574 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3284 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 19, 'TRANS': 406} Chain breaks: 2 Chain: "B" Number of atoms: 3284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3284 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 19, 'TRANS': 406} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' NA': 1} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' NA': 1} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 1.25, per 1000 atoms: 0.19 Number of scatterers: 6574 At special positions: 0 Unit cell: (101.37, 84.63, 86.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 Na 2 11.00 O 1148 8.00 N 1054 7.00 C 4324 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: 0.32 Conformation dependent library (CDL) restraints added in 243.0 milliseconds 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1588 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 0 sheets defined 76.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 42 through 65 removed outlier: 3.564A pdb=" N ALA A 55 " --> pdb=" O PHE A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 88 Processing helix chain 'A' and resid 101 through 116 Processing helix chain 'A' and resid 116 through 127 Processing helix chain 'A' and resid 179 through 216 removed outlier: 3.757A pdb=" N SER A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 227 Proline residue: A 222 - end of helix Processing helix chain 'A' and resid 229 through 244 Processing helix chain 'A' and resid 254 through 258 Processing helix chain 'A' and resid 260 through 275 Processing helix chain 'A' and resid 277 through 293 removed outlier: 3.648A pdb=" N ARG A 283 " --> pdb=" O PRO A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 304 removed outlier: 4.060A pdb=" N THR A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 342 Processing helix chain 'A' and resid 344 through 348 removed outlier: 4.216A pdb=" N ASP A 348 " --> pdb=" O SER A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 367 removed outlier: 3.882A pdb=" N ARG A 367 " --> pdb=" O VAL A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 379 Processing helix chain 'A' and resid 380 through 393 removed outlier: 3.528A pdb=" N LEU A 393 " --> pdb=" O GLY A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 427 Processing helix chain 'A' and resid 429 through 445 Processing helix chain 'A' and resid 445 through 452 Processing helix chain 'A' and resid 457 through 470 Processing helix chain 'A' and resid 479 through 485 Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 504 through 520 removed outlier: 3.525A pdb=" N LEU A 520 " --> pdb=" O LEU A 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 65 removed outlier: 3.563A pdb=" N ALA B 55 " --> pdb=" O PHE B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 88 Processing helix chain 'B' and resid 101 through 116 Processing helix chain 'B' and resid 116 through 127 Processing helix chain 'B' and resid 179 through 216 removed outlier: 3.756A pdb=" N SER B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 227 Proline residue: B 222 - end of helix Processing helix chain 'B' and resid 229 through 244 Processing helix chain 'B' and resid 254 through 258 Processing helix chain 'B' and resid 260 through 275 Processing helix chain 'B' and resid 277 through 293 removed outlier: 3.648A pdb=" N ARG B 283 " --> pdb=" O PRO B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 304 removed outlier: 4.060A pdb=" N THR B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 342 Processing helix chain 'B' and resid 344 through 348 removed outlier: 4.216A pdb=" N ASP B 348 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 367 removed outlier: 3.882A pdb=" N ARG B 367 " --> pdb=" O VAL B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 379 Processing helix chain 'B' and resid 380 through 393 removed outlier: 3.530A pdb=" N LEU B 393 " --> pdb=" O GLY B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 427 Processing helix chain 'B' and resid 429 through 445 Processing helix chain 'B' and resid 445 through 452 Processing helix chain 'B' and resid 457 through 470 Processing helix chain 'B' and resid 479 through 485 Processing helix chain 'B' and resid 498 through 503 Processing helix chain 'B' and resid 504 through 520 removed outlier: 3.526A pdb=" N LEU B 520 " --> pdb=" O LEU B 516 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1296 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: 1.01 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1365 1.33 - 1.45: 1476 1.45 - 1.57: 3803 1.57 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 6718 Sorted by residual: bond pdb=" N VAL A 89 " pdb=" CA VAL A 89 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.25e-02 6.40e+03 4.55e+00 bond pdb=" CA ARG A 367 " pdb=" CB ARG A 367 " ideal model delta sigma weight residual 1.523 1.498 0.026 1.27e-02 6.20e+03 4.06e+00 bond pdb=" CA ARG B 367 " pdb=" CB ARG B 367 " ideal model delta sigma weight residual 1.523 1.498 0.025 1.27e-02 6.20e+03 3.85e+00 bond pdb=" C SER B 90 " pdb=" O SER B 90 " ideal model delta sigma weight residual 1.235 1.212 0.023 1.23e-02 6.61e+03 3.47e+00 bond pdb=" CA ILE A 374 " pdb=" CB ILE A 374 " ideal model delta sigma weight residual 1.544 1.520 0.023 1.30e-02 5.92e+03 3.18e+00 ... (remaining 6713 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 8806 1.34 - 2.67: 251 2.67 - 4.01: 59 4.01 - 5.35: 12 5.35 - 6.68: 6 Bond angle restraints: 9134 Sorted by residual: angle pdb=" N LEU A 87 " pdb=" CA LEU A 87 " pdb=" C LEU A 87 " ideal model delta sigma weight residual 111.28 115.08 -3.80 1.09e+00 8.42e-01 1.22e+01 angle pdb=" N LEU B 87 " pdb=" CA LEU B 87 " pdb=" C LEU B 87 " ideal model delta sigma weight residual 111.28 115.01 -3.73 1.09e+00 8.42e-01 1.17e+01 angle pdb=" N ILE A 374 " pdb=" CA ILE A 374 " pdb=" CB ILE A 374 " ideal model delta sigma weight residual 112.32 108.44 3.88 1.15e+00 7.56e-01 1.14e+01 angle pdb=" N SER B 90 " pdb=" CA SER B 90 " pdb=" C SER B 90 " ideal model delta sigma weight residual 112.04 107.41 4.63 1.44e+00 4.82e-01 1.04e+01 angle pdb=" N SER A 90 " pdb=" CA SER A 90 " pdb=" C SER A 90 " ideal model delta sigma weight residual 112.04 107.91 4.13 1.44e+00 4.82e-01 8.25e+00 ... (remaining 9129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.72: 3572 15.72 - 31.43: 304 31.43 - 47.15: 72 47.15 - 62.87: 6 62.87 - 78.59: 4 Dihedral angle restraints: 3958 sinusoidal: 1500 harmonic: 2458 Sorted by residual: dihedral pdb=" CA ARG A 367 " pdb=" C ARG A 367 " pdb=" N HIS A 368 " pdb=" CA HIS A 368 " ideal model delta harmonic sigma weight residual 180.00 158.03 21.97 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ARG B 367 " pdb=" C ARG B 367 " pdb=" N HIS B 368 " pdb=" CA HIS B 368 " ideal model delta harmonic sigma weight residual 180.00 158.16 21.84 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA ASN B 365 " pdb=" C ASN B 365 " pdb=" N ALA B 366 " pdb=" CA ALA B 366 " ideal model delta harmonic sigma weight residual 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 3955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 780 0.041 - 0.081: 264 0.081 - 0.122: 56 0.122 - 0.163: 7 0.163 - 0.203: 3 Chirality restraints: 1110 Sorted by residual: chirality pdb=" CA ILE A 374 " pdb=" N ILE A 374 " pdb=" C ILE A 374 " pdb=" CB ILE A 374 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ASN A 253 " pdb=" N ASN A 253 " pdb=" C ASN A 253 " pdb=" CB ASN A 253 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.27e-01 chirality pdb=" CA ASN B 253 " pdb=" N ASN B 253 " pdb=" C ASN B 253 " pdb=" CB ASN B 253 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.90e-01 ... (remaining 1107 not shown) Planarity restraints: 1108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 88 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.00e+00 pdb=" C THR A 88 " 0.046 2.00e-02 2.50e+03 pdb=" O THR A 88 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL A 89 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 252 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.08e+00 pdb=" C GLU B 252 " -0.043 2.00e-02 2.50e+03 pdb=" O GLU B 252 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN B 253 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 252 " -0.012 2.00e-02 2.50e+03 2.45e-02 6.03e+00 pdb=" C GLU A 252 " 0.042 2.00e-02 2.50e+03 pdb=" O GLU A 252 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN A 253 " -0.014 2.00e-02 2.50e+03 ... (remaining 1105 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 83 2.65 - 3.21: 6554 3.21 - 3.78: 10886 3.78 - 4.34: 15511 4.34 - 4.90: 24867 Nonbonded interactions: 57901 Sorted by model distance: nonbonded pdb=" O GLN B 424 " pdb=" OG1 THR B 527 " model vdw 2.090 3.040 nonbonded pdb=" O GLN A 424 " pdb=" OG1 THR A 527 " model vdw 2.091 3.040 nonbonded pdb=" NH2 ARG A 367 " pdb=" O PRO A 394 " model vdw 2.189 3.120 nonbonded pdb=" NH2 ARG B 367 " pdb=" O PRO B 394 " model vdw 2.189 3.120 nonbonded pdb=" O GLY B 91 " pdb=" O HOH B 801 " model vdw 2.257 3.040 ... (remaining 57896 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.620 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:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 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 0.032 6718 Z= 0.206 Angle : 0.601 6.685 9134 Z= 0.333 Chirality : 0.043 0.203 1110 Planarity : 0.005 0.041 1108 Dihedral : 12.297 78.585 2370 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.67 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % 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: -1.88 (0.25), residues: 840 helix: -0.90 (0.18), residues: 582 sheet: None (None), residues: 0 loop : -1.73 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 450 TYR 0.015 0.002 TYR B 50 PHE 0.011 0.001 PHE A 361 TRP 0.007 0.001 TRP A 287 HIS 0.007 0.002 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.21 ( 6718) covalent geometry : angle 0.60119 / 0.33 ( 9134) hydrogen bonds : bond 0.13137 / 8.94 ( 448) hydrogen bonds : angle 6.20942 / 4.41 ( 1296) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.149 Fit side-chains REVERT: A 69 ASN cc_start: 0.7256 (t0) cc_final: 0.7047 (t0) REVERT: A 300 LEU cc_start: 0.7012 (mt) cc_final: 0.6743 (mm) REVERT: A 447 ARG cc_start: 0.6932 (mtp85) cc_final: 0.6616 (ttp-110) REVERT: B 300 LEU cc_start: 0.7012 (mt) cc_final: 0.6742 (mm) REVERT: B 447 ARG cc_start: 0.6940 (mtp85) cc_final: 0.6620 (ttp-110) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.4133 time to fit residues: 44.2910 Evaluate side-chains 75 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 253 ASN A 260 ASN A 270 GLN A 309 HIS A 312 ASN A 358 ASN A 368 HIS A 484 HIS B 69 ASN B 253 ASN B 260 ASN B 270 GLN B 309 HIS B 312 ASN B 358 ASN B 368 HIS B 484 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.142221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.124908 restraints weight = 7992.950| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.15 r_work: 0.3316 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6718 Z= 0.132 Angle : 0.524 5.909 9134 Z= 0.277 Chirality : 0.040 0.144 1110 Planarity : 0.004 0.041 1108 Dihedral : 4.398 19.514 896 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.13 % Allowed : 9.87 % Favored : 88.00 % 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: 0.39 (0.28), residues: 840 helix: 0.93 (0.21), residues: 586 sheet: None (None), residues: 0 loop : -1.24 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 367 TYR 0.015 0.002 TYR A 50 PHE 0.010 0.001 PHE A 361 TRP 0.005 0.001 TRP B 502 HIS 0.007 0.002 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 6718) covalent geometry : angle 0.52350 / 0.28 ( 9134) hydrogen bonds : bond 0.03252 / 2.16 ( 448) hydrogen bonds : angle 4.18726 / 2.96 ( 1296) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.218 Fit side-chains REVERT: A 69 ASN cc_start: 0.7239 (t0) cc_final: 0.7015 (t0) REVERT: A 117 GLU cc_start: 0.7199 (tm-30) cc_final: 0.6995 (mt-10) REVERT: A 447 ARG cc_start: 0.7437 (mtp85) cc_final: 0.7035 (ttp-110) REVERT: B 117 GLU cc_start: 0.7205 (tm-30) cc_final: 0.6981 (mt-10) REVERT: B 447 ARG cc_start: 0.7443 (mtp85) cc_final: 0.7043 (ttp-110) outliers start: 16 outliers final: 5 residues processed: 111 average time/residue: 0.3589 time to fit residues: 42.4708 Evaluate side-chains 90 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 80 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 HIS B 69 ASN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.145339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.126950 restraints weight = 7946.198| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.27 r_work: 0.3349 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 6718 Z= 0.099 Angle : 0.474 6.165 9134 Z= 0.246 Chirality : 0.038 0.135 1110 Planarity : 0.004 0.039 1108 Dihedral : 4.022 16.645 896 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.07 % Allowed : 11.60 % Favored : 87.33 % 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: 1.57 (0.28), residues: 840 helix: 1.90 (0.21), residues: 588 sheet: None (None), residues: 0 loop : -1.06 (0.35), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 448 TYR 0.014 0.002 TYR B 50 PHE 0.010 0.001 PHE A 198 TRP 0.004 0.001 TRP A 531 HIS 0.003 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 ( 6718) covalent geometry : angle 0.47353 / 0.25 ( 9134) hydrogen bonds : bond 0.02729 / 1.81 ( 448) hydrogen bonds : angle 3.79693 / 2.67 ( 1296) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.157 Fit side-chains REVERT: A 117 GLU cc_start: 0.7300 (tm-30) cc_final: 0.6805 (mt-10) REVERT: A 447 ARG cc_start: 0.7523 (mtp85) cc_final: 0.7161 (ttp-110) REVERT: B 69 ASN cc_start: 0.7131 (t0) cc_final: 0.6927 (t0) REVERT: B 117 GLU cc_start: 0.7310 (tm-30) cc_final: 0.6800 (mt-10) REVERT: B 447 ARG cc_start: 0.7517 (mtp85) cc_final: 0.7157 (ttp-110) REVERT: B 529 LYS cc_start: 0.6326 (ptmm) cc_final: 0.5862 (pttt) outliers start: 8 outliers final: 4 residues processed: 114 average time/residue: 0.3815 time to fit residues: 45.8681 Evaluate side-chains 92 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 10 optimal weight: 0.0040 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 0.0670 overall best weight: 1.3934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.142753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.123866 restraints weight = 7961.244| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.28 r_work: 0.3312 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6718 Z= 0.125 Angle : 0.504 6.350 9134 Z= 0.262 Chirality : 0.039 0.131 1110 Planarity : 0.004 0.039 1108 Dihedral : 4.188 19.304 896 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.20 % Allowed : 10.67 % Favored : 86.13 % 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: 1.86 (0.28), residues: 840 helix: 2.14 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -0.96 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 367 TYR 0.016 0.002 TYR A 76 PHE 0.010 0.001 PHE B 198 TRP 0.005 0.001 TRP A 287 HIS 0.005 0.001 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 6718) covalent geometry : angle 0.50376 / 0.26 ( 9134) hydrogen bonds : bond 0.02963 / 1.97 ( 448) hydrogen bonds : angle 3.77227 / 2.65 ( 1296) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.148 Fit side-chains REVERT: A 117 GLU cc_start: 0.7313 (tm-30) cc_final: 0.6769 (mt-10) REVERT: A 447 ARG cc_start: 0.7508 (mtp85) cc_final: 0.7153 (ttp-110) REVERT: B 69 ASN cc_start: 0.7327 (t0) cc_final: 0.7125 (t0) REVERT: B 117 GLU cc_start: 0.7305 (tm-30) cc_final: 0.6767 (mt-10) REVERT: B 447 ARG cc_start: 0.7493 (mtp85) cc_final: 0.7138 (ttp-110) outliers start: 24 outliers final: 12 residues processed: 108 average time/residue: 0.4012 time to fit residues: 45.7529 Evaluate side-chains 102 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 15 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.145152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.126338 restraints weight = 8072.565| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.30 r_work: 0.3345 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 6718 Z= 0.098 Angle : 0.469 5.739 9134 Z= 0.243 Chirality : 0.038 0.123 1110 Planarity : 0.004 0.038 1108 Dihedral : 3.958 15.805 896 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.40 % Allowed : 12.80 % Favored : 84.80 % 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: 2.33 (0.29), residues: 840 helix: 2.51 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -0.84 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 367 TYR 0.015 0.002 TYR A 81 PHE 0.011 0.001 PHE B 198 TRP 0.004 0.001 TRP B 502 HIS 0.003 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 ( 6718) covalent geometry : angle 0.46862 / 0.24 ( 9134) hydrogen bonds : bond 0.02639 / 1.75 ( 448) hydrogen bonds : angle 3.62639 / 2.53 ( 1296) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.158 Fit side-chains REVERT: A 57 LEU cc_start: 0.8253 (mt) cc_final: 0.7541 (tp) REVERT: A 117 GLU cc_start: 0.7304 (tm-30) cc_final: 0.6812 (mt-10) REVERT: A 256 ILE cc_start: 0.8344 (tt) cc_final: 0.8126 (tt) REVERT: A 447 ARG cc_start: 0.7529 (mtp85) cc_final: 0.7179 (ttp-110) REVERT: B 57 LEU cc_start: 0.8191 (mt) cc_final: 0.7492 (tp) REVERT: B 117 GLU cc_start: 0.7291 (tm-30) cc_final: 0.6802 (mt-10) REVERT: B 256 ILE cc_start: 0.8343 (tt) cc_final: 0.8131 (tt) REVERT: B 447 ARG cc_start: 0.7519 (mtp85) cc_final: 0.7168 (ttp-110) REVERT: B 529 LYS cc_start: 0.6324 (ptmm) cc_final: 0.6008 (pttt) outliers start: 18 outliers final: 9 residues processed: 106 average time/residue: 0.3694 time to fit residues: 41.4423 Evaluate side-chains 104 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 8 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 60 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.143319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.124396 restraints weight = 8001.214| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.30 r_work: 0.3320 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6718 Z= 0.120 Angle : 0.495 6.018 9134 Z= 0.257 Chirality : 0.039 0.120 1110 Planarity : 0.004 0.038 1108 Dihedral : 4.123 17.369 896 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.40 % Allowed : 13.20 % Favored : 84.40 % 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: 2.27 (0.28), residues: 840 helix: 2.45 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -0.81 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 367 TYR 0.015 0.002 TYR A 81 PHE 0.009 0.001 PHE A 198 TRP 0.004 0.001 TRP A 502 HIS 0.005 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 6718) covalent geometry : angle 0.49451 / 0.26 ( 9134) hydrogen bonds : bond 0.02882 / 1.91 ( 448) hydrogen bonds : angle 3.69917 / 2.59 ( 1296) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.158 Fit side-chains REVERT: A 57 LEU cc_start: 0.8208 (mt) cc_final: 0.7509 (tp) REVERT: A 117 GLU cc_start: 0.7280 (tm-30) cc_final: 0.6781 (mt-10) REVERT: A 256 ILE cc_start: 0.8328 (tt) cc_final: 0.8123 (tt) REVERT: A 447 ARG cc_start: 0.7522 (mtp85) cc_final: 0.7148 (ttp-110) REVERT: A 529 LYS cc_start: 0.6566 (ptmm) cc_final: 0.6019 (pttt) REVERT: B 57 LEU cc_start: 0.8202 (mt) cc_final: 0.7504 (tp) REVERT: B 117 GLU cc_start: 0.7316 (tm-30) cc_final: 0.6813 (mt-10) REVERT: B 447 ARG cc_start: 0.7510 (mtp85) cc_final: 0.7139 (ttp-110) outliers start: 18 outliers final: 12 residues processed: 106 average time/residue: 0.4011 time to fit residues: 44.8308 Evaluate side-chains 101 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 5 optimal weight: 0.0070 chunk 0 optimal weight: 6.9990 chunk 64 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 22 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.147486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.128823 restraints weight = 7958.833| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.29 r_work: 0.3372 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6718 Z= 0.088 Angle : 0.456 5.371 9134 Z= 0.236 Chirality : 0.037 0.116 1110 Planarity : 0.004 0.038 1108 Dihedral : 3.772 14.913 896 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.53 % Allowed : 12.93 % Favored : 84.53 % 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: 2.74 (0.29), residues: 840 helix: 2.82 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -0.65 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 367 TYR 0.013 0.002 TYR B 81 PHE 0.011 0.001 PHE A 198 TRP 0.005 0.001 TRP B 531 HIS 0.002 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00187 / 0.09 ( 6718) covalent geometry : angle 0.45595 / 0.24 ( 9134) hydrogen bonds : bond 0.02416 / 1.60 ( 448) hydrogen bonds : angle 3.53029 / 2.46 ( 1296) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.197 Fit side-chains REVERT: A 57 LEU cc_start: 0.8225 (mt) cc_final: 0.7544 (tp) REVERT: A 117 GLU cc_start: 0.7306 (tm-30) cc_final: 0.6771 (mt-10) REVERT: A 447 ARG cc_start: 0.7506 (mtp85) cc_final: 0.7164 (ttp-110) REVERT: A 529 LYS cc_start: 0.6454 (ptmm) cc_final: 0.5620 (ttmm) REVERT: B 57 LEU cc_start: 0.8230 (mt) cc_final: 0.7540 (tp) REVERT: B 117 GLU cc_start: 0.7315 (tm-30) cc_final: 0.6753 (mt-10) REVERT: B 447 ARG cc_start: 0.7508 (mtp85) cc_final: 0.7164 (ttp-110) REVERT: B 529 LYS cc_start: 0.6328 (ptmm) cc_final: 0.5829 (pttp) outliers start: 19 outliers final: 12 residues processed: 107 average time/residue: 0.3763 time to fit residues: 42.6308 Evaluate side-chains 102 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 HIS B 69 ASN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.147405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.128818 restraints weight = 7988.575| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.28 r_work: 0.3355 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6718 Z= 0.102 Angle : 0.473 5.596 9134 Z= 0.244 Chirality : 0.038 0.111 1110 Planarity : 0.004 0.038 1108 Dihedral : 3.890 15.680 896 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.00 % Allowed : 13.87 % Favored : 84.13 % 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: 2.71 (0.29), residues: 840 helix: 2.77 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -0.61 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 367 TYR 0.015 0.002 TYR A 81 PHE 0.010 0.001 PHE B 198 TRP 0.004 0.001 TRP B 502 HIS 0.004 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 6718) covalent geometry : angle 0.47284 / 0.24 ( 9134) hydrogen bonds : bond 0.02623 / 1.74 ( 448) hydrogen bonds : angle 3.56455 / 2.49 ( 1296) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.172 Fit side-chains REVERT: A 57 LEU cc_start: 0.8234 (mt) cc_final: 0.7559 (tp) REVERT: A 117 GLU cc_start: 0.7268 (tm-30) cc_final: 0.6816 (mt-10) REVERT: A 447 ARG cc_start: 0.7552 (mtp85) cc_final: 0.7203 (ttp-110) REVERT: A 529 LYS cc_start: 0.6556 (ptmm) cc_final: 0.5723 (ttmm) REVERT: B 57 LEU cc_start: 0.8191 (mt) cc_final: 0.7516 (tp) REVERT: B 117 GLU cc_start: 0.7251 (tm-30) cc_final: 0.6774 (mt-10) REVERT: B 447 ARG cc_start: 0.7558 (mtp85) cc_final: 0.7211 (ttp-110) REVERT: B 529 LYS cc_start: 0.6424 (ptmm) cc_final: 0.5903 (pttp) outliers start: 15 outliers final: 12 residues processed: 96 average time/residue: 0.4007 time to fit residues: 40.5059 Evaluate side-chains 98 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 21 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 HIS B 69 ASN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.143438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.124425 restraints weight = 8013.734| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.30 r_work: 0.3322 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6718 Z= 0.132 Angle : 0.515 6.031 9134 Z= 0.266 Chirality : 0.040 0.122 1110 Planarity : 0.004 0.039 1108 Dihedral : 4.131 17.917 896 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.00 % Allowed : 14.13 % Favored : 83.87 % 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: 2.42 (0.28), residues: 840 helix: 2.53 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -0.65 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 367 TYR 0.015 0.002 TYR A 76 PHE 0.010 0.001 PHE A 463 TRP 0.005 0.001 TRP B 45 HIS 0.005 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 6718) covalent geometry : angle 0.51513 / 0.27 ( 9134) hydrogen bonds : bond 0.02964 / 1.96 ( 448) hydrogen bonds : angle 3.71502 / 2.60 ( 1296) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.180 Fit side-chains REVERT: A 117 GLU cc_start: 0.7281 (tm-30) cc_final: 0.6782 (mt-10) REVERT: A 256 ILE cc_start: 0.8356 (tt) cc_final: 0.8116 (tt) REVERT: A 447 ARG cc_start: 0.7495 (mtp85) cc_final: 0.7125 (ttp-110) REVERT: B 66 LYS cc_start: 0.6771 (tptp) cc_final: 0.6546 (tptp) REVERT: B 117 GLU cc_start: 0.7283 (tm-30) cc_final: 0.6773 (mt-10) REVERT: B 367 ARG cc_start: 0.7889 (mmm-85) cc_final: 0.6667 (mmt180) REVERT: B 447 ARG cc_start: 0.7486 (mtp85) cc_final: 0.7134 (ttp-110) outliers start: 15 outliers final: 12 residues processed: 102 average time/residue: 0.4476 time to fit residues: 47.9441 Evaluate side-chains 102 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 HIS B 69 ASN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.146644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.127879 restraints weight = 7959.984| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.30 r_work: 0.3358 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6718 Z= 0.096 Angle : 0.486 6.974 9134 Z= 0.249 Chirality : 0.038 0.113 1110 Planarity : 0.004 0.038 1108 Dihedral : 3.902 16.248 896 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.73 % Allowed : 14.93 % Favored : 83.33 % 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: 2.72 (0.29), residues: 840 helix: 2.77 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -0.58 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 367 TYR 0.015 0.002 TYR A 81 PHE 0.011 0.001 PHE B 198 TRP 0.004 0.001 TRP B 531 HIS 0.003 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 ( 6718) covalent geometry : angle 0.48619 / 0.25 ( 9134) hydrogen bonds : bond 0.02566 / 1.69 ( 448) hydrogen bonds : angle 3.58139 / 2.50 ( 1296) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.170 Fit side-chains REVERT: A 57 LEU cc_start: 0.8168 (mt) cc_final: 0.7494 (tp) REVERT: A 117 GLU cc_start: 0.7291 (tm-30) cc_final: 0.6762 (mt-10) REVERT: A 256 ILE cc_start: 0.8328 (tt) cc_final: 0.8093 (tt) REVERT: A 447 ARG cc_start: 0.7510 (mtp85) cc_final: 0.7165 (ttp-110) REVERT: A 529 LYS cc_start: 0.6484 (ptmm) cc_final: 0.5606 (ttmm) REVERT: B 57 LEU cc_start: 0.8167 (mt) cc_final: 0.7486 (tp) REVERT: B 117 GLU cc_start: 0.7271 (tm-30) cc_final: 0.6736 (mt-10) REVERT: B 367 ARG cc_start: 0.7799 (mmm-85) cc_final: 0.6580 (mmt180) REVERT: B 447 ARG cc_start: 0.7512 (mtp85) cc_final: 0.7169 (ttp-110) REVERT: B 529 LYS cc_start: 0.6420 (ptmm) cc_final: 0.5630 (ttmm) outliers start: 13 outliers final: 10 residues processed: 94 average time/residue: 0.4298 time to fit residues: 42.5388 Evaluate side-chains 95 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 51 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.143936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.126331 restraints weight = 7949.809| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.16 r_work: 0.3326 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6718 Z= 0.126 Angle : 0.522 7.231 9134 Z= 0.267 Chirality : 0.040 0.119 1110 Planarity : 0.004 0.038 1108 Dihedral : 4.120 17.975 896 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.33 % Allowed : 15.20 % Favored : 83.47 % 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: 2.45 (0.28), residues: 840 helix: 2.56 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -0.66 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 367 TYR 0.015 0.002 TYR A 76 PHE 0.011 0.001 PHE B 257 TRP 0.005 0.001 TRP B 502 HIS 0.005 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 6718) covalent geometry : angle 0.52205 / 0.27 ( 9134) hydrogen bonds : bond 0.02903 / 1.92 ( 448) hydrogen bonds : angle 3.69652 / 2.59 ( 1296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1703.11 seconds wall clock time: 29 minutes 44.45 seconds (1784.45 seconds total)