Starting phenix.real_space_refine on Sun Apr 27 05:42:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hb0_34610/04_2025/8hb0_34610.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hb0_34610/04_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_34610/04_2025/8hb0_34610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hb0_34610/04_2025/8hb0_34610.map" model { file = "/net/cci-nas-00/data/ceres_data/8hb0_34610/04_2025/8hb0_34610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hb0_34610/04_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-5669/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: 3.52, per 1000 atoms: 0.74 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: 1.32 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.48 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: 1.37 Time building geometry restraints manager: 1.51 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: 0.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.410 Find NCS groups from input model: 0.050 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:12.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.240 ------------------------------------------------------------------------------- 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 : 0.017 0.318 4908 Z= 1.207 Angle : 2.311 40.549 6700 Z= 1.681 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 Details of bonding type rmsd hydrogen bonds : bond 0.19018 ( 342) hydrogen bonds : angle 8.71411 ( 1020) SS BOND : bond 0.27721 ( 4) SS BOND : angle 19.03329 ( 8) covalent geometry : bond 0.01547 ( 4904) covalent geometry : angle 2.21624 ( 6692) *********************** 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 : 0.477 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: 1.0602 time to fit residues: 106.2926 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 : 0.534 ------------------------------------------------------------------------------- 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 = 5149.990| |-----------------------------------------------------------------------------| 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: 0.2752 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 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 4908 Z= 0.157 Angle : 0.685 12.615 6700 Z= 0.350 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 Details of bonding type rmsd hydrogen bonds : bond 0.04760 ( 342) hydrogen bonds : angle 5.77228 ( 1020) SS BOND : bond 0.00649 ( 4) SS BOND : angle 1.64213 ( 8) covalent geometry : bond 0.00344 ( 4904) covalent geometry : angle 0.68263 ( 6692) *********************** 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 : 0.489 Fit side-chains REVERT: A 45 CYS cc_start: 0.7931 (m) cc_final: 0.7114 (p) REVERT: A 231 ASP cc_start: 0.8390 (p0) cc_final: 0.8129 (p0) REVERT: A 254 PHE cc_start: 0.7700 (t80) cc_final: 0.7431 (t80) REVERT: A 281 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7231 (tt) REVERT: A 300 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7362 (mmt180) REVERT: A 407 MET cc_start: 0.8885 (mmm) cc_final: 0.8674 (mmt) REVERT: A 416 ARG cc_start: 0.7299 (mpt180) cc_final: 0.7010 (mtm180) REVERT: A 420 ARG cc_start: 0.7037 (ttt180) cc_final: 0.6709 (ttm-80) REVERT: A 448 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8269 (mm-40) REVERT: A 451 GLN cc_start: 0.8156 (mt0) cc_final: 0.7673 (mt0) REVERT: A 515 SER cc_start: 0.7164 (p) cc_final: 0.6767 (m) REVERT: A 548 THR cc_start: 0.7610 (m) cc_final: 0.7330 (p) REVERT: A 661 MET cc_start: 0.8045 (mtt) cc_final: 0.7823 (mtm) outliers start: 12 outliers final: 1 residues processed: 82 average time/residue: 1.1661 time to fit residues: 99.4576 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 : 0.490 ------------------------------------------------------------------------------- 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: 0.7980 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3298 r_free = 0.3298 target = 0.122647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.099701 restraints weight = 4953.051| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.46 r_work: 0.2895 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4908 Z= 0.122 Angle : 0.608 12.954 6700 Z= 0.304 Chirality : 0.040 0.144 779 Planarity : 0.005 0.044 817 Dihedral : 4.280 17.796 722 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.49 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: 1.68 (0.35), residues: 609 helix: 1.76 (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 0.012 0.001 TRP A 65 HIS 0.003 0.001 HIS A 80 PHE 0.010 0.001 PHE A 520 TYR 0.013 0.001 TYR A 256 ARG 0.008 0.001 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.04052 ( 342) hydrogen bonds : angle 5.35545 ( 1020) SS BOND : bond 0.00283 ( 4) SS BOND : angle 1.17052 ( 8) covalent geometry : bond 0.00254 ( 4904) covalent geometry : angle 0.60713 ( 6692) *********************** 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 76 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.557 Fit side-chains REVERT: A 44 MET cc_start: 0.7477 (mtp) cc_final: 0.7177 (mtm) REVERT: A 45 CYS cc_start: 0.7898 (m) cc_final: 0.6916 (p) REVERT: A 46 ARG cc_start: 0.6173 (ttt90) cc_final: 0.5846 (ttt-90) REVERT: A 167 GLN cc_start: 0.8041 (tt0) cc_final: 0.7836 (tt0) REVERT: A 231 ASP cc_start: 0.8198 (p0) cc_final: 0.7994 (p0) REVERT: A 254 PHE cc_start: 0.7615 (t80) cc_final: 0.7329 (t80) REVERT: A 300 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7462 (mmt180) REVERT: A 407 MET cc_start: 0.8734 (mmm) cc_final: 0.8521 (mmt) REVERT: A 416 ARG cc_start: 0.7215 (mpt180) cc_final: 0.6884 (mtm180) REVERT: A 420 ARG cc_start: 0.6936 (ttt180) cc_final: 0.6614 (ttm-80) REVERT: A 448 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8250 (mm-40) REVERT: A 451 GLN cc_start: 0.8011 (mt0) cc_final: 0.7485 (mt0) REVERT: A 548 THR cc_start: 0.7456 (OUTLIER) cc_final: 0.7112 (p) REVERT: A 661 MET cc_start: 0.7894 (mtt) cc_final: 0.7634 (mtm) outliers start: 13 outliers final: 3 residues processed: 72 average time/residue: 1.2454 time to fit residues: 93.2870 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 : 0.527 ------------------------------------------------------------------------------- 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 548 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 53 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3279 r_free = 0.3279 target = 0.121183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.098773 restraints weight = 5050.076| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.39 r_work: 0.2886 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4908 Z= 0.132 Angle : 0.603 13.468 6700 Z= 0.299 Chirality : 0.041 0.146 779 Planarity : 0.005 0.046 817 Dihedral : 4.110 17.384 722 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.66 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: 1.89 (0.35), residues: 609 helix: 1.90 (0.24), residues: 452 sheet: None (None), residues: 0 loop : -0.66 (0.54), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 487 HIS 0.003 0.001 HIS A 80 PHE 0.010 0.001 PHE A 453 TYR 0.010 0.002 TYR A 410 ARG 0.005 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 342) hydrogen bonds : angle 5.29479 ( 1020) SS BOND : bond 0.00268 ( 4) SS BOND : angle 0.93975 ( 8) covalent geometry : bond 0.00287 ( 4904) covalent geometry : angle 0.60298 ( 6692) *********************** 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 76 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.512 Fit side-chains REVERT: A 44 MET cc_start: 0.7540 (mtp) cc_final: 0.7230 (mtm) REVERT: A 45 CYS cc_start: 0.7938 (m) cc_final: 0.6993 (p) REVERT: A 46 ARG cc_start: 0.6159 (ttt90) cc_final: 0.5811 (ttt-90) REVERT: A 254 PHE cc_start: 0.7573 (t80) cc_final: 0.7322 (t80) REVERT: A 281 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.6864 (tt) REVERT: A 300 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7641 (mmt180) REVERT: A 407 MET cc_start: 0.8739 (mmm) cc_final: 0.8520 (mmt) REVERT: A 416 ARG cc_start: 0.7189 (mpt180) cc_final: 0.6896 (mtm180) REVERT: A 420 ARG cc_start: 0.6924 (ttt180) cc_final: 0.6602 (ttm-80) REVERT: A 448 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8315 (mm-40) REVERT: A 451 GLN cc_start: 0.8147 (mt0) cc_final: 0.7626 (mt0) REVERT: A 548 THR cc_start: 0.7480 (OUTLIER) cc_final: 0.7149 (p) REVERT: A 661 MET cc_start: 0.8026 (mtt) cc_final: 0.7754 (mtm) outliers start: 16 outliers final: 5 residues processed: 71 average time/residue: 1.3237 time to fit residues: 97.6896 Evaluate side-chains 64 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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 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: 10.0000 chunk 16 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 54 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.116497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.094545 restraints weight = 5219.422| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.34 r_work: 0.2821 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 4908 Z= 0.199 Angle : 0.665 15.417 6700 Z= 0.333 Chirality : 0.044 0.158 779 Planarity : 0.005 0.050 817 Dihedral : 4.286 16.780 722 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.80 % Allowed : 11.80 % Favored : 85.40 % 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: 1.66 (0.35), residues: 609 helix: 1.68 (0.24), residues: 452 sheet: None (None), residues: 0 loop : -0.52 (0.56), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 487 HIS 0.004 0.001 HIS A 80 PHE 0.014 0.002 PHE A 326 TYR 0.011 0.002 TYR A 290 ARG 0.004 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.04865 ( 342) hydrogen bonds : angle 5.59959 ( 1020) SS BOND : bond 0.00341 ( 4) SS BOND : angle 0.95001 ( 8) covalent geometry : bond 0.00466 ( 4904) covalent geometry : angle 0.66417 ( 6692) *********************** 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 71 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.539 Fit side-chains REVERT: A 45 CYS cc_start: 0.7840 (m) cc_final: 0.6943 (p) REVERT: A 46 ARG cc_start: 0.6211 (ttt90) cc_final: 0.5822 (ttt-90) REVERT: A 254 PHE cc_start: 0.7626 (t80) cc_final: 0.7380 (t80) REVERT: A 281 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7129 (tt) REVERT: A 300 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7346 (mmt180) REVERT: A 407 MET cc_start: 0.8743 (mmm) cc_final: 0.8523 (mmt) REVERT: A 416 ARG cc_start: 0.7256 (mpt180) cc_final: 0.6989 (mtm180) REVERT: A 448 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8387 (mm-40) REVERT: A 451 GLN cc_start: 0.8240 (mt0) cc_final: 0.7779 (mt0) REVERT: A 548 THR cc_start: 0.7605 (OUTLIER) cc_final: 0.7268 (p) REVERT: A 568 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6417 (mt-10) REVERT: A 661 MET cc_start: 0.7899 (mtt) cc_final: 0.7625 (mtm) outliers start: 14 outliers final: 3 residues processed: 65 average time/residue: 1.4314 time to fit residues: 96.4174 Evaluate side-chains 65 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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: 8.9990 chunk 43 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.119559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.098344 restraints weight = 5115.480| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.34 r_work: 0.2879 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4908 Z= 0.130 Angle : 0.600 15.032 6700 Z= 0.297 Chirality : 0.040 0.147 779 Planarity : 0.005 0.046 817 Dihedral : 4.071 17.368 722 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 3.00 % Allowed : 11.40 % Favored : 85.60 % 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: 1.94 (0.35), residues: 609 helix: 1.87 (0.24), residues: 452 sheet: None (None), residues: 0 loop : -0.39 (0.55), 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 0.009 0.001 PHE A 453 TYR 0.011 0.001 TYR A 128 ARG 0.004 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.04088 ( 342) hydrogen bonds : angle 5.34856 ( 1020) SS BOND : bond 0.00243 ( 4) SS BOND : angle 0.79698 ( 8) covalent geometry : bond 0.00282 ( 4904) covalent geometry : angle 0.59964 ( 6692) *********************** 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 78 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.537 Fit side-chains REVERT: A 45 CYS cc_start: 0.7780 (m) cc_final: 0.6934 (p) REVERT: A 46 ARG cc_start: 0.6274 (ttt90) cc_final: 0.5909 (ttt-90) REVERT: A 254 PHE cc_start: 0.7674 (t80) cc_final: 0.7456 (t80) REVERT: A 281 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.6916 (tt) REVERT: A 300 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7293 (mmt180) REVERT: A 448 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8385 (mm-40) REVERT: A 451 GLN cc_start: 0.8280 (mt0) cc_final: 0.7816 (mt0) REVERT: A 548 THR cc_start: 0.7637 (OUTLIER) cc_final: 0.7360 (p) REVERT: A 568 GLU cc_start: 0.7053 (mt-10) cc_final: 0.6485 (mt-10) outliers start: 15 outliers final: 4 residues processed: 70 average time/residue: 1.3491 time to fit residues: 97.9536 Evaluate side-chains 65 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 56 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 23 optimal weight: 0.0040 chunk 35 optimal weight: 0.0030 chunk 41 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.5204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.123935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.103150 restraints weight = 5086.842| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.31 r_work: 0.2952 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4908 Z= 0.111 Angle : 0.575 14.932 6700 Z= 0.281 Chirality : 0.039 0.141 779 Planarity : 0.005 0.046 817 Dihedral : 3.907 17.636 722 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 2.00 % Allowed : 12.80 % 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: 2.11 (0.35), residues: 609 helix: 1.99 (0.24), residues: 453 sheet: None (None), residues: 0 loop : -0.33 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 65 HIS 0.002 0.001 HIS A 80 PHE 0.008 0.001 PHE A 534 TYR 0.011 0.001 TYR A 188 ARG 0.002 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.03656 ( 342) hydrogen bonds : angle 5.15014 ( 1020) SS BOND : bond 0.00208 ( 4) SS BOND : angle 0.70727 ( 8) covalent geometry : bond 0.00227 ( 4904) covalent geometry : angle 0.57438 ( 6692) *********************** 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 76 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.495 Fit side-chains REVERT: A 45 CYS cc_start: 0.7791 (m) cc_final: 0.6901 (p) REVERT: A 46 ARG cc_start: 0.6183 (ttt90) cc_final: 0.5856 (ttt-90) REVERT: A 451 GLN cc_start: 0.8175 (mt0) cc_final: 0.7910 (mt0) REVERT: A 548 THR cc_start: 0.7680 (OUTLIER) cc_final: 0.7407 (p) REVERT: A 568 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6285 (mt-10) outliers start: 10 outliers final: 3 residues processed: 72 average time/residue: 1.3921 time to fit residues: 103.8946 Evaluate side-chains 63 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 56 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 25 optimal weight: 0.3980 chunk 49 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 = 0.3256 r_free = 0.3256 target = 0.118543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.096766 restraints weight = 5196.634| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.42 r_work: 0.2854 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4908 Z= 0.155 Angle : 0.637 16.045 6700 Z= 0.312 Chirality : 0.042 0.149 779 Planarity : 0.005 0.048 817 Dihedral : 3.982 16.657 722 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.60 % Allowed : 13.60 % 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: 2.00 (0.35), residues: 609 helix: 1.89 (0.24), residues: 452 sheet: None (None), residues: 0 loop : -0.29 (0.55), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 487 HIS 0.004 0.001 HIS A 80 PHE 0.010 0.002 PHE A 453 TYR 0.013 0.002 TYR A 188 ARG 0.003 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.04334 ( 342) hydrogen bonds : angle 5.36002 ( 1020) SS BOND : bond 0.00234 ( 4) SS BOND : angle 0.71935 ( 8) covalent geometry : bond 0.00353 ( 4904) covalent geometry : angle 0.63731 ( 6692) *********************** 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 70 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.559 Fit side-chains REVERT: A 45 CYS cc_start: 0.7894 (m) cc_final: 0.7004 (p) REVERT: A 46 ARG cc_start: 0.6371 (ttt90) cc_final: 0.5951 (ttt-90) REVERT: A 300 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7295 (mmt180) REVERT: A 451 GLN cc_start: 0.8223 (mt0) cc_final: 0.7937 (mt0) REVERT: A 548 THR cc_start: 0.7652 (OUTLIER) cc_final: 0.7368 (p) REVERT: A 568 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6450 (mt-10) outliers start: 8 outliers final: 4 residues processed: 67 average time/residue: 1.4275 time to fit residues: 99.2058 Evaluate side-chains 65 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 391 MET Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 18 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 167 GLN ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.117328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.096139 restraints weight = 5125.811| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.34 r_work: 0.2847 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4908 Z= 0.171 Angle : 0.660 16.595 6700 Z= 0.323 Chirality : 0.043 0.152 779 Planarity : 0.005 0.050 817 Dihedral : 4.070 16.709 722 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % 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: 1.88 (0.35), residues: 609 helix: 1.80 (0.24), residues: 451 sheet: None (None), residues: 0 loop : -0.30 (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 0.017 0.002 PHE A 254 TYR 0.012 0.002 TYR A 455 ARG 0.003 0.000 ARG A 267 Details of bonding type rmsd hydrogen bonds : bond 0.04551 ( 342) hydrogen bonds : angle 5.45183 ( 1020) SS BOND : bond 0.00297 ( 4) SS BOND : angle 0.77877 ( 8) covalent geometry : bond 0.00393 ( 4904) covalent geometry : angle 0.65949 ( 6692) *********************** 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 70 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.488 Fit side-chains REVERT: A 45 CYS cc_start: 0.7894 (m) cc_final: 0.6946 (p) REVERT: A 46 ARG cc_start: 0.6307 (ttt90) cc_final: 0.5953 (ttt-90) REVERT: A 300 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7284 (mmt180) REVERT: A 451 GLN cc_start: 0.8262 (mt0) cc_final: 0.7974 (mt0) REVERT: A 548 THR cc_start: 0.7652 (OUTLIER) cc_final: 0.7367 (p) REVERT: A 568 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6500 (mt-10) outliers start: 9 outliers final: 5 residues processed: 65 average time/residue: 1.3659 time to fit residues: 92.1912 Evaluate side-chains 67 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 391 MET Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 12 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.0570 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- 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 = 0.3285 r_free = 0.3285 target = 0.121023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.099961 restraints weight = 5120.637| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.32 r_work: 0.2908 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 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 0.038 4908 Z= 0.125 Angle : 0.614 15.828 6700 Z= 0.299 Chirality : 0.040 0.146 779 Planarity : 0.005 0.047 817 Dihedral : 3.930 17.350 722 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.80 % Allowed : 14.60 % 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: 2.04 (0.35), residues: 609 helix: 1.95 (0.24), residues: 451 sheet: None (None), residues: 0 loop : -0.35 (0.54), residues: 158 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 0.009 0.001 PHE A 534 TYR 0.011 0.001 TYR A 188 ARG 0.003 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.03976 ( 342) hydrogen bonds : angle 5.26995 ( 1020) SS BOND : bond 0.00222 ( 4) SS BOND : angle 0.78858 ( 8) covalent geometry : bond 0.00269 ( 4904) covalent geometry : angle 0.61391 ( 6692) ********************** 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 70 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.654 Fit side-chains REVERT: A 45 CYS cc_start: 0.7749 (m) cc_final: 0.6695 (p) REVERT: A 46 ARG cc_start: 0.6256 (ttt90) cc_final: 0.5850 (ttt-90) REVERT: A 300 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7251 (mmt180) REVERT: A 451 GLN cc_start: 0.8190 (mt0) cc_final: 0.7956 (mt0) REVERT: A 548 THR cc_start: 0.7604 (OUTLIER) cc_final: 0.7318 (p) REVERT: A 568 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6381 (mt-10) outliers start: 4 outliers final: 2 residues processed: 68 average time/residue: 1.6201 time to fit residues: 113.8824 Evaluate side-chains 66 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 391 MET Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 33 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 55 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 50 optimal weight: 0.1980 chunk 3 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3284 r_free = 0.3284 target = 0.120978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.099937 restraints weight = 5185.163| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.31 r_work: 0.2907 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4908 Z= 0.126 Angle : 0.624 16.018 6700 Z= 0.302 Chirality : 0.040 0.147 779 Planarity : 0.005 0.047 817 Dihedral : 3.895 17.030 722 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % 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: 2.06 (0.35), residues: 609 helix: 1.96 (0.24), residues: 452 sheet: None (None), residues: 0 loop : -0.34 (0.54), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 440 HIS 0.003 0.001 HIS A 80 PHE 0.026 0.001 PHE A 206 TYR 0.010 0.001 TYR A 188 ARG 0.005 0.000 ARG A 136 Details of bonding type rmsd hydrogen bonds : bond 0.04007 ( 342) hydrogen bonds : angle 5.25521 ( 1020) SS BOND : bond 0.00208 ( 4) SS BOND : angle 0.75925 ( 8) covalent geometry : bond 0.00274 ( 4904) covalent geometry : angle 0.62406 ( 6692) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3452.91 seconds wall clock time: 60 minutes 55.79 seconds (3655.79 seconds total)