Starting phenix.real_space_refine on Thu Mar 6 03:34:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hdh_34673/03_2025/8hdh_34673.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hdh_34673/03_2025/8hdh_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_2025/8hdh_34673.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hdh_34673/03_2025/8hdh_34673.map" model { file = "/net/cci-nas-00/data/ceres_data/8hdh_34673/03_2025/8hdh_34673.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hdh_34673/03_2025/8hdh_34673.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4778 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4497 Classifications: {'peptide': 586} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 558} Chain breaks: 1 Chain: "B" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 231 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 50 Unusual residues: {' NA': 1, '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: 3.83, per 1000 atoms: 0.80 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: 1.38 Conformation dependent library (CDL) restraints added in 543.8 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: 0.44 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: 1.31 Time building geometry restraints manager: 1.33 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: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.740 Find NCS groups from input model: 0.050 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.120 ------------------------------------------------------------------------------- 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 : 0.016 0.085 4903 Z= 1.062 Angle : 2.207 10.898 6689 Z= 1.639 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (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 TRP 0.021 0.003 TRP A 65 HIS 0.007 0.002 HIS A 80 PHE 0.028 0.004 PHE A 520 TYR 0.021 0.004 TYR A 233 ARG 0.006 0.001 ARG A 300 *********************** 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 : 0.459 Fit side-chains REVERT: A 46 ARG cc_start: 0.5535 (ttt90) cc_final: 0.4409 (mmp80) REVERT: A 62 MET cc_start: 0.9096 (mmp) cc_final: 0.8808 (mmp) REVERT: A 104 PHE cc_start: 0.7000 (m-80) cc_final: 0.6434 (t80) REVERT: A 306 SER cc_start: 0.6640 (t) cc_final: 0.6392 (p) REVERT: A 308 THR cc_start: 0.7973 (t) cc_final: 0.7696 (m) REVERT: A 353 ARG cc_start: 0.7351 (ttp-110) cc_final: 0.7061 (ttm110) REVERT: A 359 VAL cc_start: 0.8251 (m) cc_final: 0.7949 (t) REVERT: A 372 LYS cc_start: 0.7916 (mmtm) cc_final: 0.7663 (mmmt) REVERT: A 412 ARG cc_start: 0.6615 (ttt90) cc_final: 0.5746 (ttt180) REVERT: A 504 PHE cc_start: 0.6786 (t80) cc_final: 0.6420 (m-80) REVERT: A 558 ARG cc_start: 0.7824 (mtm-85) cc_final: 0.7602 (mtm180) REVERT: A 645 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7001 (mt-10) REVERT: A 651 ARG cc_start: 0.6534 (ttm110) cc_final: 0.5905 (tpt170) REVERT: A 661 MET cc_start: 0.7137 (mtt) cc_final: 0.6892 (tpt) REVERT: B 31 MET cc_start: 0.5863 (ptm) cc_final: 0.5476 (mtt) outliers start: 5 outliers final: 1 residues processed: 109 average time/residue: 0.1825 time to fit residues: 24.9028 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 : 0.472 ------------------------------------------------------------------------------- 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 50 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN A 299 GLN A 399 ASN A 557 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.131849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.110132 restraints weight = 5374.696| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.50 r_work: 0.3067 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4903 Z= 0.198 Angle : 0.641 7.023 6689 Z= 0.335 Chirality : 0.043 0.150 778 Planarity : 0.004 0.038 818 Dihedral : 5.982 41.358 718 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.00 % Allowed : 9.80 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.34), residues: 609 helix: 1.20 (0.24), residues: 452 sheet: None (None), residues: 0 loop : -0.71 (0.52), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 276 HIS 0.004 0.001 HIS A 557 PHE 0.009 0.001 PHE A 476 TYR 0.014 0.002 TYR A 256 ARG 0.003 0.000 ARG A 257 *********************** 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: 10 poor density : 83 time to evaluate : 0.489 Fit side-chains REVERT: A 46 ARG cc_start: 0.6239 (ttt90) cc_final: 0.4759 (mmp80) REVERT: A 62 MET cc_start: 0.9186 (mmp) cc_final: 0.8954 (mmt) REVERT: A 104 PHE cc_start: 0.7476 (m-80) cc_final: 0.7082 (t80) REVERT: A 154 LYS cc_start: 0.8983 (mttp) cc_final: 0.8646 (mttt) REVERT: A 359 VAL cc_start: 0.8209 (m) cc_final: 0.7949 (p) REVERT: A 386 MET cc_start: 0.8152 (mmm) cc_final: 0.7852 (mpp) REVERT: A 412 ARG cc_start: 0.6387 (ttt90) cc_final: 0.5935 (tmt170) REVERT: A 419 ASP cc_start: 0.7921 (m-30) cc_final: 0.7703 (m-30) REVERT: A 421 GLU cc_start: 0.7111 (tt0) cc_final: 0.6774 (tt0) REVERT: A 504 PHE cc_start: 0.7320 (t80) cc_final: 0.6577 (m-80) REVERT: A 651 ARG cc_start: 0.7011 (ttm110) cc_final: 0.6455 (tpt170) outliers start: 10 outliers final: 7 residues processed: 91 average time/residue: 0.2180 time to fit residues: 24.5029 Evaluate side-chains 77 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 299 GLN Chi-restraints excluded: chain A residue 347 VAL 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 41 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 32 optimal weight: 0.0770 chunk 39 optimal weight: 0.0040 chunk 28 optimal weight: 5.9990 overall best weight: 0.7752 ------------------------------------------------------------------------------- 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 = 0.3432 r_free = 0.3432 target = 0.131378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.109317 restraints weight = 5359.990| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.54 r_work: 0.3073 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4903 Z= 0.164 Angle : 0.575 6.709 6689 Z= 0.297 Chirality : 0.041 0.143 778 Planarity : 0.004 0.043 818 Dihedral : 5.356 40.702 718 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.20 % Allowed : 12.20 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.35), residues: 609 helix: 1.89 (0.24), residues: 452 sheet: None (None), residues: 0 loop : -0.50 (0.53), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 440 HIS 0.002 0.000 HIS A 80 PHE 0.008 0.001 PHE A 520 TYR 0.012 0.001 TYR A 256 ARG 0.003 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.469 Fit side-chains REVERT: A 46 ARG cc_start: 0.6402 (ttt90) cc_final: 0.4852 (mmp80) REVERT: A 104 PHE cc_start: 0.7591 (m-80) cc_final: 0.7078 (t80) REVERT: A 386 MET cc_start: 0.8101 (mmm) cc_final: 0.7787 (mpp) REVERT: A 412 ARG cc_start: 0.6401 (ttt90) cc_final: 0.5940 (tmt170) REVERT: A 645 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6862 (mt-10) REVERT: A 651 ARG cc_start: 0.7031 (ttm110) cc_final: 0.6476 (tpt170) outliers start: 11 outliers final: 8 residues processed: 87 average time/residue: 0.1908 time to fit residues: 20.8658 Evaluate side-chains 79 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 147 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 347 VAL 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 53 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.0060 chunk 57 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- 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 = 0.3410 r_free = 0.3410 target = 0.129578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.108074 restraints weight = 5477.520| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.55 r_work: 0.3058 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 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 : 0.003 0.031 4903 Z= 0.175 Angle : 0.549 6.763 6689 Z= 0.284 Chirality : 0.041 0.147 778 Planarity : 0.004 0.042 818 Dihedral : 5.149 40.672 718 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.20 % Allowed : 12.40 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.35), residues: 609 helix: 2.03 (0.24), residues: 454 sheet: None (None), residues: 0 loop : -0.26 (0.56), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 276 HIS 0.002 0.001 HIS A 565 PHE 0.023 0.001 PHE A 504 TYR 0.010 0.001 TYR A 256 ARG 0.002 0.000 ARG A 379 *********************** 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 86 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.526 Fit side-chains REVERT: A 46 ARG cc_start: 0.6358 (ttt90) cc_final: 0.4902 (mmp80) REVERT: A 104 PHE cc_start: 0.6983 (m-80) cc_final: 0.6721 (t80) REVERT: A 386 MET cc_start: 0.7903 (mmm) cc_final: 0.7597 (mpp) REVERT: A 412 ARG cc_start: 0.6330 (ttt90) cc_final: 0.5860 (tmt170) REVERT: A 505 SER cc_start: 0.8191 (OUTLIER) cc_final: 0.7805 (p) REVERT: A 651 ARG cc_start: 0.7023 (ttm110) cc_final: 0.6461 (tpt170) REVERT: A 661 MET cc_start: 0.8242 (tpt) cc_final: 0.8008 (tpt) outliers start: 16 outliers final: 12 residues processed: 82 average time/residue: 0.1715 time to fit residues: 18.2217 Evaluate side-chains 81 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 347 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 475 LEU 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 33 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3388 r_free = 0.3388 target = 0.127547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.106163 restraints weight = 5557.190| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.53 r_work: 0.3047 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4903 Z= 0.208 Angle : 0.564 6.843 6689 Z= 0.291 Chirality : 0.041 0.152 778 Planarity : 0.004 0.041 818 Dihedral : 5.224 41.796 718 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.00 % Allowed : 12.80 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.35), residues: 609 helix: 2.01 (0.24), residues: 454 sheet: None (None), residues: 0 loop : -0.36 (0.55), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 440 HIS 0.003 0.001 HIS A 80 PHE 0.013 0.001 PHE A 504 TYR 0.011 0.001 TYR A 290 ARG 0.002 0.000 ARG A 379 *********************** 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: 15 poor density : 72 time to evaluate : 0.624 Fit side-chains REVERT: A 46 ARG cc_start: 0.6425 (ttt90) cc_final: 0.4963 (mmp80) REVERT: A 62 MET cc_start: 0.9240 (mmp) cc_final: 0.8925 (mmp) REVERT: A 103 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.7994 (mp) REVERT: A 104 PHE cc_start: 0.7177 (m-80) cc_final: 0.6765 (t80) REVERT: A 412 ARG cc_start: 0.6349 (ttt90) cc_final: 0.5954 (tmt170) REVERT: A 651 ARG cc_start: 0.7085 (ttm110) cc_final: 0.6516 (tpt170) REVERT: A 661 MET cc_start: 0.8391 (tpt) cc_final: 0.8158 (tpt) outliers start: 15 outliers final: 13 residues processed: 84 average time/residue: 0.1863 time to fit residues: 20.3882 Evaluate side-chains 80 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 147 LEU Chi-restraints excluded: chain A residue 170 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 391 MET Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 55 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 33 optimal weight: 0.0970 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.3407 r_free = 0.3407 target = 0.129031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.107823 restraints weight = 5472.600| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.53 r_work: 0.3054 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4903 Z= 0.177 Angle : 0.537 6.761 6689 Z= 0.277 Chirality : 0.040 0.149 778 Planarity : 0.004 0.041 818 Dihedral : 5.060 41.257 718 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.20 % Allowed : 13.00 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.35), residues: 609 helix: 2.13 (0.24), residues: 454 sheet: None (None), residues: 0 loop : -0.39 (0.55), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 276 HIS 0.002 0.001 HIS A 80 PHE 0.010 0.001 PHE A 504 TYR 0.009 0.001 TYR A 290 ARG 0.001 0.000 ARG A 379 *********************** 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 86 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.481 Fit side-chains REVERT: A 46 ARG cc_start: 0.6563 (ttt90) cc_final: 0.5174 (mmp80) REVERT: A 104 PHE cc_start: 0.7139 (m-80) cc_final: 0.6742 (t80) REVERT: A 386 MET cc_start: 0.7934 (mmm) cc_final: 0.7710 (tpp) REVERT: A 412 ARG cc_start: 0.6227 (ttt90) cc_final: 0.5866 (tmt170) REVERT: A 651 ARG cc_start: 0.7054 (ttm110) cc_final: 0.6492 (tpt170) REVERT: A 661 MET cc_start: 0.8355 (tpt) cc_final: 0.8139 (tpt) outliers start: 16 outliers final: 13 residues processed: 82 average time/residue: 0.1737 time to fit residues: 18.3644 Evaluate side-chains 80 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 181 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 56 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 23 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3420 r_free = 0.3420 target = 0.130115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.108790 restraints weight = 5453.403| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.54 r_work: 0.3069 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4903 Z= 0.162 Angle : 0.526 6.689 6689 Z= 0.269 Chirality : 0.040 0.148 778 Planarity : 0.004 0.040 818 Dihedral : 4.929 40.398 718 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.80 % Allowed : 13.20 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.35), residues: 609 helix: 2.19 (0.24), residues: 457 sheet: None (None), residues: 0 loop : -0.48 (0.55), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 276 HIS 0.002 0.001 HIS A 80 PHE 0.008 0.001 PHE A 534 TYR 0.009 0.001 TYR A 128 ARG 0.001 0.000 ARG A 379 *********************** 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 88 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.536 Fit side-chains REVERT: A 46 ARG cc_start: 0.6500 (ttt90) cc_final: 0.5156 (mmp80) REVERT: A 104 PHE cc_start: 0.7145 (m-80) cc_final: 0.6720 (t80) REVERT: A 386 MET cc_start: 0.7876 (mmm) cc_final: 0.7645 (tpp) REVERT: A 412 ARG cc_start: 0.6226 (ttt90) cc_final: 0.5842 (tmt170) REVERT: A 651 ARG cc_start: 0.7030 (ttm110) cc_final: 0.6457 (tpt170) REVERT: A 661 MET cc_start: 0.8349 (tpt) cc_final: 0.8137 (tpt) outliers start: 14 outliers final: 11 residues processed: 83 average time/residue: 0.1755 time to fit residues: 18.7086 Evaluate side-chains 82 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 181 LEU Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 56 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.124752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.103560 restraints weight = 5561.015| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.55 r_work: 0.3004 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 4903 Z= 0.315 Angle : 0.624 7.110 6689 Z= 0.322 Chirality : 0.044 0.163 778 Planarity : 0.005 0.042 818 Dihedral : 5.546 46.337 718 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.40 % Allowed : 13.80 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.34), residues: 609 helix: 1.81 (0.24), residues: 452 sheet: None (None), residues: 0 loop : -0.58 (0.53), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 429 HIS 0.003 0.001 HIS A 565 PHE 0.011 0.002 PHE A 230 TYR 0.014 0.002 TYR A 526 ARG 0.003 0.001 ARG A 267 *********************** 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 89 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.461 Fit side-chains REVERT: A 103 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8003 (mp) REVERT: A 104 PHE cc_start: 0.7348 (m-80) cc_final: 0.6877 (t80) REVERT: A 412 ARG cc_start: 0.6391 (ttt90) cc_final: 0.5934 (tmt170) REVERT: A 651 ARG cc_start: 0.7189 (ttm110) cc_final: 0.6527 (mmt180) outliers start: 17 outliers final: 16 residues processed: 85 average time/residue: 0.1537 time to fit residues: 17.0213 Evaluate side-chains 87 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 155 ILE 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 186 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 18 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3395 r_free = 0.3395 target = 0.127910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.106809 restraints weight = 5433.264| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.55 r_work: 0.3046 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4903 Z= 0.183 Angle : 0.546 6.791 6689 Z= 0.280 Chirality : 0.040 0.147 778 Planarity : 0.004 0.042 818 Dihedral : 5.150 43.091 718 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.60 % Allowed : 15.40 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.35), residues: 609 helix: 2.05 (0.24), residues: 454 sheet: None (None), residues: 0 loop : -0.47 (0.55), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 276 HIS 0.003 0.001 HIS A 80 PHE 0.008 0.001 PHE A 534 TYR 0.009 0.001 TYR A 290 ARG 0.002 0.000 ARG A 379 *********************** 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 87 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.527 Fit side-chains REVERT: A 46 ARG cc_start: 0.6390 (ttt90) cc_final: 0.4939 (mmp80) REVERT: A 103 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7953 (mp) REVERT: A 104 PHE cc_start: 0.6838 (m-80) cc_final: 0.6516 (t80) REVERT: A 386 MET cc_start: 0.8078 (mmm) cc_final: 0.7859 (tpp) REVERT: A 412 ARG cc_start: 0.6286 (ttt90) cc_final: 0.5863 (tmt170) REVERT: A 651 ARG cc_start: 0.7058 (ttm110) cc_final: 0.6451 (tpt170) outliers start: 13 outliers final: 11 residues processed: 83 average time/residue: 0.1850 time to fit residues: 19.8972 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 : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 181 LEU Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 12 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.129866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.108686 restraints weight = 5444.295| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.55 r_work: 0.3083 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4903 Z= 0.166 Angle : 0.539 6.710 6689 Z= 0.277 Chirality : 0.040 0.145 778 Planarity : 0.004 0.042 818 Dihedral : 5.014 42.260 718 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.40 % Allowed : 15.20 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.35), residues: 609 helix: 2.19 (0.24), residues: 454 sheet: None (None), residues: 0 loop : -0.43 (0.55), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 276 HIS 0.003 0.000 HIS A 80 PHE 0.009 0.001 PHE A 520 TYR 0.010 0.001 TYR A 256 ARG 0.002 0.000 ARG A 352 ********************** 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 82 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.473 Fit side-chains REVERT: A 46 ARG cc_start: 0.6443 (ttt90) cc_final: 0.5089 (mmp80) REVERT: A 104 PHE cc_start: 0.6768 (m-80) cc_final: 0.6447 (t80) REVERT: A 386 MET cc_start: 0.7866 (mmm) cc_final: 0.7662 (tpp) REVERT: A 412 ARG cc_start: 0.6315 (ttt90) cc_final: 0.5877 (tmt170) REVERT: A 651 ARG cc_start: 0.7039 (ttm110) cc_final: 0.6461 (tpt170) outliers start: 12 outliers final: 10 residues processed: 78 average time/residue: 0.1813 time to fit residues: 18.0539 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 : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 186 MET Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 33 optimal weight: 0.4980 chunk 43 optimal weight: 0.7980 chunk 52 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 3 optimal weight: 8.9990 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 = 0.3437 r_free = 0.3437 target = 0.131468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.110230 restraints weight = 5551.086| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.57 r_work: 0.3089 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4903 Z= 0.157 Angle : 0.522 6.634 6689 Z= 0.268 Chirality : 0.040 0.147 778 Planarity : 0.004 0.041 818 Dihedral : 4.884 41.569 718 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.00 % Allowed : 15.80 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.35), residues: 609 helix: 2.25 (0.24), residues: 455 sheet: None (None), residues: 0 loop : -0.45 (0.55), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 276 HIS 0.002 0.000 HIS A 80 PHE 0.008 0.001 PHE A 534 TYR 0.009 0.001 TYR A 256 ARG 0.002 0.000 ARG A 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2486.90 seconds wall clock time: 43 minutes 21.78 seconds (2601.78 seconds total)