Starting phenix.real_space_refine on Fri Aug 22 15:09:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hb0_34610/08_2025/8hb0_34610.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hb0_34610/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8hb0_34610/08_2025/8hb0_34610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hb0_34610/08_2025/8hb0_34610.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hb0_34610/08_2025/8hb0_34610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hb0_34610/08_2025/8hb0_34610.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.63, per 1000 atoms: 0.34 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: 0.59 Conformation dependent library (CDL) restraints added in 199.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.16 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: 0.80 Time building geometry restraints manager: 0.82 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: 0.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.490 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.610 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG A 368 TYR 0.021 0.005 TYR A 128 PHE 0.023 0.004 PHE A 326 TRP 0.015 0.003 TRP A 291 HIS 0.013 0.002 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.01547 ( 4904) covalent geometry : angle 2.21624 ( 6692) SS BOND : bond 0.27721 ( 4) SS BOND : angle 19.03329 ( 8) hydrogen bonds : bond 0.19018 ( 342) hydrogen bonds : angle 8.71411 ( 1020) *********************** 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 : 0.195 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: 0.5722 time to fit residues: 57.1535 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 : 0.194 ------------------------------------------------------------------------------- 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 54 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 = 0.3267 r_free = 0.3267 target = 0.119864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.098854 restraints weight = 5109.016| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.31 r_work: 0.2885 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4908 Z= 0.150 Angle : 0.679 12.520 6700 Z= 0.347 Chirality : 0.042 0.140 779 Planarity : 0.005 0.039 817 Dihedral : 4.801 18.297 726 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.20 % Allowed : 8.00 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.33), residues: 609 helix: 1.07 (0.23), residues: 451 sheet: None (None), residues: 0 loop : -0.95 (0.51), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 499 TYR 0.021 0.002 TYR A 256 PHE 0.013 0.002 PHE A 520 TRP 0.016 0.002 TRP A 65 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 4904) covalent geometry : angle 0.67736 ( 6692) SS BOND : bond 0.00446 ( 4) SS BOND : angle 1.62418 ( 8) hydrogen bonds : bond 0.04673 ( 342) hydrogen bonds : angle 5.75087 ( 1020) *********************** 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 84 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.184 Fit side-chains REVERT: A 45 CYS cc_start: 0.7862 (m) cc_final: 0.7030 (p) REVERT: A 231 ASP cc_start: 0.8378 (p0) cc_final: 0.8128 (p0) REVERT: A 254 PHE cc_start: 0.7687 (t80) cc_final: 0.7419 (t80) REVERT: A 300 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7344 (mmt180) REVERT: A 407 MET cc_start: 0.8885 (mmm) cc_final: 0.8670 (mmt) REVERT: A 416 ARG cc_start: 0.7310 (mpt180) cc_final: 0.7009 (mtm180) REVERT: A 420 ARG cc_start: 0.7029 (ttt180) cc_final: 0.6697 (ttm-80) REVERT: A 448 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8262 (mm-40) REVERT: A 451 GLN cc_start: 0.8153 (mt0) cc_final: 0.7668 (mt0) REVERT: A 515 SER cc_start: 0.7152 (p) cc_final: 0.6751 (m) REVERT: A 548 THR cc_start: 0.7563 (m) cc_final: 0.7282 (p) REVERT: A 661 MET cc_start: 0.8009 (mtt) cc_final: 0.7788 (mtm) outliers start: 11 outliers final: 1 residues processed: 81 average time/residue: 0.6118 time to fit residues: 51.4346 Evaluate side-chains 64 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 54 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 55 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.3287 r_free = 0.3287 target = 0.121882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.098869 restraints weight = 4989.304| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.47 r_work: 0.2884 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4908 Z= 0.129 Angle : 0.617 13.132 6700 Z= 0.309 Chirality : 0.041 0.148 779 Planarity : 0.005 0.044 817 Dihedral : 4.288 17.607 722 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.35), residues: 609 helix: 1.75 (0.24), residues: 453 sheet: None (None), residues: 0 loop : -0.78 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 353 TYR 0.013 0.002 TYR A 256 PHE 0.010 0.001 PHE A 520 TRP 0.011 0.001 TRP A 487 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 4904) covalent geometry : angle 0.61610 ( 6692) SS BOND : bond 0.00293 ( 4) SS BOND : angle 1.23700 ( 8) hydrogen bonds : bond 0.04191 ( 342) hydrogen bonds : angle 5.38896 ( 1020) *********************** 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 : 0.206 Fit side-chains REVERT: A 45 CYS cc_start: 0.7917 (m) cc_final: 0.6945 (p) REVERT: A 46 ARG cc_start: 0.6158 (ttt90) cc_final: 0.5819 (ttt-90) REVERT: A 231 ASP cc_start: 0.8178 (p0) cc_final: 0.7958 (p0) REVERT: A 254 PHE cc_start: 0.7623 (t80) cc_final: 0.7332 (t80) REVERT: A 300 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7612 (mmt180) REVERT: A 407 MET cc_start: 0.8737 (mmm) cc_final: 0.8525 (mmt) REVERT: A 416 ARG cc_start: 0.7190 (mpt180) cc_final: 0.6852 (mtm180) REVERT: A 420 ARG cc_start: 0.6942 (ttt180) cc_final: 0.6616 (ttm-80) REVERT: A 448 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8269 (mm-40) REVERT: A 451 GLN cc_start: 0.8077 (mt0) cc_final: 0.7527 (mt0) REVERT: A 548 THR cc_start: 0.7399 (m) cc_final: 0.7055 (p) REVERT: A 661 MET cc_start: 0.7899 (mtt) cc_final: 0.7588 (mtm) outliers start: 13 outliers final: 3 residues processed: 71 average time/residue: 0.6356 time to fit residues: 46.8501 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 : 0.179 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 22 optimal weight: 0.0170 chunk 53 optimal weight: 0.0670 chunk 12 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.3321 r_free = 0.3321 target = 0.124567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.101984 restraints weight = 4955.930| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.47 r_work: 0.2929 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4908 Z= 0.112 Angle : 0.579 13.423 6700 Z= 0.286 Chirality : 0.039 0.141 779 Planarity : 0.005 0.044 817 Dihedral : 4.036 18.018 722 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 3.00 % Allowed : 9.40 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.35), residues: 609 helix: 2.02 (0.24), residues: 453 sheet: None (None), residues: 0 loop : -0.65 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 353 TYR 0.010 0.001 TYR A 256 PHE 0.009 0.001 PHE A 520 TRP 0.010 0.001 TRP A 65 HIS 0.003 0.001 HIS A 555 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 4904) covalent geometry : angle 0.57874 ( 6692) SS BOND : bond 0.00220 ( 4) SS BOND : angle 0.90468 ( 8) hydrogen bonds : bond 0.03734 ( 342) hydrogen bonds : angle 5.14499 ( 1020) *********************** 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 82 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.196 Fit side-chains REVERT: A 45 CYS cc_start: 0.7879 (m) cc_final: 0.6916 (p) REVERT: A 46 ARG cc_start: 0.5986 (ttt90) cc_final: 0.5652 (ttt-90) REVERT: A 254 PHE cc_start: 0.7518 (t80) cc_final: 0.7277 (t80) REVERT: A 300 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7530 (mmt180) REVERT: A 407 MET cc_start: 0.8713 (mmm) cc_final: 0.8487 (mmt) REVERT: A 416 ARG cc_start: 0.7235 (mpt180) cc_final: 0.6846 (mtm180) REVERT: A 420 ARG cc_start: 0.6767 (ttt180) cc_final: 0.6428 (ttm-80) REVERT: A 448 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8195 (mm-40) REVERT: A 451 GLN cc_start: 0.8014 (mt0) cc_final: 0.7519 (mt0) REVERT: A 548 THR cc_start: 0.7342 (OUTLIER) cc_final: 0.6991 (p) REVERT: A 568 GLU cc_start: 0.6853 (mt-10) cc_final: 0.5986 (mt-10) REVERT: A 661 MET cc_start: 0.7921 (mtt) cc_final: 0.7634 (mtm) outliers start: 15 outliers final: 3 residues processed: 78 average time/residue: 0.6699 time to fit residues: 54.1503 Evaluate side-chains 66 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 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 48 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3271 r_free = 0.3271 target = 0.120325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.098389 restraints weight = 5046.778| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.34 r_work: 0.2878 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2893 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= 0.142 Angle : 0.610 15.142 6700 Z= 0.301 Chirality : 0.041 0.148 779 Planarity : 0.005 0.046 817 Dihedral : 4.045 17.036 722 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.40 % Allowed : 12.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.35), residues: 609 helix: 1.96 (0.24), residues: 452 sheet: None (None), residues: 0 loop : -0.52 (0.54), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 353 TYR 0.010 0.002 TYR A 290 PHE 0.010 0.001 PHE A 453 TRP 0.011 0.001 TRP A 487 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 4904) covalent geometry : angle 0.60927 ( 6692) SS BOND : bond 0.00252 ( 4) SS BOND : angle 0.82666 ( 8) hydrogen bonds : bond 0.04228 ( 342) hydrogen bonds : angle 5.33251 ( 1020) *********************** 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: 12 poor density : 59 time to evaluate : 0.219 Fit side-chains REVERT: A 45 CYS cc_start: 0.7825 (m) cc_final: 0.6898 (p) REVERT: A 46 ARG cc_start: 0.6115 (ttt90) cc_final: 0.5743 (ttt-90) REVERT: A 254 PHE cc_start: 0.7569 (t80) cc_final: 0.7333 (t80) REVERT: A 281 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.6860 (tt) REVERT: A 300 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7477 (mmt180) REVERT: A 349 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: A 407 MET cc_start: 0.8752 (mmm) cc_final: 0.8520 (mmt) REVERT: A 416 ARG cc_start: 0.7195 (mpt180) cc_final: 0.6915 (mtm180) REVERT: A 420 ARG cc_start: 0.6926 (ttt180) cc_final: 0.6720 (ttm-80) REVERT: A 448 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8341 (mm-40) REVERT: A 451 GLN cc_start: 0.8215 (mt0) cc_final: 0.7805 (mt0) REVERT: A 548 THR cc_start: 0.7575 (OUTLIER) cc_final: 0.7263 (p) REVERT: A 661 MET cc_start: 0.7922 (mtt) cc_final: 0.7694 (mtm) outliers start: 12 outliers final: 3 residues processed: 66 average time/residue: 0.7563 time to fit residues: 51.6613 Evaluate side-chains 66 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 359 VAL 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 36 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3278 r_free = 0.3278 target = 0.120769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.098219 restraints weight = 5161.134| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.40 r_work: 0.2880 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2995 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= 0.133 Angle : 0.600 15.223 6700 Z= 0.296 Chirality : 0.041 0.148 779 Planarity : 0.005 0.046 817 Dihedral : 3.991 17.183 722 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.40 % Allowed : 11.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.35), residues: 609 helix: 1.97 (0.24), residues: 452 sheet: None (None), residues: 0 loop : -0.45 (0.54), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 353 TYR 0.010 0.001 TYR A 290 PHE 0.025 0.001 PHE A 206 TRP 0.011 0.001 TRP A 487 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 4904) covalent geometry : angle 0.60023 ( 6692) SS BOND : bond 0.00249 ( 4) SS BOND : angle 0.76098 ( 8) hydrogen bonds : bond 0.04094 ( 342) hydrogen bonds : angle 5.30455 ( 1020) *********************** 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: 17 poor density : 63 time to evaluate : 0.202 Fit side-chains REVERT: A 45 CYS cc_start: 0.7742 (m) cc_final: 0.6820 (p) REVERT: A 46 ARG cc_start: 0.6076 (ttt90) cc_final: 0.5705 (ttt-90) REVERT: A 254 PHE cc_start: 0.7610 (t80) cc_final: 0.7389 (t80) REVERT: A 300 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7332 (mmt180) REVERT: A 349 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: A 407 MET cc_start: 0.8735 (mmm) cc_final: 0.8503 (mmt) REVERT: A 416 ARG cc_start: 0.7168 (mpt180) cc_final: 0.6956 (mtm180) REVERT: A 420 ARG cc_start: 0.6804 (ttt180) cc_final: 0.6595 (ttm-80) REVERT: A 451 GLN cc_start: 0.8195 (mt0) cc_final: 0.7836 (mt0) REVERT: A 548 THR cc_start: 0.7584 (OUTLIER) cc_final: 0.7265 (p) REVERT: A 568 GLU cc_start: 0.6857 (mt-10) cc_final: 0.6176 (mt-10) REVERT: A 661 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7707 (mtm) outliers start: 17 outliers final: 6 residues processed: 71 average time/residue: 0.6818 time to fit residues: 50.2438 Evaluate side-chains 69 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 179 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 359 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 51 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN A 168 GLN A 250 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.117522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.095877 restraints weight = 5120.061| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.33 r_work: 0.2840 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4908 Z= 0.177 Angle : 0.647 16.072 6700 Z= 0.320 Chirality : 0.043 0.154 779 Planarity : 0.005 0.050 817 Dihedral : 4.127 16.569 722 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.60 % Allowed : 12.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.35), residues: 609 helix: 1.82 (0.24), residues: 451 sheet: None (None), residues: 0 loop : -0.41 (0.55), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 267 TYR 0.011 0.002 TYR A 290 PHE 0.011 0.002 PHE A 326 TRP 0.013 0.001 TRP A 487 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 4904) covalent geometry : angle 0.64699 ( 6692) SS BOND : bond 0.00291 ( 4) SS BOND : angle 0.80228 ( 8) hydrogen bonds : bond 0.04641 ( 342) hydrogen bonds : angle 5.48139 ( 1020) *********************** 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 74 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.195 Fit side-chains REVERT: A 44 MET cc_start: 0.7835 (mtm) cc_final: 0.7541 (mtm) REVERT: A 45 CYS cc_start: 0.7926 (m) cc_final: 0.6948 (p) REVERT: A 46 ARG cc_start: 0.6129 (ttt90) cc_final: 0.5767 (ttt-90) REVERT: A 254 PHE cc_start: 0.7717 (t80) cc_final: 0.7474 (t80) REVERT: A 300 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7326 (mmt180) REVERT: A 416 ARG cc_start: 0.7162 (mpt180) cc_final: 0.6919 (mtm180) REVERT: A 420 ARG cc_start: 0.6834 (ttt180) cc_final: 0.6632 (ttm-80) REVERT: A 451 GLN cc_start: 0.8198 (mt0) cc_final: 0.7916 (mt0) REVERT: A 548 THR cc_start: 0.7633 (OUTLIER) cc_final: 0.7319 (p) REVERT: A 553 ARG cc_start: 0.6843 (OUTLIER) cc_final: 0.6636 (ttt180) REVERT: A 568 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6467 (mt-10) REVERT: A 661 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7734 (mtm) outliers start: 13 outliers final: 4 residues processed: 68 average time/residue: 0.6790 time to fit residues: 47.9573 Evaluate side-chains 67 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.190 ------------------------------------------------------------------------------- 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 281 LEU 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 553 ARG 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 10 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.120770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.098791 restraints weight = 5195.320| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.35 r_work: 0.2884 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 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 : 0.003 0.035 4908 Z= 0.128 Angle : 0.601 15.182 6700 Z= 0.296 Chirality : 0.040 0.146 779 Planarity : 0.005 0.047 817 Dihedral : 3.989 17.067 722 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.20 % Allowed : 13.60 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.35), residues: 609 helix: 1.94 (0.24), residues: 451 sheet: None (None), residues: 0 loop : -0.33 (0.55), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 353 TYR 0.011 0.001 TYR A 128 PHE 0.009 0.001 PHE A 453 TRP 0.011 0.001 TRP A 276 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 4904) covalent geometry : angle 0.60124 ( 6692) SS BOND : bond 0.00235 ( 4) SS BOND : angle 0.75046 ( 8) hydrogen bonds : bond 0.04074 ( 342) hydrogen bonds : angle 5.30790 ( 1020) *********************** 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: 11 poor density : 63 time to evaluate : 0.187 Fit side-chains REVERT: A 44 MET cc_start: 0.7819 (mtm) cc_final: 0.7556 (mtm) REVERT: A 45 CYS cc_start: 0.7795 (m) cc_final: 0.6804 (p) REVERT: A 46 ARG cc_start: 0.6081 (ttt90) cc_final: 0.5731 (ttt-90) REVERT: A 300 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7217 (mmt180) REVERT: A 420 ARG cc_start: 0.6841 (ttt180) cc_final: 0.6535 (ttp80) REVERT: A 451 GLN cc_start: 0.8203 (mt0) cc_final: 0.7912 (mt0) REVERT: A 548 THR cc_start: 0.7601 (OUTLIER) cc_final: 0.7290 (p) REVERT: A 568 GLU cc_start: 0.6844 (mt-10) cc_final: 0.6246 (mt-10) REVERT: A 661 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7729 (mtm) outliers start: 11 outliers final: 3 residues processed: 69 average time/residue: 0.7274 time to fit residues: 51.9167 Evaluate side-chains 66 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.185 ------------------------------------------------------------------------------- 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 494 LEU 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 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.119306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.097495 restraints weight = 5087.230| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.33 r_work: 0.2866 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4908 Z= 0.149 Angle : 0.628 15.875 6700 Z= 0.308 Chirality : 0.042 0.149 779 Planarity : 0.005 0.048 817 Dihedral : 4.010 16.759 722 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.40 % Allowed : 13.40 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.35), residues: 609 helix: 1.89 (0.24), residues: 451 sheet: None (None), residues: 0 loop : -0.31 (0.55), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 136 TYR 0.011 0.002 TYR A 188 PHE 0.025 0.002 PHE A 206 TRP 0.011 0.001 TRP A 487 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 4904) covalent geometry : angle 0.62745 ( 6692) SS BOND : bond 0.00249 ( 4) SS BOND : angle 0.74759 ( 8) hydrogen bonds : bond 0.04330 ( 342) hydrogen bonds : angle 5.35878 ( 1020) *********************** 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 73 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.187 Fit side-chains REVERT: A 44 MET cc_start: 0.7857 (mtm) cc_final: 0.7623 (mtm) REVERT: A 45 CYS cc_start: 0.7836 (m) cc_final: 0.6840 (p) REVERT: A 46 ARG cc_start: 0.6132 (ttt90) cc_final: 0.5782 (ttt-90) REVERT: A 300 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7243 (mmt180) REVERT: A 420 ARG cc_start: 0.6835 (ttt180) cc_final: 0.6551 (ttp80) REVERT: A 451 GLN cc_start: 0.8200 (mt0) cc_final: 0.7898 (mt0) REVERT: A 548 THR cc_start: 0.7575 (OUTLIER) cc_final: 0.7267 (p) REVERT: A 568 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6488 (mt-10) REVERT: A 661 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7732 (mtm) outliers start: 12 outliers final: 4 residues processed: 68 average time/residue: 0.6827 time to fit residues: 48.1081 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 : 0.176 ------------------------------------------------------------------------------- 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 281 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 33 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.122244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.100468 restraints weight = 5129.650| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.33 r_work: 0.2911 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3266 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= 0.123 Angle : 0.606 15.420 6700 Z= 0.296 Chirality : 0.040 0.145 779 Planarity : 0.005 0.047 817 Dihedral : 3.908 17.128 722 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.20 % Allowed : 14.60 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.09 (0.35), residues: 609 helix: 1.97 (0.24), residues: 452 sheet: None (None), residues: 0 loop : -0.29 (0.55), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 136 TYR 0.011 0.001 TYR A 188 PHE 0.017 0.001 PHE A 254 TRP 0.011 0.001 TRP A 276 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 4904) covalent geometry : angle 0.60590 ( 6692) SS BOND : bond 0.00221 ( 4) SS BOND : angle 0.76634 ( 8) hydrogen bonds : bond 0.03977 ( 342) hydrogen bonds : angle 5.25137 ( 1020) ********************** 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: 6 poor density : 64 time to evaluate : 0.200 Fit side-chains REVERT: A 44 MET cc_start: 0.7825 (mtm) cc_final: 0.7594 (mtm) REVERT: A 45 CYS cc_start: 0.7790 (m) cc_final: 0.6670 (p) REVERT: A 46 ARG cc_start: 0.6188 (ttt90) cc_final: 0.5775 (ttt-90) REVERT: A 300 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7178 (mmt180) REVERT: A 420 ARG cc_start: 0.6847 (ttt180) cc_final: 0.6546 (ttp80) REVERT: A 451 GLN cc_start: 0.8170 (mt0) cc_final: 0.7917 (mt0) REVERT: A 548 THR cc_start: 0.7583 (OUTLIER) cc_final: 0.7282 (p) REVERT: A 568 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6295 (mt-10) REVERT: A 661 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7729 (mtm) outliers start: 6 outliers final: 2 residues processed: 67 average time/residue: 0.6319 time to fit residues: 44.0153 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 : 0.200 ------------------------------------------------------------------------------- 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 1 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 15 optimal weight: 0.0040 chunk 25 optimal weight: 0.0040 chunk 41 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 0.7406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.124001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.101605 restraints weight = 5087.119| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.41 r_work: 0.2932 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4908 Z= 0.118 Angle : 0.598 15.471 6700 Z= 0.292 Chirality : 0.040 0.143 779 Planarity : 0.005 0.046 817 Dihedral : 3.825 17.050 722 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.40 % Allowed : 14.20 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.35), residues: 609 helix: 2.04 (0.24), residues: 453 sheet: None (None), residues: 0 loop : -0.28 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 136 TYR 0.010 0.001 TYR A 188 PHE 0.009 0.001 PHE A 534 TRP 0.012 0.001 TRP A 440 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 4904) covalent geometry : angle 0.59803 ( 6692) SS BOND : bond 0.00187 ( 4) SS BOND : angle 0.75043 ( 8) hydrogen bonds : bond 0.03832 ( 342) hydrogen bonds : angle 5.15894 ( 1020) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1763.07 seconds wall clock time: 30 minutes 59.02 seconds (1859.02 seconds total)