Starting phenix.real_space_refine on Tue Feb 11 07:42:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hb0_34610/02_2025/8hb0_34610.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hb0_34610/02_2025/8hb0_34610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hb0_34610/02_2025/8hb0_34610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hb0_34610/02_2025/8hb0_34610.map" model { file = "/net/cci-nas-00/data/ceres_data/8hb0_34610/02_2025/8hb0_34610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hb0_34610/02_2025/8hb0_34610.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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: 6 Type Number sf(0) Gaussians S 37 5.16 5 Na 1 4.78 5 C 3153 2.51 5 N 777 2.21 5 O 809 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4778 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4497 Classifications: {'peptide': 586} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 558} Chain breaks: 1 Chain: "B" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 231 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 50 Unusual residues: {' NA': 1, 'KZ3': 1, 'NAG': 1} Classifications: {'undetermined': 3, 'water': 4} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.18, per 1000 atoms: 0.67 Number of scatterers: 4778 At special positions: 0 Unit cell: (73.0402, 75.2536, 92.9603, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 37 16.00 Na 1 11.00 F 1 9.00 O 809 8.00 N 777 7.00 C 3153 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 511 " distance=2.20 Simple disulfide: pdb=" SG CYS A 345 " - pdb=" SG CYS A 351 " distance=2.32 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 361 " distance=2.33 Simple disulfide: pdb=" SG CYS A 517 " - pdb=" SG CYS A 522 " distance=2.35 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: 1.15 Conformation dependent library (CDL) restraints added in 607.4 milliseconds 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1116 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 0 sheets defined 82.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 22 through 47 removed outlier: 3.997A pdb=" N ILE A 26 " --> pdb=" O ASN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 58 Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 77 through 92 removed outlier: 3.760A pdb=" N PHE A 81 " --> pdb=" O GLY A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 112 removed outlier: 4.115A pdb=" N GLU A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 103 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE A 104 " --> pdb=" O TRP A 100 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A 108 " --> pdb=" O PHE A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 121 removed outlier: 4.095A pdb=" N VAL A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 136 through 154 removed outlier: 3.643A pdb=" N LEU A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 170 removed outlier: 3.569A pdb=" N ASP A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 192 removed outlier: 4.180A pdb=" N GLY A 192 " --> pdb=" O TYR A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 224 removed outlier: 3.736A pdb=" N LEU A 197 " --> pdb=" O GLY A 193 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 203 " --> pdb=" O TYR A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 233 removed outlier: 3.504A pdb=" N LEU A 229 " --> pdb=" O GLY A 225 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A 230 " --> pdb=" O TYR A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.721A pdb=" N TYR A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 257' Processing helix chain 'A' and resid 275 through 293 Processing helix chain 'A' and resid 294 through 299 Processing helix chain 'A' and resid 306 through 323 removed outlier: 3.758A pdb=" N THR A 323 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 328 through 339 Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 347 through 355 Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 364 through 374 removed outlier: 3.560A pdb=" N LEU A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 371 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 409 removed outlier: 4.025A pdb=" N LEU A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 414 Processing helix chain 'A' and resid 420 through 446 removed outlier: 3.539A pdb=" N VAL A 430 " --> pdb=" O GLY A 426 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) Proline residue: A 442 - end of helix Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.646A pdb=" N ASP A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 477 Processing helix chain 'A' and resid 481 through 507 Proline residue: A 502 - end of helix Processing helix chain 'A' and resid 518 through 524 removed outlier: 4.243A pdb=" N VAL A 524 " --> pdb=" O PHE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 548 removed outlier: 3.625A pdb=" N ILE A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 556 Processing helix chain 'A' and resid 646 through 671 Processing helix chain 'B' and resid 29 through 55 342 hydrogen bonds defined for protein. 1020 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: 1.28 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 701 1.28 - 1.42: 1349 1.42 - 1.56: 2797 1.56 - 1.70: 0 1.70 - 1.84: 57 Bond restraints: 4904 Sorted by residual: bond pdb=" C PRO A 324 " pdb=" O PRO A 324 " ideal model delta sigma weight residual 1.237 1.139 0.099 1.26e-02 6.30e+03 6.14e+01 bond pdb=" C PRO A 502 " pdb=" O PRO A 502 " ideal model delta sigma weight residual 1.235 1.145 0.090 1.30e-02 5.92e+03 4.78e+01 bond pdb=" C LEU A 497 " pdb=" O LEU A 497 " ideal model delta sigma weight residual 1.237 1.170 0.066 1.19e-02 7.06e+03 3.10e+01 bond pdb=" C PRO A 66 " pdb=" O PRO A 66 " ideal model delta sigma weight residual 1.237 1.170 0.067 1.29e-02 6.01e+03 2.68e+01 bond pdb=" C PHE A 520 " pdb=" O PHE A 520 " ideal model delta sigma weight residual 1.235 1.299 -0.063 1.26e-02 6.30e+03 2.53e+01 ... (remaining 4899 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 4600 2.24 - 4.48: 1803 4.48 - 6.72: 264 6.72 - 8.96: 17 8.96 - 11.20: 8 Bond angle restraints: 6692 Sorted by residual: angle pdb=" CA ASP A 261 " pdb=" CB ASP A 261 " pdb=" CG ASP A 261 " ideal model delta sigma weight residual 112.60 119.21 -6.61 1.00e+00 1.00e+00 4.37e+01 angle pdb=" CA PHE A 326 " pdb=" CB PHE A 326 " pdb=" CG PHE A 326 " ideal model delta sigma weight residual 113.80 107.31 6.49 1.00e+00 1.00e+00 4.22e+01 angle pdb=" CA PHE A 520 " pdb=" CB PHE A 520 " pdb=" CG PHE A 520 " ideal model delta sigma weight residual 113.80 120.25 -6.45 1.00e+00 1.00e+00 4.16e+01 angle pdb=" C SER A 227 " pdb=" N GLY A 228 " pdb=" CA GLY A 228 " ideal model delta sigma weight residual 120.03 127.10 -7.07 1.12e+00 7.97e-01 3.98e+01 angle pdb=" C ARG A 420 " pdb=" N GLU A 421 " pdb=" CA GLU A 421 " ideal model delta sigma weight residual 120.44 128.50 -8.06 1.30e+00 5.92e-01 3.85e+01 ... (remaining 6687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.08: 2572 16.08 - 32.16: 219 32.16 - 48.24: 45 48.24 - 64.33: 14 64.33 - 80.41: 4 Dihedral angle restraints: 2854 sinusoidal: 1102 harmonic: 1752 Sorted by residual: dihedral pdb=" CB CYS A 517 " pdb=" SG CYS A 517 " pdb=" SG CYS A 522 " pdb=" CB CYS A 522 " ideal model delta sinusoidal sigma weight residual 93.00 12.59 80.41 1 1.00e+01 1.00e-02 8.00e+01 dihedral pdb=" CA GLY A 418 " pdb=" C GLY A 418 " pdb=" N ASP A 419 " pdb=" CA ASP A 419 " ideal model delta harmonic sigma weight residual 180.00 -154.03 -25.97 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" C GLU A 503 " pdb=" N GLU A 503 " pdb=" CA GLU A 503 " pdb=" CB GLU A 503 " ideal model delta harmonic sigma weight residual -122.60 -110.19 -12.41 0 2.50e+00 1.60e-01 2.46e+01 ... (remaining 2851 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 387 0.059 - 0.118: 232 0.118 - 0.177: 116 0.177 - 0.236: 39 0.236 - 0.295: 5 Chirality restraints: 779 Sorted by residual: chirality pdb=" CA PRO A 269 " pdb=" N PRO A 269 " pdb=" C PRO A 269 " pdb=" CB PRO A 269 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CB VAL A 106 " pdb=" CA VAL A 106 " pdb=" CG1 VAL A 106 " pdb=" CG2 VAL A 106 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA VAL A 560 " pdb=" N VAL A 560 " pdb=" C VAL A 560 " pdb=" CB VAL A 560 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 776 not shown) Planarity restraints: 817 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 801 " -0.043 2.00e-02 2.50e+03 3.51e-02 1.54e+01 pdb=" C7 NAG A 801 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG A 801 " -0.033 2.00e-02 2.50e+03 pdb=" N2 NAG A 801 " 0.055 2.00e-02 2.50e+03 pdb=" O7 NAG A 801 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 521 " 0.016 2.00e-02 2.50e+03 3.08e-02 9.46e+00 pdb=" C LEU A 521 " -0.053 2.00e-02 2.50e+03 pdb=" O LEU A 521 " 0.019 2.00e-02 2.50e+03 pdb=" N CYS A 522 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 520 " -0.014 2.00e-02 2.50e+03 2.87e-02 8.25e+00 pdb=" C PHE A 520 " 0.050 2.00e-02 2.50e+03 pdb=" O PHE A 520 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU A 521 " -0.017 2.00e-02 2.50e+03 ... (remaining 814 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 104 2.70 - 3.25: 4833 3.25 - 3.80: 7942 3.80 - 4.35: 10878 4.35 - 4.90: 17609 Nonbonded interactions: 41366 Sorted by model distance: nonbonded pdb=" O ALA A 73 " pdb="NA NA A 803 " model vdw 2.153 2.470 nonbonded pdb=" O ILE A 76 " pdb="NA NA A 803 " model vdw 2.267 2.470 nonbonded pdb=" OG SER A 392 " pdb="NA NA A 803 " model vdw 2.299 2.470 nonbonded pdb=" O GLY A 332 " pdb=" OG SER A 335 " model vdw 2.309 3.040 nonbonded pdb=" ND2 ASN A 250 " pdb=" C1 NAG A 801 " model vdw 2.344 3.550 ... (remaining 41361 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: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.820 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 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 : 0.015 0.099 4904 Z= 1.022 Angle : 2.216 11.197 6692 Z= 1.653 Chirality : 0.091 0.295 779 Planarity : 0.005 0.035 817 Dihedral : 13.362 80.313 1726 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.94 % Favored : 95.89 % Rotamer: Outliers : 0.80 % Allowed : 5.80 % Favored : 93.40 % Cbeta Deviations : 0.72 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.30), residues: 609 helix: -1.34 (0.20), residues: 444 sheet: None (None), residues: 0 loop : -1.52 (0.50), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 291 HIS 0.013 0.002 HIS A 80 PHE 0.023 0.004 PHE A 326 TYR 0.021 0.005 TYR A 128 ARG 0.006 0.001 ARG A 368 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.490 Fit side-chains REVERT: A 45 CYS cc_start: 0.8008 (m) cc_final: 0.7036 (p) REVERT: A 49 ARG cc_start: 0.7408 (mtp-110) cc_final: 0.7151 (mtm180) REVERT: A 148 PHE cc_start: 0.8062 (m-10) cc_final: 0.7841 (m-80) REVERT: A 150 TYR cc_start: 0.8407 (m-10) cc_final: 0.8106 (m-10) REVERT: A 167 GLN cc_start: 0.8132 (tt0) cc_final: 0.7689 (tm-30) REVERT: A 254 PHE cc_start: 0.7582 (t80) cc_final: 0.7347 (t80) REVERT: A 274 LEU cc_start: 0.8571 (mt) cc_final: 0.8362 (mt) REVERT: A 325 MET cc_start: 0.8894 (tpp) cc_final: 0.8633 (tpp) REVERT: A 353 ARG cc_start: 0.7686 (ttp-110) cc_final: 0.7140 (ttm110) REVERT: A 407 MET cc_start: 0.8652 (mmm) cc_final: 0.8382 (mmm) REVERT: A 420 ARG cc_start: 0.7444 (ttt180) cc_final: 0.6617 (ttp-110) REVERT: A 548 THR cc_start: 0.7959 (m) cc_final: 0.7389 (p) REVERT: A 560 VAL cc_start: 0.8474 (OUTLIER) cc_final: 0.8097 (m) REVERT: A 568 GLU cc_start: 0.6580 (mt-10) cc_final: 0.6109 (mt-10) REVERT: A 641 GLU cc_start: 0.5285 (mm-30) cc_final: 0.4478 (pm20) REVERT: A 661 MET cc_start: 0.7934 (mtt) cc_final: 0.7720 (mtm) outliers start: 4 outliers final: 1 residues processed: 96 average time/residue: 1.0894 time to fit residues: 109.1801 Evaluate side-chains 57 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 502 PRO Chi-restraints excluded: chain A residue 560 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 295 GLN A 483 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.119196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.098116 restraints weight = 5149.987| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.31 r_work: 0.2873 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4904 Z= 0.225 Angle : 0.683 12.615 6692 Z= 0.349 Chirality : 0.043 0.143 779 Planarity : 0.005 0.039 817 Dihedral : 4.833 18.144 726 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.40 % Allowed : 8.00 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.33), residues: 609 helix: 1.05 (0.23), residues: 451 sheet: None (None), residues: 0 loop : -0.94 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 65 HIS 0.004 0.001 HIS A 80 PHE 0.015 0.002 PHE A 520 TYR 0.021 0.002 TYR A 256 ARG 0.004 0.001 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.648 Fit side-chains REVERT: A 45 CYS cc_start: 0.7935 (m) cc_final: 0.7117 (p) REVERT: A 231 ASP cc_start: 0.8390 (p0) cc_final: 0.8129 (p0) REVERT: A 254 PHE cc_start: 0.7698 (t80) cc_final: 0.7429 (t80) REVERT: A 281 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7230 (tt) REVERT: A 300 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7359 (mmt180) REVERT: A 407 MET cc_start: 0.8883 (mmm) cc_final: 0.8673 (mmt) REVERT: A 416 ARG cc_start: 0.7301 (mpt180) cc_final: 0.7010 (mtm180) REVERT: A 420 ARG cc_start: 0.7038 (ttt180) cc_final: 0.6709 (ttm-80) REVERT: A 448 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8267 (mm-40) REVERT: A 451 GLN cc_start: 0.8155 (mt0) cc_final: 0.7672 (mt0) REVERT: A 515 SER cc_start: 0.7162 (p) cc_final: 0.6765 (m) REVERT: A 548 THR cc_start: 0.7609 (m) cc_final: 0.7329 (p) REVERT: A 661 MET cc_start: 0.8043 (mtt) cc_final: 0.7821 (mtm) outliers start: 12 outliers final: 1 residues processed: 82 average time/residue: 1.2063 time to fit residues: 103.1256 Evaluate side-chains 65 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 494 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.121811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.099187 restraints weight = 4973.486| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.39 r_work: 0.2894 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4904 Z= 0.180 Angle : 0.615 13.052 6692 Z= 0.308 Chirality : 0.041 0.146 779 Planarity : 0.005 0.044 817 Dihedral : 4.299 17.678 722 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.60 % Allowed : 10.00 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.35), residues: 609 helix: 1.73 (0.24), residues: 453 sheet: None (None), residues: 0 loop : -0.78 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 65 HIS 0.003 0.001 HIS A 80 PHE 0.011 0.001 PHE A 520 TYR 0.013 0.002 TYR A 256 ARG 0.008 0.001 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.515 Fit side-chains REVERT: A 44 MET cc_start: 0.7581 (mtp) cc_final: 0.7277 (mtm) REVERT: A 45 CYS cc_start: 0.7918 (m) cc_final: 0.6974 (p) REVERT: A 46 ARG cc_start: 0.6226 (ttt90) cc_final: 0.5885 (ttt-90) REVERT: A 231 ASP cc_start: 0.8286 (p0) cc_final: 0.8055 (p0) REVERT: A 254 PHE cc_start: 0.7633 (t80) cc_final: 0.7359 (t80) REVERT: A 281 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.6953 (tt) REVERT: A 300 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7523 (mmt180) REVERT: A 407 MET cc_start: 0.8775 (mmm) cc_final: 0.8563 (mmt) REVERT: A 416 ARG cc_start: 0.7193 (mpt180) cc_final: 0.6905 (mtm180) REVERT: A 420 ARG cc_start: 0.6918 (ttt180) cc_final: 0.6619 (ttm-80) REVERT: A 448 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8307 (mm-40) REVERT: A 451 GLN cc_start: 0.8105 (mt0) cc_final: 0.7586 (mt0) REVERT: A 548 THR cc_start: 0.7466 (OUTLIER) cc_final: 0.7150 (p) REVERT: A 661 MET cc_start: 0.7973 (mtt) cc_final: 0.7725 (mtm) outliers start: 13 outliers final: 3 residues processed: 69 average time/residue: 1.2525 time to fit residues: 89.9343 Evaluate side-chains 66 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 53 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.0570 chunk 57 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.0570 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.123678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.101048 restraints weight = 5029.123| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.47 r_work: 0.2914 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4904 Z= 0.160 Angle : 0.583 13.312 6692 Z= 0.287 Chirality : 0.039 0.142 779 Planarity : 0.005 0.044 817 Dihedral : 4.030 17.805 722 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 3.20 % Allowed : 9.80 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.35), residues: 609 helix: 1.99 (0.24), residues: 453 sheet: None (None), residues: 0 loop : -0.64 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 65 HIS 0.003 0.001 HIS A 80 PHE 0.009 0.001 PHE A 520 TYR 0.010 0.001 TYR A 410 ARG 0.006 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.503 Fit side-chains REVERT: A 44 MET cc_start: 0.7403 (mtp) cc_final: 0.7113 (mtm) REVERT: A 45 CYS cc_start: 0.7915 (m) cc_final: 0.6906 (p) REVERT: A 46 ARG cc_start: 0.6116 (ttt90) cc_final: 0.5774 (ttt-90) REVERT: A 254 PHE cc_start: 0.7534 (t80) cc_final: 0.7293 (t80) REVERT: A 300 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7549 (mmt180) REVERT: A 407 MET cc_start: 0.8713 (mmm) cc_final: 0.8488 (mmt) REVERT: A 416 ARG cc_start: 0.7244 (mpt180) cc_final: 0.6840 (mtm180) REVERT: A 420 ARG cc_start: 0.6769 (ttt180) cc_final: 0.6426 (ttm-80) REVERT: A 448 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8220 (mm-40) REVERT: A 451 GLN cc_start: 0.8031 (mt0) cc_final: 0.7529 (mt0) REVERT: A 548 THR cc_start: 0.7466 (OUTLIER) cc_final: 0.7111 (p) REVERT: A 661 MET cc_start: 0.7924 (mtt) cc_final: 0.7637 (mtm) outliers start: 16 outliers final: 4 residues processed: 79 average time/residue: 1.2338 time to fit residues: 101.5177 Evaluate side-chains 68 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 33 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN A 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.116180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.094210 restraints weight = 5224.144| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.34 r_work: 0.2820 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 4904 Z= 0.332 Angle : 0.676 15.428 6692 Z= 0.338 Chirality : 0.045 0.159 779 Planarity : 0.005 0.050 817 Dihedral : 4.267 16.731 722 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.00 % Allowed : 11.80 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.35), residues: 609 helix: 1.72 (0.24), residues: 450 sheet: None (None), residues: 0 loop : -0.56 (0.55), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 487 HIS 0.004 0.002 HIS A 80 PHE 0.015 0.002 PHE A 326 TYR 0.012 0.002 TYR A 290 ARG 0.004 0.001 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.528 Fit side-chains REVERT: A 45 CYS cc_start: 0.7870 (m) cc_final: 0.6955 (p) REVERT: A 46 ARG cc_start: 0.6213 (ttt90) cc_final: 0.5834 (ttt-90) REVERT: A 254 PHE cc_start: 0.7633 (t80) cc_final: 0.7392 (t80) REVERT: A 281 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7130 (tt) REVERT: A 300 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7357 (mmt180) REVERT: A 407 MET cc_start: 0.8743 (mmm) cc_final: 0.8519 (mmt) REVERT: A 416 ARG cc_start: 0.7234 (mpt180) cc_final: 0.7030 (mtm180) REVERT: A 448 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8399 (mm-40) REVERT: A 451 GLN cc_start: 0.8233 (mt0) cc_final: 0.7781 (mt0) REVERT: A 548 THR cc_start: 0.7602 (OUTLIER) cc_final: 0.7267 (p) REVERT: A 568 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6380 (mt-10) REVERT: A 661 MET cc_start: 0.7899 (mtt) cc_final: 0.7622 (mtm) outliers start: 15 outliers final: 3 residues processed: 69 average time/residue: 1.4316 time to fit residues: 102.3911 Evaluate side-chains 66 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 55 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 22 optimal weight: 0.1980 chunk 46 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 173 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.121675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.100690 restraints weight = 5102.136| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.31 r_work: 0.2915 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4904 Z= 0.162 Angle : 0.587 15.018 6692 Z= 0.289 Chirality : 0.039 0.141 779 Planarity : 0.005 0.045 817 Dihedral : 3.992 17.702 722 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 2.60 % Allowed : 12.20 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.35), residues: 609 helix: 1.95 (0.24), residues: 452 sheet: None (None), residues: 0 loop : -0.42 (0.54), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 276 HIS 0.003 0.001 HIS A 80 PHE 0.008 0.001 PHE A 453 TYR 0.010 0.001 TYR A 290 ARG 0.003 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.561 Fit side-chains REVERT: A 45 CYS cc_start: 0.7772 (m) cc_final: 0.6907 (p) REVERT: A 46 ARG cc_start: 0.6269 (ttt90) cc_final: 0.5904 (ttt-90) REVERT: A 300 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7294 (mmt180) REVERT: A 407 MET cc_start: 0.8772 (mmm) cc_final: 0.8553 (mmt) REVERT: A 416 ARG cc_start: 0.7223 (mpt180) cc_final: 0.7006 (mtm180) REVERT: A 451 GLN cc_start: 0.8248 (mt0) cc_final: 0.7895 (mt0) REVERT: A 548 THR cc_start: 0.7691 (OUTLIER) cc_final: 0.7426 (p) REVERT: A 568 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6364 (mt-10) REVERT: A 661 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7698 (mtm) outliers start: 13 outliers final: 1 residues processed: 72 average time/residue: 1.3097 time to fit residues: 97.9824 Evaluate side-chains 64 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 661 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 56 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 chunk 41 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN A 557 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.122742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.101813 restraints weight = 5099.756| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.33 r_work: 0.2937 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4904 Z= 0.161 Angle : 0.583 15.125 6692 Z= 0.285 Chirality : 0.039 0.141 779 Planarity : 0.005 0.045 817 Dihedral : 3.874 17.334 722 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.20 % Allowed : 12.60 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.35), residues: 609 helix: 2.07 (0.24), residues: 452 sheet: None (None), residues: 0 loop : -0.39 (0.54), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 276 HIS 0.003 0.001 HIS A 80 PHE 0.008 0.001 PHE A 534 TYR 0.010 0.001 TYR A 188 ARG 0.004 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.524 Fit side-chains REVERT: A 45 CYS cc_start: 0.7874 (m) cc_final: 0.6962 (p) REVERT: A 46 ARG cc_start: 0.6175 (ttt90) cc_final: 0.5838 (ttt-90) REVERT: A 300 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7262 (mmt180) REVERT: A 416 ARG cc_start: 0.7232 (mpt180) cc_final: 0.6998 (mtm180) REVERT: A 451 GLN cc_start: 0.8176 (mt0) cc_final: 0.7900 (mt0) REVERT: A 548 THR cc_start: 0.7691 (OUTLIER) cc_final: 0.7419 (p) REVERT: A 568 GLU cc_start: 0.7024 (mt-10) cc_final: 0.6368 (mt-10) REVERT: A 661 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7705 (mtm) outliers start: 11 outliers final: 2 residues processed: 73 average time/residue: 1.2821 time to fit residues: 97.3715 Evaluate side-chains 67 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 661 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 56 optimal weight: 2.9990 chunk 32 optimal weight: 0.0770 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.0744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN A 376 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.121202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.100003 restraints weight = 5180.051| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.34 r_work: 0.2904 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4904 Z= 0.181 Angle : 0.600 15.723 6692 Z= 0.293 Chirality : 0.040 0.144 779 Planarity : 0.005 0.046 817 Dihedral : 3.869 17.120 722 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.00 % Allowed : 13.00 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.35), residues: 609 helix: 2.07 (0.24), residues: 452 sheet: None (None), residues: 0 loop : -0.38 (0.54), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 487 HIS 0.003 0.001 HIS A 80 PHE 0.015 0.001 PHE A 254 TYR 0.013 0.001 TYR A 188 ARG 0.003 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.492 Fit side-chains REVERT: A 44 MET cc_start: 0.7889 (mtm) cc_final: 0.7671 (mtm) REVERT: A 45 CYS cc_start: 0.7854 (m) cc_final: 0.6952 (p) REVERT: A 46 ARG cc_start: 0.6260 (ttt90) cc_final: 0.5851 (ttt-90) REVERT: A 300 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7213 (mmt180) REVERT: A 325 MET cc_start: 0.9195 (OUTLIER) cc_final: 0.7316 (tpt) REVERT: A 416 ARG cc_start: 0.7225 (mpt180) cc_final: 0.6924 (mtm180) REVERT: A 451 GLN cc_start: 0.8195 (mt0) cc_final: 0.7981 (mt0) REVERT: A 548 THR cc_start: 0.7593 (OUTLIER) cc_final: 0.7326 (p) REVERT: A 568 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6323 (mt-10) REVERT: A 661 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7695 (mtm) outliers start: 10 outliers final: 2 residues processed: 69 average time/residue: 1.3266 time to fit residues: 95.1630 Evaluate side-chains 67 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 661 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 18 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 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 = 0.3242 r_free = 0.3242 target = 0.117426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.096148 restraints weight = 5130.954| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.35 r_work: 0.2847 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4904 Z= 0.257 Angle : 0.655 16.602 6692 Z= 0.320 Chirality : 0.043 0.149 779 Planarity : 0.005 0.049 817 Dihedral : 4.023 16.428 722 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.80 % Allowed : 13.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.35), residues: 609 helix: 1.90 (0.24), residues: 451 sheet: None (None), residues: 0 loop : -0.34 (0.55), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 487 HIS 0.004 0.001 HIS A 80 PHE 0.023 0.002 PHE A 206 TYR 0.011 0.002 TYR A 290 ARG 0.003 0.000 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.542 Fit side-chains REVERT: A 44 MET cc_start: 0.7969 (mtm) cc_final: 0.7686 (mtm) REVERT: A 45 CYS cc_start: 0.7922 (m) cc_final: 0.7014 (p) REVERT: A 46 ARG cc_start: 0.6299 (ttt90) cc_final: 0.5885 (ttt-90) REVERT: A 300 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7296 (mmt180) REVERT: A 416 ARG cc_start: 0.7340 (mpt180) cc_final: 0.6918 (mtm180) REVERT: A 451 GLN cc_start: 0.8236 (mt0) cc_final: 0.7947 (mt0) REVERT: A 548 THR cc_start: 0.7644 (OUTLIER) cc_final: 0.7366 (p) REVERT: A 568 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6463 (mt-10) REVERT: A 661 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7718 (mtm) outliers start: 9 outliers final: 2 residues processed: 68 average time/residue: 1.3036 time to fit residues: 92.1408 Evaluate side-chains 65 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 661 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 12 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 0.0010 chunk 42 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 overall best weight: 0.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 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 = 0.3292 r_free = 0.3292 target = 0.121590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.100774 restraints weight = 5121.176| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.30 r_work: 0.2917 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4904 Z= 0.170 Angle : 0.608 15.683 6692 Z= 0.296 Chirality : 0.040 0.144 779 Planarity : 0.005 0.046 817 Dihedral : 3.895 17.291 722 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.20 % Allowed : 14.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.35), residues: 609 helix: 1.98 (0.24), residues: 453 sheet: None (None), residues: 0 loop : -0.31 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 65 HIS 0.003 0.001 HIS A 80 PHE 0.008 0.001 PHE A 534 TYR 0.011 0.001 TYR A 188 ARG 0.003 0.000 ARG A 353 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.533 Fit side-chains REVERT: A 44 MET cc_start: 0.7890 (mtm) cc_final: 0.7639 (mtm) REVERT: A 45 CYS cc_start: 0.7864 (m) cc_final: 0.6936 (p) REVERT: A 46 ARG cc_start: 0.6286 (ttt90) cc_final: 0.5880 (ttt-90) REVERT: A 300 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7196 (mmt180) REVERT: A 416 ARG cc_start: 0.7332 (mpt180) cc_final: 0.6891 (mtm180) REVERT: A 451 GLN cc_start: 0.8175 (mt0) cc_final: 0.7936 (mt0) REVERT: A 548 THR cc_start: 0.7598 (OUTLIER) cc_final: 0.7330 (p) REVERT: A 568 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6377 (mt-10) REVERT: A 661 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7699 (mtm) outliers start: 6 outliers final: 2 residues processed: 65 average time/residue: 1.3467 time to fit residues: 91.1046 Evaluate side-chains 63 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 661 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 0.2980 chunk 13 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 3 optimal weight: 8.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 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 = 0.3287 r_free = 0.3287 target = 0.121248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.100303 restraints weight = 5203.099| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.33 r_work: 0.2910 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4904 Z= 0.184 Angle : 0.623 15.912 6692 Z= 0.301 Chirality : 0.040 0.146 779 Planarity : 0.005 0.047 817 Dihedral : 3.868 16.966 722 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.20 % Allowed : 14.20 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.35), residues: 609 helix: 2.00 (0.24), residues: 453 sheet: None (None), residues: 0 loop : -0.29 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 440 HIS 0.003 0.001 HIS A 80 PHE 0.009 0.001 PHE A 534 TYR 0.012 0.001 TYR A 188 ARG 0.005 0.000 ARG A 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3261.06 seconds wall clock time: 58 minutes 15.83 seconds (3495.83 seconds total)