Starting phenix.real_space_refine on Thu Oct 22 19:16:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x2n_66480/10_2026/9x2n_66480.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x2n_66480/10_2026/9x2n_66480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9x2n_66480/10_2026/9x2n_66480.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x2n_66480/10_2026/9x2n_66480.map" model { file = "/net/cci-nas-00/data/ceres_data/9x2n_66480/10_2026/9x2n_66480.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x2n_66480/10_2026/9x2n_66480.cif" } resolution = 3.2 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= 0.026 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 22 5.16 5 C 2753 2.51 5 N 667 2.21 5 O 686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s 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: 4128 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3894 Classifications: {'peptide': 511} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 486} Chain: "B" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 234 Classifications: {'peptide': 30} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 28} Time building chain proxies: 0.66, per 1000 atoms: 0.16 Number of scatterers: 4128 At special positions: 0 Unit cell: (73.696, 65.424, 73.696, 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 22 16.00 O 686 8.00 N 667 7.00 C 2753 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: 0.19 Conformation dependent library (CDL) restraints added in 100.5 milliseconds 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1006 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 85.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 1 through 32 removed outlier: 3.558A pdb=" N ALA A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE A 31 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE A 32 " --> pdb=" O VAL A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 51 removed outlier: 3.777A pdb=" N PHE A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL A 43 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU A 47 " --> pdb=" O VAL A 43 " (cutoff:3.500A) Proline residue: A 48 - end of helix Processing helix chain 'A' and resid 51 through 56 removed outlier: 3.640A pdb=" N PHE A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 75 Proline residue: A 66 - end of helix Processing helix chain 'A' and resid 76 through 105 removed outlier: 3.702A pdb=" N VAL A 82 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 85 " --> pdb=" O ARG A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 114 Processing helix chain 'A' and resid 120 through 135 removed outlier: 3.875A pdb=" N GLN A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 154 removed outlier: 3.763A pdb=" N ALA A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 177 removed outlier: 3.543A pdb=" N ALA A 161 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Proline residue: A 164 - end of helix removed outlier: 3.810A pdb=" N LEU A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN A 168 " --> pdb=" O PRO A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 211 removed outlier: 3.697A pdb=" N ALA A 190 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN A 204 " --> pdb=" O GLN A 200 " (cutoff:3.500A) Proline residue: A 206 - end of helix removed outlier: 3.765A pdb=" N ILE A 211 " --> pdb=" O HIS A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 256 removed outlier: 3.560A pdb=" N VAL A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 4.086A pdb=" N PHE A 256 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.672A pdb=" N LEU A 271 " --> pdb=" O TYR A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 279 Processing helix chain 'A' and resid 279 through 298 removed outlier: 3.765A pdb=" N ILE A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 299 through 328 Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 328 through 338 removed outlier: 3.718A pdb=" N GLN A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 376 removed outlier: 4.183A pdb=" N MET A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL A 359 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLY A 360 " --> pdb=" O ALA A 356 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY A 363 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 366 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Proline residue: A 372 - end of helix Processing helix chain 'A' and resid 380 through 403 removed outlier: 3.998A pdb=" N GLN A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 432 removed outlier: 3.634A pdb=" N LEU A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 466 removed outlier: 3.704A pdb=" N LEU A 463 " --> pdb=" O LEU A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 499 removed outlier: 3.647A pdb=" N LEU A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 484 " --> pdb=" O ARG A 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 45 removed outlier: 4.022A pdb=" N SER B 31 " --> pdb=" O LEU B 27 " (cutoff:3.500A) 307 hydrogen bonds defined for protein. 921 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: 0.58 Time building geometry restraints manager: 0.27 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: 1228 1.34 - 1.46: 605 1.46 - 1.57: 2353 1.57 - 1.69: 0 1.69 - 1.80: 42 Bond restraints: 4228 Sorted by residual: bond pdb=" CA TYR B 48 " pdb=" C TYR B 48 " ideal model delta sigma weight residual 1.522 1.473 0.050 1.08e-02 8.57e+03 2.10e+01 bond pdb=" CA SER B 31 " pdb=" CB SER B 31 " ideal model delta sigma weight residual 1.528 1.481 0.048 1.56e-02 4.11e+03 9.42e+00 bond pdb=" N ILE A 237 " pdb=" CA ILE A 237 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.76e+00 bond pdb=" CA SER B 47 " pdb=" CB SER B 47 " ideal model delta sigma weight residual 1.528 1.483 0.046 1.56e-02 4.11e+03 8.64e+00 bond pdb=" N VAL A 100 " pdb=" CA VAL A 100 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.30e-02 5.92e+03 8.36e+00 ... (remaining 4223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 5544 1.98 - 3.96: 172 3.96 - 5.94: 36 5.94 - 7.92: 6 7.92 - 9.90: 1 Bond angle restraints: 5759 Sorted by residual: angle pdb=" N TYR B 48 " pdb=" CA TYR B 48 " pdb=" CB TYR B 48 " ideal model delta sigma weight residual 110.27 100.37 9.90 1.88e+00 2.83e-01 2.78e+01 angle pdb=" C TYR B 48 " pdb=" CA TYR B 48 " pdb=" CB TYR B 48 " ideal model delta sigma weight residual 110.13 103.51 6.62 1.34e+00 5.57e-01 2.44e+01 angle pdb=" C PRO B 49 " pdb=" CA PRO B 49 " pdb=" CB PRO B 49 " ideal model delta sigma weight residual 110.98 117.12 -6.14 1.31e+00 5.83e-01 2.20e+01 angle pdb=" N LEU B 35 " pdb=" CA LEU B 35 " pdb=" C LEU B 35 " ideal model delta sigma weight residual 110.97 106.09 4.88 1.09e+00 8.42e-01 2.00e+01 angle pdb=" C ALA B 54 " pdb=" N VAL B 55 " pdb=" CA VAL B 55 " ideal model delta sigma weight residual 121.70 113.93 7.77 1.80e+00 3.09e-01 1.86e+01 ... (remaining 5754 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.50: 2099 14.50 - 29.01: 239 29.01 - 43.51: 108 43.51 - 58.01: 30 58.01 - 72.52: 6 Dihedral angle restraints: 2482 sinusoidal: 921 harmonic: 1561 Sorted by residual: dihedral pdb=" N TYR B 48 " pdb=" C TYR B 48 " pdb=" CA TYR B 48 " pdb=" CB TYR B 48 " ideal model delta harmonic sigma weight residual 122.80 106.36 16.44 0 2.50e+00 1.60e-01 4.32e+01 dihedral pdb=" C TYR B 48 " pdb=" N TYR B 48 " pdb=" CA TYR B 48 " pdb=" CB TYR B 48 " ideal model delta harmonic sigma weight residual -122.60 -108.48 -14.12 0 2.50e+00 1.60e-01 3.19e+01 dihedral pdb=" N TRP B 53 " pdb=" C TRP B 53 " pdb=" CA TRP B 53 " pdb=" CB TRP B 53 " ideal model delta harmonic sigma weight residual 122.80 114.06 8.74 0 2.50e+00 1.60e-01 1.22e+01 ... (remaining 2479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 627 0.077 - 0.154: 62 0.154 - 0.231: 7 0.231 - 0.307: 2 0.307 - 0.384: 1 Chirality restraints: 699 Sorted by residual: chirality pdb=" CA TYR B 48 " pdb=" N TYR B 48 " pdb=" C TYR B 48 " pdb=" CB TYR B 48 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CG LEU A 306 " pdb=" CB LEU A 306 " pdb=" CD1 LEU A 306 " pdb=" CD2 LEU A 306 " both_signs ideal model delta sigma weight residual False -2.59 -2.82 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CG LEU B 27 " pdb=" CB LEU B 27 " pdb=" CD1 LEU B 27 " pdb=" CD2 LEU B 27 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 696 not shown) Planarity restraints: 696 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 29 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.88e+00 pdb=" C ALA B 29 " 0.038 2.00e-02 2.50e+03 pdb=" O ALA B 29 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU B 30 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 53 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" C TRP B 53 " -0.032 2.00e-02 2.50e+03 pdb=" O TRP B 53 " 0.012 2.00e-02 2.50e+03 pdb=" N ALA B 54 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 305 " -0.141 9.50e-02 1.11e+02 6.33e-02 2.46e+00 pdb=" NE ARG A 305 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG A 305 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 305 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 305 " -0.005 2.00e-02 2.50e+03 ... (remaining 693 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1354 2.83 - 3.35: 4339 3.35 - 3.87: 7008 3.87 - 4.38: 8461 4.38 - 4.90: 14031 Nonbonded interactions: 35193 Sorted by model distance: nonbonded pdb=" O ALA A 8 " pdb=" OG SER A 12 " model vdw 2.313 3.040 nonbonded pdb=" O LEU A 288 " pdb=" OG SER A 292 " model vdw 2.330 3.040 nonbonded pdb=" O GLY A 326 " pdb=" OG SER A 329 " model vdw 2.341 3.040 nonbonded pdb=" OH TYR A 303 " pdb=" O GLY A 373 " model vdw 2.367 3.040 nonbonded pdb=" O TYR B 36 " pdb=" OG SER B 40 " model vdw 2.375 3.040 ... (remaining 35188 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.770 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:0.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 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 0.050 4228 Z= 0.346 Angle : 0.780 9.904 5759 Z= 0.495 Chirality : 0.051 0.384 699 Planarity : 0.005 0.063 696 Dihedral : 15.953 72.519 1476 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.23 % Allowed : 24.60 % Favored : 75.17 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 4.00 % 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: -0.16 (0.37), residues: 537 helix: 0.27 (0.26), residues: 420 sheet: None (None), residues: 0 loop : -1.10 (0.58), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 218 TYR 0.009 0.001 TYR B 36 PHE 0.012 0.001 PHE A 32 TRP 0.003 0.001 TRP B 53 HIS 0.004 0.001 HIS A 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.35 ( 4228) covalent geometry : angle 0.78039 / 0.50 ( 5759) hydrogen bonds : bond 0.25705 / 17.19 ( 307) hydrogen bonds : angle 8.78219 / 6.27 ( 921) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 0.142 Fit side-chains REVERT: A 111 MET cc_start: 0.7118 (ptp) cc_final: 0.6843 (tmm) REVERT: A 210 LYS cc_start: 0.7026 (mtpt) cc_final: 0.6405 (mmmt) REVERT: A 231 LYS cc_start: 0.6977 (mmpt) cc_final: 0.6755 (mmtt) REVERT: A 442 MET cc_start: 0.7711 (ttp) cc_final: 0.7057 (mpp) outliers start: 1 outliers final: 0 residues processed: 83 average time/residue: 0.0364 time to fit residues: 4.0390 Evaluate side-chains 58 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: [24, 48, 26, 2, 16, 32, 31, 25, 50, 53, 19] chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 ASN A 464 HIS B 45 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.158022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.126279 restraints weight = 4648.640| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.41 r_work: 0.3342 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4228 Z= 0.166 Angle : 0.617 7.721 5759 Z= 0.306 Chirality : 0.040 0.140 699 Planarity : 0.004 0.035 696 Dihedral : 3.917 36.494 576 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.37 % Allowed : 22.07 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 (0.37), residues: 537 helix: 1.08 (0.25), residues: 431 sheet: None (None), residues: 0 loop : -0.88 (0.67), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 352 TYR 0.011 0.001 TYR A 426 PHE 0.011 0.001 PHE A 124 TRP 0.006 0.001 TRP B 53 HIS 0.005 0.001 HIS A 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 ( 4228) covalent geometry : angle 0.61699 / 0.31 ( 5759) hydrogen bonds : bond 0.05489 / 3.70 ( 307) hydrogen bonds : angle 4.99388 / 3.46 ( 921) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.150 Fit side-chains REVERT: A 90 LEU cc_start: 0.8327 (mp) cc_final: 0.8114 (mp) REVERT: A 111 MET cc_start: 0.7219 (OUTLIER) cc_final: 0.6334 (tmm) REVERT: A 203 TYR cc_start: 0.7684 (t80) cc_final: 0.7373 (t80) REVERT: A 210 LYS cc_start: 0.6489 (mtpt) cc_final: 0.6084 (mmmt) REVERT: A 233 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7715 (tpt) REVERT: A 270 ARG cc_start: 0.6819 (mmp-170) cc_final: 0.5961 (tmt170) REVERT: A 369 VAL cc_start: 0.8322 (OUTLIER) cc_final: 0.7962 (t) REVERT: A 442 MET cc_start: 0.6983 (ttp) cc_final: 0.6211 (mpp) REVERT: A 482 MET cc_start: 0.7630 (tpp) cc_final: 0.7321 (mmm) outliers start: 19 outliers final: 8 residues processed: 103 average time/residue: 0.0460 time to fit residues: 6.5910 Evaluate side-chains 80 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain B residue 55 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: [41, 11, 0, 33, 43, 27, 18, 25, 28, 19, 34] chunk 41 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 28 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 398 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 = 0.3827 r_free = 0.3827 target = 0.156081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.124441 restraints weight = 4667.948| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.46 r_work: 0.3317 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4228 Z= 0.152 Angle : 0.616 9.322 5759 Z= 0.287 Chirality : 0.040 0.171 699 Planarity : 0.004 0.036 696 Dihedral : 3.767 31.833 576 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.68 % Allowed : 22.76 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.33 (0.37), residues: 537 helix: 1.32 (0.25), residues: 432 sheet: None (None), residues: 0 loop : -0.76 (0.68), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 480 TYR 0.009 0.001 TYR A 426 PHE 0.009 0.001 PHE A 32 TRP 0.007 0.001 TRP B 53 HIS 0.003 0.001 HIS A 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 4228) covalent geometry : angle 0.61584 / 0.29 ( 5759) hydrogen bonds : bond 0.04813 / 3.22 ( 307) hydrogen bonds : angle 4.61118 / 3.17 ( 921) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.132 Fit side-chains REVERT: A 90 LEU cc_start: 0.8236 (mp) cc_final: 0.7995 (mp) REVERT: A 111 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6326 (tmm) REVERT: A 203 TYR cc_start: 0.7770 (t80) cc_final: 0.7450 (t80) REVERT: A 210 LYS cc_start: 0.6469 (mtpt) cc_final: 0.6101 (mmmt) REVERT: A 270 ARG cc_start: 0.6996 (mmp-170) cc_final: 0.6039 (tmt170) REVERT: A 442 MET cc_start: 0.6890 (ttp) cc_final: 0.6202 (mpp) REVERT: A 496 LEU cc_start: 0.6051 (OUTLIER) cc_final: 0.5538 (mm) outliers start: 16 outliers final: 10 residues processed: 83 average time/residue: 0.0434 time to fit residues: 5.0428 Evaluate side-chains 76 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain B residue 55 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: [11, 4, 52, 2, 17, 21, 1, 45, 19, 25, 6] chunk 11 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 ASN A 432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.154966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.123503 restraints weight = 4617.026| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.45 r_work: 0.3311 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4228 Z= 0.152 Angle : 0.592 8.212 5759 Z= 0.281 Chirality : 0.039 0.155 699 Planarity : 0.004 0.036 696 Dihedral : 3.685 25.566 576 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.83 % Allowed : 22.30 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.59 (0.37), residues: 537 helix: 1.54 (0.25), residues: 432 sheet: None (None), residues: 0 loop : -0.87 (0.67), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 270 TYR 0.011 0.001 TYR A 426 PHE 0.010 0.001 PHE A 135 TRP 0.004 0.001 TRP A 469 HIS 0.002 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 4228) covalent geometry : angle 0.59215 / 0.28 ( 5759) hydrogen bonds : bond 0.04446 / 2.96 ( 307) hydrogen bonds : angle 4.48716 / 3.08 ( 921) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.106 Fit side-chains revert: symmetry clash REVERT: A 90 LEU cc_start: 0.8123 (mp) cc_final: 0.7864 (mp) REVERT: A 111 MET cc_start: 0.7198 (OUTLIER) cc_final: 0.6426 (tmm) REVERT: A 123 LYS cc_start: 0.6844 (mttt) cc_final: 0.6330 (mptt) REVERT: A 203 TYR cc_start: 0.7910 (t80) cc_final: 0.7667 (t80) REVERT: A 227 MET cc_start: 0.6494 (mmp) cc_final: 0.5397 (ttt) REVERT: A 270 ARG cc_start: 0.7114 (mmp-170) cc_final: 0.6068 (tmt170) REVERT: A 442 MET cc_start: 0.6764 (ttp) cc_final: 0.6087 (mpp) REVERT: A 496 LEU cc_start: 0.6176 (OUTLIER) cc_final: 0.5682 (mm) outliers start: 21 outliers final: 15 residues processed: 87 average time/residue: 0.0426 time to fit residues: 5.0509 Evaluate side-chains 79 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 314 CYS Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain B residue 55 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: [29, 4, 1, 31, 48, 8, 22, 51, 27, 24, 41] chunk 29 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 27 optimal weight: 0.0670 chunk 24 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.165586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.137333 restraints weight = 4712.342| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.12 r_work: 0.3535 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4228 Z= 0.140 Angle : 0.569 8.688 5759 Z= 0.271 Chirality : 0.039 0.160 699 Planarity : 0.004 0.035 696 Dihedral : 3.607 22.199 576 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.68 % Allowed : 24.60 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.84 (0.37), residues: 537 helix: 1.75 (0.25), residues: 429 sheet: None (None), residues: 0 loop : -0.86 (0.66), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 270 TYR 0.009 0.001 TYR A 426 PHE 0.008 0.001 PHE A 135 TRP 0.010 0.001 TRP B 53 HIS 0.001 0.000 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 4228) covalent geometry : angle 0.56920 / 0.27 ( 5759) hydrogen bonds : bond 0.04307 / 2.86 ( 307) hydrogen bonds : angle 4.40988 / 3.03 ( 921) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: A 90 LEU cc_start: 0.8558 (mp) cc_final: 0.8326 (mp) REVERT: A 111 MET cc_start: 0.7301 (OUTLIER) cc_final: 0.6657 (tmm) REVERT: A 123 LYS cc_start: 0.7154 (mttt) cc_final: 0.6639 (mptt) REVERT: A 203 TYR cc_start: 0.8006 (t80) cc_final: 0.7795 (t80) REVERT: A 227 MET cc_start: 0.6559 (mmp) cc_final: 0.5542 (ttt) REVERT: A 270 ARG cc_start: 0.7482 (mmp-170) cc_final: 0.6479 (tmt170) REVERT: A 442 MET cc_start: 0.7042 (ttp) cc_final: 0.6443 (mpp) REVERT: A 496 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6272 (mm) outliers start: 16 outliers final: 11 residues processed: 77 average time/residue: 0.0460 time to fit residues: 4.9487 Evaluate side-chains 73 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 314 CYS Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain B residue 55 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: [41, 52, 29, 49, 44, 26, 15, 45, 5, 50, 53] chunk 41 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 0.0020 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.165499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.137012 restraints weight = 4756.619| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.14 r_work: 0.3534 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4228 Z= 0.137 Angle : 0.561 8.909 5759 Z= 0.267 Chirality : 0.038 0.163 699 Planarity : 0.004 0.035 696 Dihedral : 3.570 19.439 576 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.60 % Allowed : 24.60 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.95 (0.37), residues: 537 helix: 1.84 (0.25), residues: 429 sheet: None (None), residues: 0 loop : -0.89 (0.65), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 270 TYR 0.009 0.001 TYR A 426 PHE 0.008 0.001 PHE A 135 TRP 0.006 0.001 TRP B 53 HIS 0.001 0.000 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 4228) covalent geometry : angle 0.56124 / 0.27 ( 5759) hydrogen bonds : bond 0.04233 / 2.81 ( 307) hydrogen bonds : angle 4.35365 / 2.98 ( 921) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: A 90 LEU cc_start: 0.8576 (mp) cc_final: 0.8342 (mp) REVERT: A 111 MET cc_start: 0.7270 (OUTLIER) cc_final: 0.6689 (tmm) REVERT: A 123 LYS cc_start: 0.7122 (mttt) cc_final: 0.6745 (mttp) REVERT: A 227 MET cc_start: 0.6578 (mmp) cc_final: 0.5565 (ttt) REVERT: A 270 ARG cc_start: 0.7508 (mmp-170) cc_final: 0.6471 (tmt170) REVERT: A 420 LEU cc_start: 0.7856 (tt) cc_final: 0.7401 (tp) REVERT: A 442 MET cc_start: 0.7047 (ttp) cc_final: 0.6438 (mpp) outliers start: 20 outliers final: 15 residues processed: 80 average time/residue: 0.0473 time to fit residues: 5.2786 Evaluate side-chains 79 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 314 CYS Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain B residue 55 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: [1, 36, 33, 53, 13, 46, 3, 51, 24, 30, 18] chunk 1 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.165569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.136382 restraints weight = 4763.195| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.21 r_work: 0.3512 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4228 Z= 0.156 Angle : 0.578 9.186 5759 Z= 0.276 Chirality : 0.040 0.173 699 Planarity : 0.004 0.035 696 Dihedral : 3.611 16.033 576 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 5.06 % Allowed : 24.37 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.82 (0.37), residues: 537 helix: 1.73 (0.25), residues: 433 sheet: None (None), residues: 0 loop : -0.95 (0.66), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 270 TYR 0.013 0.001 TYR A 426 PHE 0.009 0.001 PHE A 135 TRP 0.007 0.001 TRP A 108 HIS 0.002 0.001 HIS A 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 4228) covalent geometry : angle 0.57841 / 0.28 ( 5759) hydrogen bonds : bond 0.04266 / 2.82 ( 307) hydrogen bonds : angle 4.38720 / 2.99 ( 921) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.139 Fit side-chains REVERT: A 90 LEU cc_start: 0.8516 (mp) cc_final: 0.8266 (mp) REVERT: A 111 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.6617 (tmm) REVERT: A 123 LYS cc_start: 0.6994 (mttt) cc_final: 0.6632 (mttp) REVERT: A 227 MET cc_start: 0.6617 (mmp) cc_final: 0.5552 (ttt) REVERT: A 270 ARG cc_start: 0.7524 (mmp-170) cc_final: 0.6431 (tmt170) REVERT: A 442 MET cc_start: 0.7009 (ttp) cc_final: 0.6398 (mpp) outliers start: 22 outliers final: 15 residues processed: 83 average time/residue: 0.0437 time to fit residues: 5.1217 Evaluate side-chains 81 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 314 CYS Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain B residue 55 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: [52, 46, 49, 33, 11, 2, 35, 36, 21, 23, 0] chunk 52 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 36 optimal weight: 0.3980 chunk 21 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.165080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.137433 restraints weight = 4680.645| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.06 r_work: 0.3536 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4228 Z= 0.135 Angle : 0.582 10.181 5759 Z= 0.273 Chirality : 0.039 0.176 699 Planarity : 0.004 0.035 696 Dihedral : 3.583 14.094 576 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.68 % Allowed : 25.52 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.97 (0.37), residues: 537 helix: 1.86 (0.25), residues: 429 sheet: None (None), residues: 0 loop : -0.94 (0.65), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 270 TYR 0.010 0.001 TYR A 203 PHE 0.008 0.001 PHE A 135 TRP 0.005 0.001 TRP A 108 HIS 0.002 0.001 HIS A 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 4228) covalent geometry : angle 0.58152 / 0.27 ( 5759) hydrogen bonds : bond 0.04175 / 2.77 ( 307) hydrogen bonds : angle 4.30660 / 2.93 ( 921) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.141 Fit side-chains REVERT: A 90 LEU cc_start: 0.8556 (mp) cc_final: 0.8318 (mp) REVERT: A 111 MET cc_start: 0.7191 (OUTLIER) cc_final: 0.6666 (tmm) REVERT: A 123 LYS cc_start: 0.6989 (mttt) cc_final: 0.6638 (mttp) REVERT: A 227 MET cc_start: 0.6567 (mmp) cc_final: 0.5549 (ttt) REVERT: A 270 ARG cc_start: 0.7575 (mmp-170) cc_final: 0.6505 (tmt170) REVERT: A 442 MET cc_start: 0.7051 (ttp) cc_final: 0.6470 (mpp) outliers start: 16 outliers final: 13 residues processed: 80 average time/residue: 0.0498 time to fit residues: 5.4575 Evaluate side-chains 78 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 314 CYS Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain B residue 55 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: [35, 24, 33, 18, 51, 40, 38, 15, 29, 30, 46] chunk 35 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.163562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.135104 restraints weight = 4741.341| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.14 r_work: 0.3517 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4228 Z= 0.152 Angle : 0.588 9.895 5759 Z= 0.279 Chirality : 0.040 0.181 699 Planarity : 0.004 0.035 696 Dihedral : 3.576 13.670 576 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.68 % Allowed : 25.52 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.90 (0.37), residues: 537 helix: 1.82 (0.25), residues: 431 sheet: None (None), residues: 0 loop : -1.06 (0.66), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 480 TYR 0.011 0.001 TYR A 426 PHE 0.008 0.001 PHE A 135 TRP 0.018 0.001 TRP B 53 HIS 0.002 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 ( 4228) covalent geometry : angle 0.58792 / 0.28 ( 5759) hydrogen bonds : bond 0.04233 / 2.80 ( 307) hydrogen bonds : angle 4.34089 / 2.96 ( 921) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.101 Fit side-chains REVERT: A 90 LEU cc_start: 0.8557 (mp) cc_final: 0.8319 (mp) REVERT: A 111 MET cc_start: 0.7191 (OUTLIER) cc_final: 0.6664 (tmm) REVERT: A 123 LYS cc_start: 0.6978 (mttt) cc_final: 0.6695 (mttp) REVERT: A 227 MET cc_start: 0.6581 (mmp) cc_final: 0.5599 (ttt) REVERT: A 270 ARG cc_start: 0.7523 (mmp-170) cc_final: 0.6447 (tmt170) REVERT: A 442 MET cc_start: 0.7081 (ttp) cc_final: 0.6469 (mpp) outliers start: 16 outliers final: 14 residues processed: 78 average time/residue: 0.0484 time to fit residues: 5.1806 Evaluate side-chains 78 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 314 CYS Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain B residue 55 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: [40, 47, 52, 44, 6, 16, 38, 8, 45, 10, 23] chunk 40 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.164483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.136473 restraints weight = 4712.448| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.11 r_work: 0.3523 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4228 Z= 0.144 Angle : 0.608 10.522 5759 Z= 0.283 Chirality : 0.039 0.181 699 Planarity : 0.004 0.035 696 Dihedral : 3.577 13.616 576 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.68 % Allowed : 25.75 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.90 (0.37), residues: 537 helix: 1.83 (0.25), residues: 430 sheet: None (None), residues: 0 loop : -1.09 (0.65), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 270 TYR 0.010 0.001 TYR A 426 PHE 0.008 0.001 PHE A 135 TRP 0.013 0.001 TRP B 53 HIS 0.002 0.001 HIS A 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 4228) covalent geometry : angle 0.60800 / 0.28 ( 5759) hydrogen bonds : bond 0.04213 / 2.80 ( 307) hydrogen bonds : angle 4.29106 / 2.92 ( 921) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.130 Fit side-chains REVERT: A 90 LEU cc_start: 0.8560 (mp) cc_final: 0.8323 (mp) REVERT: A 111 MET cc_start: 0.7156 (OUTLIER) cc_final: 0.6646 (tmm) REVERT: A 123 LYS cc_start: 0.7005 (mttt) cc_final: 0.6562 (mttp) REVERT: A 227 MET cc_start: 0.6556 (mmp) cc_final: 0.5573 (ttt) REVERT: A 270 ARG cc_start: 0.7522 (mmp-170) cc_final: 0.6431 (tmt170) REVERT: A 442 MET cc_start: 0.7055 (ttp) cc_final: 0.6462 (mpp) outliers start: 16 outliers final: 14 residues processed: 78 average time/residue: 0.0458 time to fit residues: 5.0300 Evaluate side-chains 79 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 314 CYS Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain B residue 55 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: [48, 4, 16, 31, 45, 22, 12, 40, 50, 19, 49] chunk 48 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 50 optimal weight: 0.0010 chunk 19 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.165730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.137551 restraints weight = 4730.314| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.13 r_work: 0.3545 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4228 Z= 0.129 Angle : 0.594 10.556 5759 Z= 0.277 Chirality : 0.039 0.180 699 Planarity : 0.004 0.034 696 Dihedral : 3.544 13.291 576 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.45 % Allowed : 25.52 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 2.07 (0.37), residues: 537 helix: 1.95 (0.25), residues: 428 sheet: None (None), residues: 0 loop : -0.94 (0.65), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 305 TYR 0.009 0.001 TYR A 203 PHE 0.008 0.001 PHE A 135 TRP 0.012 0.001 TRP B 53 HIS 0.001 0.000 HIS A 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 4228) covalent geometry : angle 0.59448 / 0.28 ( 5759) hydrogen bonds : bond 0.04110 / 2.73 ( 307) hydrogen bonds : angle 4.22691 / 2.88 ( 921) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 945.62 seconds wall clock time: 16 minutes 53.71 seconds (1013.71 seconds total)