Starting phenix.real_space_refine on Thu Jul 2 00:32:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hb0_34610/07_2026/8hb0_34610.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hb0_34610/07_2026/8hb0_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_34610/07_2026/8hb0_34610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hb0_34610/07_2026/8hb0_34610.map" model { file = "/net/cci-nas-00/data/ceres_data/8hb0_34610/07_2026/8hb0_34610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hb0_34610/07_2026/8hb0_34610.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hb0_34610/07_2026/8hb0_34610.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hb0_34610/07_2026/8hb0_34610.cif" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 chiralities: 1 Time building chain proxies: 1.10, per 1000 atoms: 0.23 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: 0.47 Conformation dependent library (CDL) restraints added in 115.6 milliseconds 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1116 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 0 sheets defined 82.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 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: 0.67 Time building geometry restraints manager: 0.55 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: 2551 16.08 - 32.16: 219 32.16 - 48.24: 45 48.24 - 64.33: 14 64.33 - 80.41: 4 Dihedral angle restraints: 2833 sinusoidal: 1081 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 2830 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 387 0.059 - 0.118: 232 0.118 - 0.177: 116 0.177 - 0.236: 39 0.236 - 0.295: 5 Chirality restraints: 779 Sorted by residual: chirality pdb=" CA PRO A 269 " pdb=" N PRO A 269 " pdb=" C PRO A 269 " pdb=" CB PRO A 269 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CB VAL A 106 " pdb=" CA VAL A 106 " pdb=" CG1 VAL A 106 " pdb=" CG2 VAL A 106 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA VAL A 560 " pdb=" N VAL A 560 " pdb=" C VAL A 560 " pdb=" CB VAL A 560 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 776 not shown) Planarity restraints: 817 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 801 " -0.043 2.00e-02 2.50e+03 3.51e-02 1.54e+01 pdb=" C7 NAG A 801 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG A 801 " -0.033 2.00e-02 2.50e+03 pdb=" N2 NAG A 801 " 0.055 2.00e-02 2.50e+03 pdb=" O7 NAG A 801 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 521 " 0.016 2.00e-02 2.50e+03 3.08e-02 9.46e+00 pdb=" C LEU A 521 " -0.053 2.00e-02 2.50e+03 pdb=" O LEU A 521 " 0.019 2.00e-02 2.50e+03 pdb=" N CYS A 522 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 520 " -0.014 2.00e-02 2.50e+03 2.87e-02 8.25e+00 pdb=" C PHE A 520 " 0.050 2.00e-02 2.50e+03 pdb=" O PHE A 520 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU A 521 " -0.017 2.00e-02 2.50e+03 ... (remaining 814 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 104 2.70 - 3.25: 4833 3.25 - 3.80: 7942 3.80 - 4.35: 10878 4.35 - 4.90: 17609 Nonbonded interactions: 41366 Sorted by model distance: nonbonded pdb=" O ALA A 73 " pdb="NA NA A 803 " model vdw 2.153 2.470 nonbonded pdb=" O ILE A 76 " pdb="NA NA A 803 " model vdw 2.267 2.470 nonbonded pdb=" OG SER A 392 " pdb="NA NA A 803 " model vdw 2.299 2.470 nonbonded pdb=" O GLY A 332 " pdb=" OG SER A 335 " model vdw 2.309 3.040 nonbonded pdb=" ND2 ASN A 250 " pdb=" C1 NAG A 801 " model vdw 2.344 3.550 ... (remaining 41361 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 5.580 Find NCS groups from input model: 0.010 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:5.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 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 : 13.432 80.313 1705 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 are 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/Z covalent geometry : bond 0.01547 / 1.14 ( 4904) covalent geometry : angle 2.21624 / 1.65 ( 6692) SS BOND : bond 0.27721 / 13.76 ( 4) SS BOND : angle 19.03329 / 10.06 ( 8) hydrogen bonds : bond 0.19018 / 12.80 ( 342) hydrogen bonds : angle 8.71411 / 6.49 ( 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 : 0.176 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: 0.4137 time to fit residues: 41.4734 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 : 0.100 ------------------------------------------------------------------------------- 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... 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 = 0.3263 r_free = 0.3263 target = 0.119438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.098437 restraints weight = 5112.235| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.31 r_work: 0.2878 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4908 Z= 0.151 Angle : 0.684 12.385 6700 Z= 0.350 Chirality : 0.043 0.143 779 Planarity : 0.005 0.039 817 Dihedral : 4.887 18.263 705 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.00 % Allowed : 8.00 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.33), residues: 609 helix: 1.06 (0.23), residues: 451 sheet: None (None), residues: 0 loop : -0.96 (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 0.014 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/Z covalent geometry : bond 0.00329 / 0.15 ( 4904) covalent geometry : angle 0.68214 / 0.35 ( 6692) SS BOND : bond 0.00662 / 0.33 ( 4) SS BOND : angle 1.69167 / 0.84 ( 8) hydrogen bonds : bond 0.04751 / 3.13 ( 342) hydrogen bonds : angle 5.77440 / 4.35 ( 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: 10 poor density : 74 time to evaluate : 0.162 Fit side-chains REVERT: A 45 CYS cc_start: 0.7892 (m) cc_final: 0.7065 (p) REVERT: A 231 ASP cc_start: 0.8377 (p0) cc_final: 0.8128 (p0) REVERT: A 254 PHE cc_start: 0.7683 (t80) cc_final: 0.7423 (t80) REVERT: A 281 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7245 (tt) REVERT: A 300 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7342 (mmt180) REVERT: A 407 MET cc_start: 0.8886 (mmm) cc_final: 0.8671 (mmt) REVERT: A 408 ASP cc_start: 0.8653 (m-30) cc_final: 0.8447 (m-30) REVERT: A 416 ARG cc_start: 0.7320 (mpt180) cc_final: 0.7009 (mtm180) REVERT: A 420 ARG cc_start: 0.7042 (ttt180) cc_final: 0.6703 (ttm-80) REVERT: A 448 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8258 (mm-40) REVERT: A 451 GLN cc_start: 0.8156 (mt0) cc_final: 0.7675 (mt0) REVERT: A 515 SER cc_start: 0.7125 (p) cc_final: 0.6742 (m) REVERT: A 548 THR cc_start: 0.7593 (m) cc_final: 0.7301 (p) REVERT: A 661 MET cc_start: 0.8031 (mtt) cc_final: 0.7807 (mtm) outliers start: 10 outliers final: 1 residues processed: 81 average time/residue: 0.4488 time to fit residues: 37.8086 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 : 0.151 ------------------------------------------------------------------------------- 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 54 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.119188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.097823 restraints weight = 5075.917| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.35 r_work: 0.2866 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2528 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= 0.145 Angle : 0.636 13.377 6700 Z= 0.320 Chirality : 0.042 0.150 779 Planarity : 0.005 0.045 817 Dihedral : 4.436 17.499 701 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.80 % Allowed : 10.00 % Favored : 87.20 % 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 are not related in a simple way. whole: 1.52 (0.35), residues: 609 helix: 1.63 (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 0.007 0.001 ARG A 353 TYR 0.014 0.002 TYR A 256 PHE 0.011 0.002 PHE A 453 TRP 0.013 0.001 TRP A 487 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 ( 4904) covalent geometry : angle 0.63469 / 0.32 ( 6692) SS BOND : bond 0.00343 / 0.17 ( 4) SS BOND : angle 1.25037 / 0.61 ( 8) hydrogen bonds : bond 0.04433 / 2.94 ( 342) hydrogen bonds : angle 5.48651 / 4.13 ( 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 71 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.201 Fit side-chains REVERT: A 45 CYS cc_start: 0.7920 (m) cc_final: 0.7054 (p) REVERT: A 46 ARG cc_start: 0.6272 (ttt90) cc_final: 0.5925 (ttt-90) REVERT: A 231 ASP cc_start: 0.8303 (p0) cc_final: 0.8034 (p0) REVERT: A 254 PHE cc_start: 0.7708 (t80) cc_final: 0.7458 (t80) REVERT: A 281 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7090 (tt) REVERT: A 300 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7696 (mmt180) REVERT: A 407 MET cc_start: 0.8827 (mmm) cc_final: 0.8608 (mmt) REVERT: A 416 ARG cc_start: 0.7316 (mpt180) cc_final: 0.6981 (mtm180) REVERT: A 420 ARG cc_start: 0.7010 (ttt180) cc_final: 0.6722 (ttm-80) REVERT: A 448 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8324 (mm-40) REVERT: A 451 GLN cc_start: 0.8207 (mt0) cc_final: 0.7699 (mt0) REVERT: A 548 THR cc_start: 0.7548 (m) cc_final: 0.7274 (p) REVERT: A 661 MET cc_start: 0.8008 (mtt) cc_final: 0.7741 (mtm) outliers start: 14 outliers final: 4 residues processed: 67 average time/residue: 0.5419 time to fit residues: 37.7990 Evaluate side-chains 63 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 644 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 21 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 53 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.123544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.100701 restraints weight = 4950.264| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.47 r_work: 0.2912 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2896 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= 0.116 Angle : 0.587 14.036 6700 Z= 0.289 Chirality : 0.039 0.141 779 Planarity : 0.005 0.044 817 Dihedral : 4.143 17.968 701 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 3.00 % Allowed : 9.80 % Favored : 87.20 % 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 are not related in a simple way. whole: 1.95 (0.35), residues: 609 helix: 1.95 (0.24), residues: 453 sheet: None (None), residues: 0 loop : -0.65 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 353 TYR 0.011 0.001 TYR A 410 PHE 0.009 0.001 PHE A 520 TRP 0.010 0.001 TRP A 65 HIS 0.002 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 ( 4904) covalent geometry : angle 0.58632 / 0.29 ( 6692) SS BOND : bond 0.00226 / 0.11 ( 4) SS BOND : angle 0.93967 / 0.46 ( 8) hydrogen bonds : bond 0.03836 / 2.54 ( 342) hydrogen bonds : angle 5.18549 / 3.90 ( 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 83 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.103 Fit side-chains REVERT: A 45 CYS cc_start: 0.7923 (m) cc_final: 0.6914 (p) REVERT: A 46 ARG cc_start: 0.5975 (ttt90) cc_final: 0.5633 (ttt-90) REVERT: A 254 PHE cc_start: 0.7551 (t80) cc_final: 0.7296 (t80) REVERT: A 300 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7484 (mmt180) REVERT: A 407 MET cc_start: 0.8693 (mmm) cc_final: 0.8437 (mmt) REVERT: A 416 ARG cc_start: 0.7191 (mpt180) cc_final: 0.6841 (mtm180) REVERT: A 420 ARG cc_start: 0.6672 (ttt180) cc_final: 0.6326 (ttm-80) REVERT: A 448 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8189 (mm-40) REVERT: A 451 GLN cc_start: 0.8031 (mt0) cc_final: 0.7459 (mt0) REVERT: A 548 THR cc_start: 0.7373 (OUTLIER) cc_final: 0.7021 (p) REVERT: A 661 MET cc_start: 0.7954 (mtt) cc_final: 0.7675 (mtm) outliers start: 15 outliers final: 2 residues processed: 78 average time/residue: 0.4235 time to fit residues: 34.3853 Evaluate side-chains 62 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.102 ------------------------------------------------------------------------------- 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 548 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 25 optimal weight: 0.0020 chunk 4 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.121760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.100080 restraints weight = 5039.761| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.32 r_work: 0.2901 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2917 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= 0.125 Angle : 0.595 14.659 6700 Z= 0.292 Chirality : 0.040 0.145 779 Planarity : 0.005 0.046 817 Dihedral : 4.057 17.398 701 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % 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 are not related in a simple way. whole: 2.04 (0.35), residues: 609 helix: 1.99 (0.24), residues: 452 sheet: None (None), residues: 0 loop : -0.54 (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 128 PHE 0.023 0.001 PHE A 206 TRP 0.010 0.001 TRP A 487 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 ( 4904) covalent geometry : angle 0.59511 / 0.29 ( 6692) SS BOND : bond 0.00231 / 0.12 ( 4) SS BOND : angle 0.80305 / 0.41 ( 8) hydrogen bonds : bond 0.03982 / 2.64 ( 342) hydrogen bonds : angle 5.24923 / 3.95 ( 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 75 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.147 Fit side-chains REVERT: A 44 MET cc_start: 0.7929 (mtm) cc_final: 0.7644 (mtm) REVERT: A 45 CYS cc_start: 0.7825 (m) cc_final: 0.6916 (p) REVERT: A 46 ARG cc_start: 0.6093 (ttt90) cc_final: 0.5740 (ttt-90) REVERT: A 281 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.6837 (tt) REVERT: A 300 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7544 (mmt180) REVERT: A 349 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7422 (mp0) REVERT: A 416 ARG cc_start: 0.7198 (mpt180) cc_final: 0.6924 (mtm180) REVERT: A 451 GLN cc_start: 0.8222 (mt0) cc_final: 0.7832 (mt0) REVERT: A 548 THR cc_start: 0.7498 (OUTLIER) cc_final: 0.7175 (p) REVERT: A 661 MET cc_start: 0.7937 (mtt) cc_final: 0.7698 (mtm) outliers start: 17 outliers final: 4 residues processed: 68 average time/residue: 0.5161 time to fit residues: 36.4015 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 : 0.176 ------------------------------------------------------------------------------- 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 349 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 391 MET 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: 1.9990 chunk 47 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 250 ASN A 557 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.118142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.096890 restraints weight = 5239.524| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.36 r_work: 0.2856 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4908 Z= 0.157 Angle : 0.629 15.441 6700 Z= 0.311 Chirality : 0.042 0.152 779 Planarity : 0.005 0.048 817 Dihedral : 4.102 16.844 701 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.35), residues: 609 helix: 1.89 (0.24), residues: 451 sheet: None (None), residues: 0 loop : -0.48 (0.55), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 353 TYR 0.011 0.002 TYR A 290 PHE 0.011 0.002 PHE A 453 TRP 0.012 0.001 TRP A 487 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 4904) covalent geometry : angle 0.62898 / 0.31 ( 6692) SS BOND : bond 0.00274 / 0.14 ( 4) SS BOND : angle 0.83566 / 0.46 ( 8) hydrogen bonds : bond 0.04419 / 2.94 ( 342) hydrogen bonds : angle 5.40509 / 4.07 ( 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 75 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.111 Fit side-chains REVERT: A 44 MET cc_start: 0.8010 (mtm) cc_final: 0.7702 (mtm) REVERT: A 45 CYS cc_start: 0.7880 (m) cc_final: 0.6943 (p) REVERT: A 46 ARG cc_start: 0.6178 (ttt90) cc_final: 0.5816 (ttt-90) REVERT: A 281 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.6980 (tt) REVERT: A 300 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7443 (mmt180) REVERT: A 349 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7488 (mp0) REVERT: A 416 ARG cc_start: 0.7251 (mpt180) cc_final: 0.6997 (mtm180) REVERT: A 451 GLN cc_start: 0.8284 (mt0) cc_final: 0.7866 (mt0) REVERT: A 548 THR cc_start: 0.7660 (OUTLIER) cc_final: 0.7386 (p) REVERT: A 568 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6380 (mt-10) REVERT: A 661 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7705 (mtm) outliers start: 15 outliers final: 5 residues processed: 68 average time/residue: 0.5099 time to fit residues: 36.0631 Evaluate side-chains 67 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.133 ------------------------------------------------------------------------------- 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 349 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 391 MET 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: 9.9990 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 ASN A 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.117693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.096021 restraints weight = 5177.775| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.42 r_work: 0.2839 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2977 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= 0.158 Angle : 0.632 15.697 6700 Z= 0.312 Chirality : 0.042 0.151 779 Planarity : 0.005 0.049 817 Dihedral : 4.105 16.813 701 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.80 % Allowed : 12.00 % 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 are not related in a simple way. whole: 1.89 (0.35), residues: 609 helix: 1.84 (0.24), residues: 451 sheet: None (None), residues: 0 loop : -0.38 (0.55), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 353 TYR 0.011 0.002 TYR A 290 PHE 0.015 0.002 PHE A 254 TRP 0.012 0.001 TRP A 487 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 4904) covalent geometry : angle 0.63201 / 0.31 ( 6692) SS BOND : bond 0.00283 / 0.14 ( 4) SS BOND : angle 0.82345 / 0.48 ( 8) hydrogen bonds : bond 0.04417 / 2.93 ( 342) hydrogen bonds : angle 5.41226 / 4.09 ( 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 75 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.169 Fit side-chains REVERT: A 45 CYS cc_start: 0.7945 (m) cc_final: 0.7033 (p) REVERT: A 46 ARG cc_start: 0.6208 (ttt90) cc_final: 0.5855 (ttt-90) REVERT: A 300 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7312 (mmt180) REVERT: A 349 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7435 (mp0) REVERT: A 416 ARG cc_start: 0.7253 (mpt180) cc_final: 0.7002 (mtm180) REVERT: A 451 GLN cc_start: 0.8308 (mt0) cc_final: 0.7987 (mt0) REVERT: A 548 THR cc_start: 0.7640 (OUTLIER) cc_final: 0.7360 (p) REVERT: A 568 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6483 (mt-10) REVERT: A 661 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7717 (mtm) outliers start: 14 outliers final: 6 residues processed: 69 average time/residue: 0.4804 time to fit residues: 34.4986 Evaluate side-chains 68 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.104 ------------------------------------------------------------------------------- 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 349 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 661 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 10 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 49 optimal weight: 0.0980 chunk 34 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 13 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 376 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.121825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.100962 restraints weight = 5210.201| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.31 r_work: 0.2918 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3223 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= 0.118 Angle : 0.590 15.021 6700 Z= 0.289 Chirality : 0.039 0.145 779 Planarity : 0.005 0.046 817 Dihedral : 3.973 17.377 701 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 2.00 % Allowed : 13.20 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.35), residues: 609 helix: 2.01 (0.24), residues: 452 sheet: None (None), residues: 0 loop : -0.35 (0.54), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 353 TYR 0.011 0.001 TYR A 188 PHE 0.008 0.001 PHE A 534 TRP 0.011 0.001 TRP A 65 HIS 0.003 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 ( 4904) covalent geometry : angle 0.58995 / 0.29 ( 6692) SS BOND : bond 0.00198 / 0.10 ( 4) SS BOND : angle 0.76450 / 0.43 ( 8) hydrogen bonds : bond 0.03857 / 2.55 ( 342) hydrogen bonds : angle 5.22638 / 3.94 ( 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 72 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.123 Fit side-chains REVERT: A 44 MET cc_start: 0.7978 (mtm) cc_final: 0.7680 (mtm) REVERT: A 45 CYS cc_start: 0.7850 (m) cc_final: 0.6942 (p) REVERT: A 46 ARG cc_start: 0.6210 (ttt90) cc_final: 0.5869 (ttt-90) REVERT: A 349 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7445 (mp0) REVERT: A 416 ARG cc_start: 0.7204 (mpt180) cc_final: 0.6896 (mtm180) REVERT: A 451 GLN cc_start: 0.8257 (mt0) cc_final: 0.7908 (mt0) REVERT: A 548 THR cc_start: 0.7615 (OUTLIER) cc_final: 0.7364 (p) REVERT: A 568 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6347 (mt-10) REVERT: A 661 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7733 (mtm) outliers start: 10 outliers final: 3 residues processed: 69 average time/residue: 0.4839 time to fit residues: 34.7165 Evaluate side-chains 69 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.158 ------------------------------------------------------------------------------- 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 349 GLU Chi-restraints excluded: chain A residue 359 VAL 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: 7.9990 chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 0.1980 chunk 16 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.119254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.097978 restraints weight = 5136.021| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.36 r_work: 0.2870 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3103 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= 0.143 Angle : 0.624 16.209 6700 Z= 0.305 Chirality : 0.041 0.147 779 Planarity : 0.005 0.048 817 Dihedral : 3.977 16.772 701 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.20 % Allowed : 12.60 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.35), residues: 609 helix: 1.97 (0.24), residues: 451 sheet: None (None), residues: 0 loop : -0.29 (0.55), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 353 TYR 0.013 0.002 TYR A 188 PHE 0.019 0.002 PHE A 254 TRP 0.011 0.001 TRP A 487 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 4904) covalent geometry : angle 0.62355 / 0.30 ( 6692) SS BOND : bond 0.00240 / 0.12 ( 4) SS BOND : angle 0.75615 / 0.43 ( 8) hydrogen bonds : bond 0.04253 / 2.82 ( 342) hydrogen bonds : angle 5.31267 / 4.01 ( 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 74 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.172 Fit side-chains REVERT: A 45 CYS cc_start: 0.7883 (m) cc_final: 0.6935 (p) REVERT: A 46 ARG cc_start: 0.6193 (ttt90) cc_final: 0.5855 (ttt-90) REVERT: A 300 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7251 (mmt180) REVERT: A 349 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7426 (mp0) REVERT: A 416 ARG cc_start: 0.7265 (mpt180) cc_final: 0.6915 (mtm180) REVERT: A 451 GLN cc_start: 0.8207 (mt0) cc_final: 0.7966 (mt0) REVERT: A 548 THR cc_start: 0.7636 (OUTLIER) cc_final: 0.7365 (p) REVERT: A 568 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6457 (mt-10) REVERT: A 661 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7736 (mtm) outliers start: 11 outliers final: 3 residues processed: 72 average time/residue: 0.4667 time to fit residues: 35.0297 Evaluate side-chains 66 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.158 ------------------------------------------------------------------------------- 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 349 GLU Chi-restraints excluded: chain A residue 359 VAL 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: 10.0000 chunk 56 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 44 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 376 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.119698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.098374 restraints weight = 5180.107| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.36 r_work: 0.2878 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3163 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= 0.139 Angle : 0.626 16.103 6700 Z= 0.305 Chirality : 0.041 0.143 779 Planarity : 0.005 0.047 817 Dihedral : 3.963 16.873 701 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.60 % Allowed : 13.40 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.35), residues: 609 helix: 1.96 (0.24), residues: 451 sheet: None (None), residues: 0 loop : -0.29 (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 188 PHE 0.009 0.001 PHE A 453 TRP 0.011 0.001 TRP A 487 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 4904) covalent geometry : angle 0.62609 / 0.31 ( 6692) SS BOND : bond 0.00236 / 0.12 ( 4) SS BOND : angle 0.78442 / 0.45 ( 8) hydrogen bonds : bond 0.04223 / 2.80 ( 342) hydrogen bonds : angle 5.31158 / 4.01 ( 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 69 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.145 Fit side-chains REVERT: A 45 CYS cc_start: 0.7862 (m) cc_final: 0.6927 (p) REVERT: A 46 ARG cc_start: 0.6301 (ttt90) cc_final: 0.5896 (ttt-90) REVERT: A 300 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7252 (mmt180) REVERT: A 349 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: A 416 ARG cc_start: 0.7342 (mpt180) cc_final: 0.6878 (mtm180) REVERT: A 451 GLN cc_start: 0.8208 (mt0) cc_final: 0.7970 (mt0) REVERT: A 548 THR cc_start: 0.7630 (OUTLIER) cc_final: 0.7361 (p) REVERT: A 568 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6440 (mt-10) REVERT: A 661 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7734 (mtm) outliers start: 8 outliers final: 3 residues processed: 67 average time/residue: 0.5082 time to fit residues: 35.4594 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 : 0.167 ------------------------------------------------------------------------------- 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 349 GLU Chi-restraints excluded: chain A residue 359 VAL 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: 5.9990 chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 25 optimal weight: 0.0670 chunk 41 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 376 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.123078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.102364 restraints weight = 5139.446| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.31 r_work: 0.2939 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4908 Z= 0.117 Angle : 0.595 15.443 6700 Z= 0.290 Chirality : 0.039 0.139 779 Planarity : 0.005 0.046 817 Dihedral : 3.870 17.292 701 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.35), residues: 609 helix: 2.08 (0.24), residues: 451 sheet: None (None), residues: 0 loop : -0.26 (0.54), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 353 TYR 0.013 0.001 TYR A 188 PHE 0.023 0.001 PHE A 254 TRP 0.011 0.001 TRP A 65 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 ( 4904) covalent geometry : angle 0.59436 / 0.29 ( 6692) SS BOND : bond 0.00199 / 0.10 ( 4) SS BOND : angle 0.75267 / 0.41 ( 8) hydrogen bonds : bond 0.03822 / 2.54 ( 342) hydrogen bonds : angle 5.16540 / 3.89 ( 1020) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1325.66 seconds wall clock time: 23 minutes 23.03 seconds (1403.03 seconds total)