Starting phenix.real_space_refine on Tue Mar 3 13:00:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hdh_34673/03_2026/8hdh_34673.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hdh_34673/03_2026/8hdh_34673.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hdh_34673/03_2026/8hdh_34673.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hdh_34673/03_2026/8hdh_34673.map" model { file = "/net/cci-nas-00/data/ceres_data/8hdh_34673/03_2026/8hdh_34673.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hdh_34673/03_2026/8hdh_34673.cif" } resolution = 3.1 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= 0.000 sd= 0.006 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 38 5.16 5 Na 1 4.78 5 C 3153 2.51 5 N 776 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 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/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, 'L3R': 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: 1.36, per 1000 atoms: 0.28 Number of scatterers: 4778 At special positions: 0 Unit cell: (75, 76, 93, 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 38 16.00 Na 1 11.00 F 1 9.00 O 809 8.00 N 776 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=2.28 Simple disulfide: pdb=" SG CYS A 345 " - pdb=" SG CYS A 351 " distance=2.36 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 361 " distance=2.24 Simple disulfide: pdb=" SG CYS A 517 " - pdb=" SG CYS A 522 " distance=2.39 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: 0.41 Conformation dependent library (CDL) restraints added in 327.1 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 82.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 22 through 47 removed outlier: 3.941A 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: 3.848A pdb=" N PHE A 81 " --> pdb=" O GLY A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 112 removed outlier: 4.053A pdb=" N GLU A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 103 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE A 104 " --> pdb=" O TRP A 100 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 108 " --> pdb=" O PHE A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 121 removed outlier: 4.088A 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: 3.700A pdb=" N LEU A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 170 removed outlier: 3.624A pdb=" N ASP A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 192 removed outlier: 4.104A pdb=" N GLY A 192 " --> pdb=" O TYR A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 224 removed outlier: 3.524A pdb=" N LEU A 197 " --> pdb=" O GLY A 193 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 203 " --> pdb=" O TYR A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 233 removed outlier: 3.836A pdb=" N GLY A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE A 230 " --> pdb=" O TYR A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 293 Processing helix chain 'A' and resid 294 through 303 removed outlier: 4.484A pdb=" N ARG A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N CYS A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 321 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 356 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: 3.641A pdb=" N LEU A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 371 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 409 removed outlier: 4.024A 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: 3.540A 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: 3.536A 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 501 removed outlier: 3.695A pdb=" N ARG A 499 " --> pdb=" O MET A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 507 Processing helix chain 'A' and resid 518 through 523 Processing helix chain 'A' and resid 525 through 548 removed outlier: 3.671A 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 55 345 hydrogen bonds defined for protein. 1029 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: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 703 1.29 - 1.43: 1387 1.43 - 1.57: 2754 1.57 - 1.71: 0 1.71 - 1.85: 59 Bond restraints: 4903 Sorted by residual: bond pdb=" C LEU A 497 " pdb=" O LEU A 497 " ideal model delta sigma weight residual 1.236 1.152 0.085 1.32e-02 5.74e+03 4.12e+01 bond pdb=" C PHE A 98 " pdb=" O PHE A 98 " ideal model delta sigma weight residual 1.236 1.303 -0.066 1.15e-02 7.56e+03 3.30e+01 bond pdb=" C PRO A 502 " pdb=" O PRO A 502 " ideal model delta sigma weight residual 1.235 1.162 0.073 1.30e-02 5.92e+03 3.15e+01 bond pdb=" C PHE A 453 " pdb=" O PHE A 453 " ideal model delta sigma weight residual 1.236 1.294 -0.057 1.15e-02 7.56e+03 2.49e+01 bond pdb=" C HIS A 80 " pdb=" O HIS A 80 " ideal model delta sigma weight residual 1.236 1.178 0.058 1.22e-02 6.72e+03 2.27e+01 ... (remaining 4898 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 4563 2.18 - 4.36: 1779 4.36 - 6.54: 313 6.54 - 8.72: 31 8.72 - 10.90: 3 Bond angle restraints: 6689 Sorted by residual: angle pdb=" CA PHE A 520 " pdb=" CB PHE A 520 " pdb=" CG PHE A 520 " ideal model delta sigma weight residual 113.80 104.85 8.95 1.00e+00 1.00e+00 8.01e+01 angle pdb=" CA PHE A 520 " pdb=" C PHE A 520 " pdb=" O PHE A 520 " ideal model delta sigma weight residual 119.97 111.62 8.35 1.15e+00 7.56e-01 5.27e+01 angle pdb=" C LEU A 182 " pdb=" N GLY A 183 " pdb=" CA GLY A 183 " ideal model delta sigma weight residual 119.94 127.85 -7.91 1.09e+00 8.42e-01 5.27e+01 angle pdb=" CA GLY A 360 " pdb=" C GLY A 360 " pdb=" O GLY A 360 " ideal model delta sigma weight residual 121.86 115.61 6.25 1.04e+00 9.25e-01 3.61e+01 angle pdb=" CA ASP A 261 " pdb=" CB ASP A 261 " pdb=" CG ASP A 261 " ideal model delta sigma weight residual 112.60 118.54 -5.94 1.00e+00 1.00e+00 3.53e+01 ... (remaining 6684 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.85: 2537 15.85 - 31.70: 228 31.70 - 47.55: 65 47.55 - 63.40: 14 63.40 - 79.24: 5 Dihedral angle restraints: 2849 sinusoidal: 1097 harmonic: 1752 Sorted by residual: dihedral pdb=" CB CYS A 255 " pdb=" SG CYS A 255 " pdb=" SG CYS A 511 " pdb=" CB CYS A 511 " ideal model delta sinusoidal sigma weight residual -86.00 -30.53 -55.47 1 1.00e+01 1.00e-02 4.16e+01 dihedral pdb=" CA ARG A 136 " pdb=" C ARG A 136 " pdb=" N ARG A 137 " pdb=" CA ARG A 137 " ideal model delta harmonic sigma weight residual 180.00 -150.72 -29.28 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA ALA A 247 " pdb=" C ALA A 247 " pdb=" N VAL A 248 " pdb=" CA VAL A 248 " ideal model delta harmonic sigma weight residual 180.00 152.53 27.47 0 5.00e+00 4.00e-02 3.02e+01 ... (remaining 2846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 381 0.064 - 0.127: 253 0.127 - 0.191: 117 0.191 - 0.255: 22 0.255 - 0.318: 5 Chirality restraints: 778 Sorted by residual: chirality pdb=" CB VAL A 434 " pdb=" CA VAL A 434 " pdb=" CG1 VAL A 434 " pdb=" CG2 VAL A 434 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA ILE A 251 " pdb=" N ILE A 251 " pdb=" C ILE A 251 " pdb=" CB ILE A 251 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA ILE A 501 " pdb=" N ILE A 501 " pdb=" C ILE A 501 " pdb=" CB ILE A 501 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 775 not shown) Planarity restraints: 818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 L3R A 802 " 0.023 2.00e-02 2.50e+03 8.68e-02 1.32e+02 pdb=" C10 L3R A 802 " -0.127 2.00e-02 2.50e+03 pdb=" C17 L3R A 802 " 0.002 2.00e-02 2.50e+03 pdb=" C18 L3R A 802 " -0.061 2.00e-02 2.50e+03 pdb=" C19 L3R A 802 " -0.070 2.00e-02 2.50e+03 pdb=" C2 L3R A 802 " 0.108 2.00e-02 2.50e+03 pdb=" S1 L3R A 802 " 0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 801 " -0.105 2.00e-02 2.50e+03 8.66e-02 9.37e+01 pdb=" C7 NAG A 801 " 0.029 2.00e-02 2.50e+03 pdb=" C8 NAG A 801 " -0.079 2.00e-02 2.50e+03 pdb=" N2 NAG A 801 " 0.137 2.00e-02 2.50e+03 pdb=" O7 NAG A 801 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 502 " 0.020 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C PRO A 502 " -0.068 2.00e-02 2.50e+03 pdb=" O PRO A 502 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU A 503 " 0.024 2.00e-02 2.50e+03 ... (remaining 815 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 36 2.61 - 3.18: 4045 3.18 - 3.75: 7645 3.75 - 4.33: 10802 4.33 - 4.90: 17627 Nonbonded interactions: 40155 Sorted by model distance: nonbonded pdb=" O ALA A 73 " pdb="NA NA A 803 " model vdw 2.036 2.470 nonbonded pdb=" OG SER A 393 " pdb="NA NA A 803 " model vdw 2.260 2.470 nonbonded pdb=" ND2 ASN A 250 " pdb=" C1 NAG A 801 " model vdw 2.283 3.550 nonbonded pdb=" O MET A 407 " pdb=" OG1 THR A 411 " model vdw 2.314 3.040 nonbonded pdb=" O GLY A 332 " pdb=" OG SER A 335 " model vdw 2.332 3.040 ... (remaining 40150 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: 0.140 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.990 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: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 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 : 0.018 0.363 4907 Z= 1.268 Angle : 2.228 17.012 6697 Z= 1.645 Chirality : 0.093 0.318 778 Planarity : 0.007 0.103 818 Dihedral : 14.061 79.244 1721 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.49 % Allowed : 3.94 % Favored : 95.57 % Rotamer: Outliers : 1.00 % Allowed : 8.00 % Favored : 91.00 % Cbeta Deviations : 0.18 % 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: -2.42 (0.30), residues: 609 helix: -1.47 (0.20), residues: 442 sheet: None (None), residues: 0 loop : -1.43 (0.50), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 300 TYR 0.021 0.004 TYR A 233 PHE 0.028 0.004 PHE A 520 TRP 0.021 0.003 TRP A 65 HIS 0.007 0.002 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.01616 ( 4903) covalent geometry : angle 2.20730 ( 6689) SS BOND : bond 0.29352 ( 4) SS BOND : angle 9.07763 ( 8) hydrogen bonds : bond 0.20386 ( 345) hydrogen bonds : angle 8.92492 ( 1029) *********************** 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 110 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 0.163 Fit side-chains REVERT: A 46 ARG cc_start: 0.5532 (ttt90) cc_final: 0.4406 (mmp80) REVERT: A 62 MET cc_start: 0.9094 (mmp) cc_final: 0.8806 (mmp) REVERT: A 104 PHE cc_start: 0.7000 (m-80) cc_final: 0.6436 (t80) REVERT: A 306 SER cc_start: 0.6641 (t) cc_final: 0.6392 (p) REVERT: A 308 THR cc_start: 0.7974 (t) cc_final: 0.7696 (m) REVERT: A 353 ARG cc_start: 0.7349 (ttp-110) cc_final: 0.7060 (ttm110) REVERT: A 359 VAL cc_start: 0.8249 (m) cc_final: 0.7946 (t) REVERT: A 372 LYS cc_start: 0.7917 (mmtm) cc_final: 0.7664 (mmmt) REVERT: A 412 ARG cc_start: 0.6614 (ttt90) cc_final: 0.5748 (ttt180) REVERT: A 504 PHE cc_start: 0.6789 (t80) cc_final: 0.6423 (m-80) REVERT: A 558 ARG cc_start: 0.7827 (mtm-85) cc_final: 0.7602 (mtm180) REVERT: A 645 GLU cc_start: 0.7650 (mt-10) cc_final: 0.6999 (mt-10) REVERT: A 651 ARG cc_start: 0.6535 (ttm110) cc_final: 0.5904 (tpt170) REVERT: A 661 MET cc_start: 0.7136 (mtt) cc_final: 0.6891 (tpt) REVERT: B 31 MET cc_start: 0.5864 (ptm) cc_final: 0.5477 (mtt) outliers start: 5 outliers final: 1 residues processed: 109 average time/residue: 0.0833 time to fit residues: 11.3466 Evaluate side-chains 77 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN A 295 GLN A 299 GLN A 399 ASN A 557 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.131879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.110238 restraints weight = 5362.974| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.48 r_work: 0.3082 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4907 Z= 0.137 Angle : 0.635 6.895 6697 Z= 0.334 Chirality : 0.042 0.146 778 Planarity : 0.004 0.039 818 Dihedral : 5.987 39.326 718 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.60 % Allowed : 10.00 % Favored : 88.40 % 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 are not related in a simple way. whole: 1.01 (0.34), residues: 609 helix: 1.19 (0.24), residues: 452 sheet: None (None), residues: 0 loop : -0.72 (0.52), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 257 TYR 0.015 0.002 TYR A 256 PHE 0.010 0.001 PHE A 476 TRP 0.012 0.001 TRP A 65 HIS 0.004 0.001 HIS A 557 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 4903) covalent geometry : angle 0.63386 ( 6689) SS BOND : bond 0.00300 ( 4) SS BOND : angle 1.11364 ( 8) hydrogen bonds : bond 0.04670 ( 345) hydrogen bonds : angle 5.68205 ( 1029) *********************** 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 93 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.240 Fit side-chains REVERT: A 46 ARG cc_start: 0.6321 (ttt90) cc_final: 0.4956 (mmp80) REVERT: A 62 MET cc_start: 0.9172 (mmp) cc_final: 0.8916 (mmt) REVERT: A 104 PHE cc_start: 0.7419 (m-80) cc_final: 0.7014 (t80) REVERT: A 154 LYS cc_start: 0.8953 (mttp) cc_final: 0.8610 (mttt) REVERT: A 352 ARG cc_start: 0.7305 (ttp80) cc_final: 0.6992 (ttp-110) REVERT: A 353 ARG cc_start: 0.7585 (ttp-110) cc_final: 0.7384 (mtm110) REVERT: A 374 MET cc_start: 0.8592 (mmm) cc_final: 0.8296 (mmp) REVERT: A 412 ARG cc_start: 0.6325 (ttt90) cc_final: 0.5781 (ttt180) REVERT: A 419 ASP cc_start: 0.7988 (m-30) cc_final: 0.7761 (m-30) REVERT: A 421 GLU cc_start: 0.7002 (tt0) cc_final: 0.6623 (mm-30) REVERT: A 504 PHE cc_start: 0.7301 (t80) cc_final: 0.6567 (m-80) REVERT: A 645 GLU cc_start: 0.7412 (mt-10) cc_final: 0.7183 (mt-10) REVERT: A 651 ARG cc_start: 0.6799 (ttm110) cc_final: 0.6228 (tpt170) outliers start: 8 outliers final: 5 residues processed: 91 average time/residue: 0.0949 time to fit residues: 10.5357 Evaluate side-chains 77 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 299 GLN Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.3402 r_free = 0.3402 target = 0.128816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.106871 restraints weight = 5413.005| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.54 r_work: 0.3043 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4907 Z= 0.140 Angle : 0.602 6.852 6697 Z= 0.313 Chirality : 0.042 0.146 778 Planarity : 0.004 0.044 818 Dihedral : 5.511 42.317 718 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.40 % Allowed : 12.00 % 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: 1.75 (0.34), residues: 609 helix: 1.77 (0.24), residues: 451 sheet: None (None), residues: 0 loop : -0.57 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 412 TYR 0.013 0.001 TYR A 128 PHE 0.009 0.001 PHE A 113 TRP 0.011 0.001 TRP A 440 HIS 0.002 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 4903) covalent geometry : angle 0.60132 ( 6689) SS BOND : bond 0.00580 ( 4) SS BOND : angle 1.20993 ( 8) hydrogen bonds : bond 0.04360 ( 345) hydrogen bonds : angle 5.43487 ( 1029) *********************** 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 88 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.167 Fit side-chains REVERT: A 46 ARG cc_start: 0.6413 (ttt90) cc_final: 0.4878 (mmp80) REVERT: A 62 MET cc_start: 0.9275 (mmp) cc_final: 0.9017 (mmp) REVERT: A 104 PHE cc_start: 0.7593 (m-80) cc_final: 0.7084 (t80) REVERT: A 198 MET cc_start: 0.7256 (mtt) cc_final: 0.6915 (mtt) REVERT: A 374 MET cc_start: 0.8478 (mmm) cc_final: 0.8251 (mmp) REVERT: A 386 MET cc_start: 0.8161 (mmm) cc_final: 0.7871 (mpp) REVERT: A 412 ARG cc_start: 0.6425 (ttt90) cc_final: 0.5944 (tmt170) REVERT: A 421 GLU cc_start: 0.7105 (tt0) cc_final: 0.6768 (tt0) REVERT: A 572 ASP cc_start: 0.7522 (m-30) cc_final: 0.7297 (t0) REVERT: A 645 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6537 (mt-10) REVERT: A 651 ARG cc_start: 0.7010 (ttm110) cc_final: 0.6473 (tpt170) outliers start: 12 outliers final: 9 residues processed: 85 average time/residue: 0.0801 time to fit residues: 8.6547 Evaluate side-chains 80 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 20 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 22 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 58 optimal weight: 0.1980 chunk 19 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3441 r_free = 0.3441 target = 0.132042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.110478 restraints weight = 5402.462| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.55 r_work: 0.3094 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4907 Z= 0.110 Angle : 0.530 6.653 6697 Z= 0.273 Chirality : 0.040 0.144 778 Planarity : 0.004 0.042 818 Dihedral : 4.997 39.610 718 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.40 % Allowed : 12.00 % 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 are not related in a simple way. whole: 2.26 (0.35), residues: 609 helix: 2.10 (0.24), residues: 454 sheet: None (None), residues: 0 loop : -0.29 (0.55), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.011 0.001 TYR A 256 PHE 0.022 0.001 PHE A 504 TRP 0.009 0.001 TRP A 440 HIS 0.002 0.000 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 4903) covalent geometry : angle 0.52953 ( 6689) SS BOND : bond 0.00143 ( 4) SS BOND : angle 0.64571 ( 8) hydrogen bonds : bond 0.03512 ( 345) hydrogen bonds : angle 5.17450 ( 1029) *********************** 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 92 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.162 Fit side-chains REVERT: A 46 ARG cc_start: 0.6462 (ttt90) cc_final: 0.5110 (mmp80) REVERT: A 62 MET cc_start: 0.9296 (mmp) cc_final: 0.8956 (mmp) REVERT: A 104 PHE cc_start: 0.6914 (m-80) cc_final: 0.6674 (t80) REVERT: A 198 MET cc_start: 0.7202 (mtt) cc_final: 0.6926 (mtt) REVERT: A 386 MET cc_start: 0.7886 (mmm) cc_final: 0.7597 (tpp) REVERT: A 412 ARG cc_start: 0.6347 (ttt90) cc_final: 0.5897 (tmt170) REVERT: A 505 SER cc_start: 0.8308 (OUTLIER) cc_final: 0.7971 (p) REVERT: A 645 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6684 (mt-10) REVERT: A 651 ARG cc_start: 0.6998 (ttm110) cc_final: 0.6439 (tpt170) REVERT: A 661 MET cc_start: 0.8187 (tpt) cc_final: 0.7944 (tpt) outliers start: 17 outliers final: 12 residues processed: 87 average time/residue: 0.0842 time to fit residues: 9.1553 Evaluate side-chains 79 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 515 SER 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: 0.7980 chunk 15 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.131186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.109278 restraints weight = 5376.154| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.58 r_work: 0.3089 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4907 Z= 0.111 Angle : 0.528 6.693 6697 Z= 0.271 Chirality : 0.040 0.146 778 Planarity : 0.004 0.041 818 Dihedral : 4.989 40.407 718 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.60 % Allowed : 14.00 % Favored : 83.40 % 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 are not related in a simple way. whole: 2.26 (0.35), residues: 609 helix: 2.10 (0.24), residues: 457 sheet: None (None), residues: 0 loop : -0.37 (0.55), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 379 TYR 0.009 0.001 TYR A 256 PHE 0.012 0.001 PHE A 504 TRP 0.009 0.001 TRP A 276 HIS 0.002 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 4903) covalent geometry : angle 0.52784 ( 6689) SS BOND : bond 0.00230 ( 4) SS BOND : angle 0.49521 ( 8) hydrogen bonds : bond 0.03614 ( 345) hydrogen bonds : angle 5.12736 ( 1029) *********************** 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 87 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.149 Fit side-chains REVERT: A 46 ARG cc_start: 0.6481 (ttt90) cc_final: 0.5133 (mmp80) REVERT: A 62 MET cc_start: 0.9289 (mmp) cc_final: 0.8950 (mmp) REVERT: A 104 PHE cc_start: 0.7153 (m-80) cc_final: 0.6750 (t80) REVERT: A 386 MET cc_start: 0.7918 (mmm) cc_final: 0.7586 (mpp) REVERT: A 412 ARG cc_start: 0.6319 (ttt90) cc_final: 0.5869 (tmt170) REVERT: A 645 GLU cc_start: 0.6854 (mt-10) cc_final: 0.6505 (mt-10) REVERT: A 651 ARG cc_start: 0.7005 (ttm110) cc_final: 0.6427 (tpt170) REVERT: A 661 MET cc_start: 0.8350 (tpt) cc_final: 0.8087 (tpt) outliers start: 13 outliers final: 9 residues processed: 83 average time/residue: 0.0720 time to fit residues: 7.5513 Evaluate side-chains 78 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 387 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: 4.9990 chunk 24 optimal weight: 0.0060 chunk 51 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 overall best weight: 0.7602 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.132554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.110712 restraints weight = 5533.335| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.58 r_work: 0.3107 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4907 Z= 0.106 Angle : 0.519 6.416 6697 Z= 0.264 Chirality : 0.039 0.147 778 Planarity : 0.004 0.040 818 Dihedral : 4.826 39.632 718 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.40 % Allowed : 14.20 % Favored : 83.40 % 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 are not related in a simple way. whole: 2.39 (0.35), residues: 609 helix: 2.20 (0.24), residues: 457 sheet: None (None), residues: 0 loop : -0.31 (0.56), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 379 TYR 0.009 0.001 TYR A 256 PHE 0.012 0.001 PHE A 504 TRP 0.012 0.001 TRP A 65 HIS 0.002 0.000 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 4903) covalent geometry : angle 0.51866 ( 6689) SS BOND : bond 0.00178 ( 4) SS BOND : angle 0.43418 ( 8) hydrogen bonds : bond 0.03417 ( 345) hydrogen bonds : angle 5.03879 ( 1029) *********************** 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 84 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.111 Fit side-chains REVERT: A 46 ARG cc_start: 0.6529 (ttt90) cc_final: 0.5278 (mmp80) REVERT: A 62 MET cc_start: 0.9268 (mmp) cc_final: 0.8917 (mmp) REVERT: A 104 PHE cc_start: 0.7137 (m-80) cc_final: 0.6755 (t80) REVERT: A 386 MET cc_start: 0.7758 (mmm) cc_final: 0.7496 (tpp) REVERT: A 412 ARG cc_start: 0.6268 (ttt90) cc_final: 0.5842 (tmt170) REVERT: A 651 ARG cc_start: 0.7039 (ttm110) cc_final: 0.6474 (tpt170) REVERT: A 661 MET cc_start: 0.8348 (tpt) cc_final: 0.8121 (tpt) outliers start: 12 outliers final: 10 residues processed: 80 average time/residue: 0.0768 time to fit residues: 7.7629 Evaluate side-chains 79 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 51 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 40 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.3388 r_free = 0.3388 target = 0.127633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.105982 restraints weight = 5490.193| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.57 r_work: 0.3029 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4907 Z= 0.144 Angle : 0.569 6.399 6697 Z= 0.293 Chirality : 0.042 0.155 778 Planarity : 0.004 0.040 818 Dihedral : 5.201 42.432 718 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.60 % Allowed : 14.20 % Favored : 83.20 % 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: 2.21 (0.35), residues: 609 helix: 2.09 (0.24), residues: 454 sheet: None (None), residues: 0 loop : -0.41 (0.55), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 267 TYR 0.012 0.001 TYR A 290 PHE 0.009 0.001 PHE A 504 TRP 0.010 0.001 TRP A 429 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 4903) covalent geometry : angle 0.56870 ( 6689) SS BOND : bond 0.00321 ( 4) SS BOND : angle 0.58833 ( 8) hydrogen bonds : bond 0.04188 ( 345) hydrogen bonds : angle 5.27845 ( 1029) *********************** 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 89 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.176 Fit side-chains REVERT: A 46 ARG cc_start: 0.6553 (ttt90) cc_final: 0.5169 (mmp80) REVERT: A 62 MET cc_start: 0.9250 (mmp) cc_final: 0.8907 (mmp) REVERT: A 104 PHE cc_start: 0.7210 (m-80) cc_final: 0.6754 (t80) REVERT: A 359 VAL cc_start: 0.8413 (m) cc_final: 0.8185 (p) REVERT: A 386 MET cc_start: 0.8024 (mmm) cc_final: 0.7697 (mpp) REVERT: A 412 ARG cc_start: 0.6267 (ttt90) cc_final: 0.5860 (tmt170) REVERT: A 421 GLU cc_start: 0.7030 (tt0) cc_final: 0.6738 (mm-30) REVERT: A 645 GLU cc_start: 0.6852 (mt-10) cc_final: 0.6424 (mt-10) REVERT: A 651 ARG cc_start: 0.7124 (ttm110) cc_final: 0.6519 (tpt170) REVERT: A 661 MET cc_start: 0.8332 (tpt) cc_final: 0.8124 (tpt) outliers start: 13 outliers final: 12 residues processed: 86 average time/residue: 0.0805 time to fit residues: 8.7502 Evaluate side-chains 82 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 10 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 59 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3433 r_free = 0.3433 target = 0.131278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.109753 restraints weight = 5532.355| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.57 r_work: 0.3090 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4907 Z= 0.106 Angle : 0.514 6.348 6697 Z= 0.263 Chirality : 0.039 0.147 778 Planarity : 0.004 0.041 818 Dihedral : 4.870 39.500 718 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.00 % Allowed : 15.00 % Favored : 83.00 % 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: 2.36 (0.35), residues: 609 helix: 2.23 (0.24), residues: 456 sheet: None (None), residues: 0 loop : -0.49 (0.55), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.009 0.001 TYR A 290 PHE 0.009 0.001 PHE A 504 TRP 0.009 0.001 TRP A 276 HIS 0.002 0.000 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 4903) covalent geometry : angle 0.51408 ( 6689) SS BOND : bond 0.00173 ( 4) SS BOND : angle 0.41819 ( 8) hydrogen bonds : bond 0.03445 ( 345) hydrogen bonds : angle 5.08636 ( 1029) *********************** 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 81 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.183 Fit side-chains REVERT: A 46 ARG cc_start: 0.6408 (ttt90) cc_final: 0.5139 (mmp80) REVERT: A 104 PHE cc_start: 0.7155 (m-80) cc_final: 0.6757 (t80) REVERT: A 359 VAL cc_start: 0.8333 (m) cc_final: 0.8069 (p) REVERT: A 386 MET cc_start: 0.7778 (mmm) cc_final: 0.7508 (mpp) REVERT: A 412 ARG cc_start: 0.6275 (ttt90) cc_final: 0.5891 (tmt170) REVERT: A 651 ARG cc_start: 0.7057 (ttm110) cc_final: 0.6488 (tpt170) REVERT: A 661 MET cc_start: 0.8372 (tpt) cc_final: 0.8156 (tpt) outliers start: 10 outliers final: 9 residues processed: 78 average time/residue: 0.0801 time to fit residues: 7.9120 Evaluate side-chains 79 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.2980 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3437 r_free = 0.3437 target = 0.131639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.110083 restraints weight = 5443.846| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.56 r_work: 0.3097 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4907 Z= 0.106 Angle : 0.511 6.374 6697 Z= 0.262 Chirality : 0.040 0.147 778 Planarity : 0.004 0.040 818 Dihedral : 4.834 40.917 718 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.80 % Allowed : 14.80 % Favored : 83.40 % 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 are not related in a simple way. whole: 2.49 (0.35), residues: 609 helix: 2.28 (0.24), residues: 456 sheet: None (None), residues: 0 loop : -0.30 (0.56), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.009 0.001 TYR A 290 PHE 0.008 0.001 PHE A 534 TRP 0.009 0.001 TRP A 276 HIS 0.002 0.000 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 4903) covalent geometry : angle 0.51128 ( 6689) SS BOND : bond 0.00178 ( 4) SS BOND : angle 0.43276 ( 8) hydrogen bonds : bond 0.03427 ( 345) hydrogen bonds : angle 5.04669 ( 1029) *********************** 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 82 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.175 Fit side-chains REVERT: A 46 ARG cc_start: 0.6388 (ttt90) cc_final: 0.5127 (mmp80) REVERT: A 104 PHE cc_start: 0.7157 (m-80) cc_final: 0.6752 (t80) REVERT: A 359 VAL cc_start: 0.8379 (m) cc_final: 0.8133 (p) REVERT: A 412 ARG cc_start: 0.6299 (ttt90) cc_final: 0.5897 (tmt170) REVERT: A 651 ARG cc_start: 0.7069 (ttm110) cc_final: 0.6487 (tpt170) REVERT: A 661 MET cc_start: 0.8340 (tpt) cc_final: 0.8140 (tpt) outliers start: 9 outliers final: 8 residues processed: 80 average time/residue: 0.0822 time to fit residues: 8.2632 Evaluate side-chains 78 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 33 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 2 optimal weight: 8.9990 chunk 47 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3448 r_free = 0.3448 target = 0.132704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.110885 restraints weight = 5489.025| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.59 r_work: 0.3097 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 4907 Z= 0.110 Angle : 0.527 6.401 6697 Z= 0.269 Chirality : 0.040 0.151 778 Planarity : 0.004 0.041 818 Dihedral : 4.814 40.727 718 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.80 % Allowed : 14.60 % Favored : 83.60 % 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: 2.54 (0.35), residues: 609 helix: 2.34 (0.24), residues: 455 sheet: None (None), residues: 0 loop : -0.34 (0.56), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.009 0.001 TYR A 256 PHE 0.008 0.001 PHE A 534 TRP 0.010 0.001 TRP A 65 HIS 0.002 0.000 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 4903) covalent geometry : angle 0.52382 ( 6689) SS BOND : bond 0.00364 ( 4) SS BOND : angle 1.85429 ( 8) hydrogen bonds : bond 0.03397 ( 345) hydrogen bonds : angle 5.03352 ( 1029) ********************** 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 85 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.162 Fit side-chains REVERT: A 46 ARG cc_start: 0.6445 (ttt90) cc_final: 0.5206 (mmp80) REVERT: A 103 LEU cc_start: 0.8122 (tp) cc_final: 0.7672 (mt) REVERT: A 104 PHE cc_start: 0.6832 (m-80) cc_final: 0.6439 (t80) REVERT: A 164 VAL cc_start: 0.8066 (t) cc_final: 0.7853 (t) REVERT: A 359 VAL cc_start: 0.8343 (m) cc_final: 0.8085 (p) REVERT: A 386 MET cc_start: 0.7865 (mmm) cc_final: 0.7619 (tpp) REVERT: A 412 ARG cc_start: 0.6245 (ttt90) cc_final: 0.5826 (tmt170) REVERT: A 651 ARG cc_start: 0.7032 (ttm110) cc_final: 0.6444 (tpt170) REVERT: A 661 MET cc_start: 0.8241 (tpt) cc_final: 0.8030 (tpt) outliers start: 9 outliers final: 9 residues processed: 83 average time/residue: 0.0784 time to fit residues: 8.2227 Evaluate side-chains 81 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 1 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3435 r_free = 0.3435 target = 0.131424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.109952 restraints weight = 5456.255| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.54 r_work: 0.3087 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4907 Z= 0.119 Angle : 0.537 6.418 6697 Z= 0.274 Chirality : 0.040 0.150 778 Planarity : 0.004 0.040 818 Dihedral : 4.881 39.177 718 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.80 % Allowed : 15.00 % Favored : 83.20 % 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: 2.46 (0.35), residues: 609 helix: 2.27 (0.24), residues: 454 sheet: None (None), residues: 0 loop : -0.30 (0.56), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.010 0.001 TYR A 290 PHE 0.008 0.001 PHE A 534 TRP 0.008 0.001 TRP A 65 HIS 0.002 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 4903) covalent geometry : angle 0.53313 ( 6689) SS BOND : bond 0.00406 ( 4) SS BOND : angle 1.82284 ( 8) hydrogen bonds : bond 0.03588 ( 345) hydrogen bonds : angle 5.07560 ( 1029) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1220.72 seconds wall clock time: 21 minutes 34.33 seconds (1294.33 seconds total)