Starting phenix.real_space_refine on Sun Apr 27 05:45:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hdh_34673/04_2025/8hdh_34673.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hdh_34673/04_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_34673/04_2025/8hdh_34673.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hdh_34673/04_2025/8hdh_34673.map" model { file = "/net/cci-nas-00/data/ceres_data/8hdh_34673/04_2025/8hdh_34673.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hdh_34673/04_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-5669/modules/chem_data/mon_lib" Total number of atoms: 4778 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4497 Classifications: {'peptide': 586} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 558} Chain breaks: 1 Chain: "B" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 231 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 50 Unusual residues: {' NA': 1, '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: 3.70, per 1000 atoms: 0.77 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: 1.42 Conformation dependent library (CDL) restraints added in 637.5 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: 0.56 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: 1.51 Time building geometry restraints manager: 1.62 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: 0.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.060 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.630 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.20386 ( 345) hydrogen bonds : angle 8.92492 ( 1029) SS BOND : bond 0.29352 ( 4) SS BOND : angle 9.07763 ( 8) covalent geometry : bond 0.01616 ( 4903) covalent geometry : angle 2.20730 ( 6689) *********************** 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 : 0.553 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: 0.1963 time to fit residues: 26.5785 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 : 0.566 ------------------------------------------------------------------------------- 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 4907 Z= 0.146 Angle : 0.641 7.023 6697 Z= 0.336 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 Details of bonding type rmsd hydrogen bonds : bond 0.04541 ( 345) hydrogen bonds : angle 5.65362 ( 1029) SS BOND : bond 0.00415 ( 4) SS BOND : angle 1.06474 ( 8) covalent geometry : bond 0.00295 ( 4903) covalent geometry : angle 0.64062 ( 6689) *********************** 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 : 0.478 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: 0.2095 time to fit residues: 23.4477 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 : 0.488 ------------------------------------------------------------------------------- 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: 0.3980 chunk 39 optimal weight: 0.0040 chunk 28 optimal weight: 5.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN 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 = 0.131069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.108953 restraints weight = 5353.384| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.54 r_work: 0.3068 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2849 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= 0.121 Angle : 0.581 7.462 6697 Z= 0.300 Chirality : 0.041 0.143 778 Planarity : 0.004 0.043 818 Dihedral : 5.401 40.886 718 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.20 % Allowed : 12.40 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.35), residues: 609 helix: 1.86 (0.24), residues: 452 sheet: None (None), residues: 0 loop : -0.51 (0.53), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 440 HIS 0.002 0.001 HIS A 80 PHE 0.008 0.001 PHE A 113 TYR 0.012 0.001 TYR A 256 ARG 0.002 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.03976 ( 345) hydrogen bonds : angle 5.35632 ( 1029) SS BOND : bond 0.00439 ( 4) SS BOND : angle 1.15223 ( 8) covalent geometry : bond 0.00254 ( 4903) covalent geometry : angle 0.57967 ( 6689) *********************** 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 89 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.507 Fit side-chains REVERT: A 46 ARG cc_start: 0.6371 (ttt90) cc_final: 0.4808 (mmp80) REVERT: A 104 PHE cc_start: 0.7582 (m-80) cc_final: 0.7047 (t80) REVERT: A 386 MET cc_start: 0.8113 (mmm) cc_final: 0.7801 (mpp) REVERT: A 412 ARG cc_start: 0.6407 (ttt90) cc_final: 0.5944 (tmt170) REVERT: A 645 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6855 (mt-10) REVERT: A 651 ARG cc_start: 0.7035 (ttm110) cc_final: 0.6482 (tpt170) outliers start: 11 outliers final: 9 residues processed: 86 average time/residue: 0.1947 time to fit residues: 21.0410 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 : 0.506 ------------------------------------------------------------------------------- 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 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 53 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.3358 r_free = 0.3358 target = 0.125009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.103592 restraints weight = 5534.267| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.54 r_work: 0.2995 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4907 Z= 0.179 Angle : 0.620 7.064 6697 Z= 0.323 Chirality : 0.044 0.155 778 Planarity : 0.005 0.046 818 Dihedral : 5.652 44.668 718 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.00 % Allowed : 12.40 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.34), residues: 609 helix: 1.75 (0.24), residues: 450 sheet: None (None), residues: 0 loop : -0.53 (0.52), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 440 HIS 0.003 0.001 HIS A 565 PHE 0.020 0.002 PHE A 504 TYR 0.012 0.002 TYR A 290 ARG 0.002 0.000 ARG A 379 Details of bonding type rmsd hydrogen bonds : bond 0.04801 ( 345) hydrogen bonds : angle 5.54973 ( 1029) SS BOND : bond 0.00436 ( 4) SS BOND : angle 0.98362 ( 8) covalent geometry : bond 0.00424 ( 4903) covalent geometry : angle 0.61957 ( 6689) *********************** 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 84 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.547 Fit side-chains REVERT: A 46 ARG cc_start: 0.6319 (ttt90) cc_final: 0.5755 (ttm-80) REVERT: A 103 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8002 (mp) REVERT: A 104 PHE cc_start: 0.7225 (m-80) cc_final: 0.6833 (t80) REVERT: A 412 ARG cc_start: 0.6467 (ttt90) cc_final: 0.5984 (tmt170) REVERT: A 651 ARG cc_start: 0.7093 (ttm110) cc_final: 0.6485 (tpt170) REVERT: A 661 MET cc_start: 0.8344 (tpt) cc_final: 0.8048 (tpt) outliers start: 15 outliers final: 12 residues processed: 82 average time/residue: 0.1800 time to fit residues: 18.9303 Evaluate side-chains 78 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 147 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 475 LEU 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: 0.5980 chunk 16 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 53 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.128832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.107283 restraints weight = 5529.923| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.57 r_work: 0.3056 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4907 Z= 0.115 Angle : 0.537 6.788 6697 Z= 0.277 Chirality : 0.040 0.148 778 Planarity : 0.004 0.045 818 Dihedral : 5.149 40.444 718 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.40 % Allowed : 12.40 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.35), residues: 609 helix: 1.99 (0.24), residues: 454 sheet: None (None), residues: 0 loop : -0.37 (0.55), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 276 HIS 0.002 0.001 HIS A 80 PHE 0.007 0.001 PHE A 534 TYR 0.009 0.001 TYR A 256 ARG 0.002 0.000 ARG A 379 Details of bonding type rmsd hydrogen bonds : bond 0.03813 ( 345) hydrogen bonds : angle 5.24168 ( 1029) SS BOND : bond 0.00209 ( 4) SS BOND : angle 0.48956 ( 8) covalent geometry : bond 0.00248 ( 4903) covalent geometry : angle 0.53718 ( 6689) *********************** 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 89 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.490 Fit side-chains REVERT: A 46 ARG cc_start: 0.6421 (ttt90) cc_final: 0.4934 (mmp80) REVERT: A 103 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7921 (mp) REVERT: A 104 PHE cc_start: 0.7105 (m-80) cc_final: 0.6686 (t80) REVERT: A 386 MET cc_start: 0.7917 (mmm) cc_final: 0.7687 (tpp) REVERT: A 412 ARG cc_start: 0.6291 (ttt90) cc_final: 0.5825 (tmt170) REVERT: A 651 ARG cc_start: 0.7041 (ttm110) cc_final: 0.6469 (tpt170) REVERT: A 661 MET cc_start: 0.8348 (tpt) cc_final: 0.8104 (tpt) outliers start: 17 outliers final: 13 residues processed: 84 average time/residue: 0.1762 time to fit residues: 18.9679 Evaluate side-chains 82 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 299 GLN 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 475 LEU Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 55 optimal weight: 0.0470 chunk 43 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 22 optimal weight: 0.4980 chunk 46 optimal weight: 4.9990 overall best weight: 0.9082 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.129578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.108205 restraints weight = 5478.915| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.56 r_work: 0.3067 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4907 Z= 0.112 Angle : 0.527 6.727 6697 Z= 0.271 Chirality : 0.040 0.147 778 Planarity : 0.004 0.043 818 Dihedral : 5.006 40.641 718 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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: 2.26 (0.35), residues: 609 helix: 2.12 (0.24), residues: 454 sheet: None (None), residues: 0 loop : -0.34 (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 520 TYR 0.009 0.001 TYR A 256 ARG 0.001 0.000 ARG A 379 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 345) hydrogen bonds : angle 5.16442 ( 1029) SS BOND : bond 0.00222 ( 4) SS BOND : angle 0.44423 ( 8) covalent geometry : bond 0.00239 ( 4903) covalent geometry : angle 0.52710 ( 6689) *********************** 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 87 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.513 Fit side-chains REVERT: A 46 ARG cc_start: 0.6410 (ttt90) cc_final: 0.4915 (mmp80) REVERT: A 104 PHE cc_start: 0.7174 (m-80) cc_final: 0.6755 (t80) REVERT: A 386 MET cc_start: 0.7846 (mmm) cc_final: 0.7631 (tpp) REVERT: A 412 ARG cc_start: 0.6314 (ttt90) cc_final: 0.5902 (tmt170) REVERT: A 651 ARG cc_start: 0.7035 (ttm110) cc_final: 0.6462 (tpt170) REVERT: A 661 MET cc_start: 0.8355 (tpt) cc_final: 0.8126 (tpt) outliers start: 16 outliers final: 12 residues processed: 82 average time/residue: 0.1784 time to fit residues: 18.7261 Evaluate side-chains 79 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 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 387 LEU 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: 7.9990 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 35 optimal weight: 0.2980 chunk 41 optimal weight: 2.9990 chunk 53 optimal weight: 0.0050 chunk 48 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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 = 0.3454 r_free = 0.3454 target = 0.132933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.111605 restraints weight = 5418.589| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.56 r_work: 0.3106 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4907 Z= 0.103 Angle : 0.506 6.597 6697 Z= 0.260 Chirality : 0.039 0.145 778 Planarity : 0.004 0.042 818 Dihedral : 4.775 39.423 718 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.60 % Allowed : 13.00 % 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: 2.46 (0.35), residues: 609 helix: 2.26 (0.24), residues: 458 sheet: None (None), residues: 0 loop : -0.35 (0.55), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 0.001 0.000 ARG A 379 Details of bonding type rmsd hydrogen bonds : bond 0.03281 ( 345) hydrogen bonds : angle 5.02874 ( 1029) SS BOND : bond 0.00148 ( 4) SS BOND : angle 0.34672 ( 8) covalent geometry : bond 0.00212 ( 4903) covalent geometry : angle 0.50660 ( 6689) *********************** 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 : 0.514 Fit side-chains REVERT: A 46 ARG cc_start: 0.6469 (ttt90) cc_final: 0.5136 (mmp80) REVERT: A 104 PHE cc_start: 0.7133 (m-80) cc_final: 0.6725 (t80) REVERT: A 154 LYS cc_start: 0.8698 (mttp) cc_final: 0.8491 (mttt) REVERT: A 412 ARG cc_start: 0.6250 (ttt90) cc_final: 0.5859 (tmt170) REVERT: A 651 ARG cc_start: 0.7029 (ttm110) cc_final: 0.6458 (tpt170) REVERT: A 661 MET cc_start: 0.8316 (tpt) cc_final: 0.8099 (tpt) outliers start: 13 outliers final: 11 residues processed: 86 average time/residue: 0.1753 time to fit residues: 19.2878 Evaluate side-chains 79 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 155 ILE 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 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: 0.5980 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 55 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.126547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.105244 restraints weight = 5520.496| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.54 r_work: 0.3025 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4907 Z= 0.155 Angle : 0.588 6.927 6697 Z= 0.305 Chirality : 0.043 0.156 778 Planarity : 0.004 0.041 818 Dihedral : 5.328 44.032 718 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.80 % Allowed : 14.40 % 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: 2.18 (0.35), residues: 609 helix: 2.05 (0.24), residues: 454 sheet: None (None), residues: 0 loop : -0.35 (0.55), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 429 HIS 0.003 0.001 HIS A 80 PHE 0.008 0.001 PHE A 534 TYR 0.012 0.001 TYR A 128 ARG 0.002 0.000 ARG A 267 Details of bonding type rmsd hydrogen bonds : bond 0.04371 ( 345) hydrogen bonds : angle 5.32733 ( 1029) SS BOND : bond 0.00389 ( 4) SS BOND : angle 2.04355 ( 8) covalent geometry : bond 0.00363 ( 4903) covalent geometry : angle 0.58434 ( 6689) *********************** 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 87 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.486 Fit side-chains REVERT: A 46 ARG cc_start: 0.6362 (ttt90) cc_final: 0.4853 (mmp80) REVERT: A 104 PHE cc_start: 0.7320 (m-80) cc_final: 0.6907 (t80) REVERT: A 412 ARG cc_start: 0.6392 (ttt90) cc_final: 0.5965 (tmt170) REVERT: A 651 ARG cc_start: 0.7100 (ttm110) cc_final: 0.6491 (tpt170) outliers start: 14 outliers final: 14 residues processed: 85 average time/residue: 0.1667 time to fit residues: 18.1628 Evaluate side-chains 79 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 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 274 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 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: 1.9990 chunk 31 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.128080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.107119 restraints weight = 5410.521| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.52 r_work: 0.3050 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4907 Z= 0.125 Angle : 0.548 6.788 6697 Z= 0.283 Chirality : 0.041 0.150 778 Planarity : 0.004 0.041 818 Dihedral : 5.137 42.374 718 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.00 % Allowed : 15.20 % Favored : 81.80 % 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: 2.29 (0.35), residues: 609 helix: 2.14 (0.24), residues: 454 sheet: None (None), residues: 0 loop : -0.35 (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 0.008 0.001 PHE A 534 TYR 0.010 0.001 TYR A 290 ARG 0.002 0.000 ARG A 553 Details of bonding type rmsd hydrogen bonds : bond 0.03911 ( 345) hydrogen bonds : angle 5.22692 ( 1029) SS BOND : bond 0.00426 ( 4) SS BOND : angle 1.53683 ( 8) covalent geometry : bond 0.00282 ( 4903) covalent geometry : angle 0.54548 ( 6689) *********************** 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: 15 poor density : 72 time to evaluate : 0.506 Fit side-chains REVERT: A 46 ARG cc_start: 0.6579 (ttt90) cc_final: 0.5183 (mmp80) REVERT: A 103 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7991 (mp) REVERT: A 104 PHE cc_start: 0.6911 (m-80) cc_final: 0.6581 (t80) REVERT: A 412 ARG cc_start: 0.6308 (ttt90) cc_final: 0.5889 (tmt170) REVERT: A 651 ARG cc_start: 0.7080 (ttm110) cc_final: 0.6486 (tpt170) outliers start: 15 outliers final: 13 residues processed: 83 average time/residue: 0.1774 time to fit residues: 18.9708 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 : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 52 VAL 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 181 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 387 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 12 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 24 optimal weight: 0.0980 chunk 15 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3453 r_free = 0.3453 target = 0.132729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.111733 restraints weight = 5416.526| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.53 r_work: 0.3108 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4907 Z= 0.104 Angle : 0.512 6.610 6697 Z= 0.261 Chirality : 0.039 0.144 778 Planarity : 0.004 0.042 818 Dihedral : 4.817 40.218 718 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 : 2.60 % 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: 2.54 (0.35), residues: 609 helix: 2.34 (0.24), residues: 456 sheet: None (None), residues: 0 loop : -0.35 (0.55), residues: 153 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 Details of bonding type rmsd hydrogen bonds : bond 0.03297 ( 345) hydrogen bonds : angle 5.01010 ( 1029) SS BOND : bond 0.00276 ( 4) SS BOND : angle 1.12677 ( 8) covalent geometry : bond 0.00217 ( 4903) covalent geometry : angle 0.51044 ( 6689) ********************** 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 86 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.528 Fit side-chains REVERT: A 46 ARG cc_start: 0.6410 (ttt90) cc_final: 0.5144 (mmp80) REVERT: A 164 VAL cc_start: 0.8119 (t) cc_final: 0.7894 (t) REVERT: A 412 ARG cc_start: 0.6238 (ttt90) cc_final: 0.5861 (tmt170) REVERT: A 651 ARG cc_start: 0.7044 (ttm110) cc_final: 0.6482 (tpt170) outliers start: 13 outliers final: 11 residues processed: 80 average time/residue: 0.1904 time to fit residues: 19.5146 Evaluate side-chains 83 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL 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 155 ILE 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 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: 0.9980 chunk 43 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 55 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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 = 0.3417 r_free = 0.3417 target = 0.129817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.108362 restraints weight = 5531.478| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.58 r_work: 0.3060 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4907 Z= 0.126 Angle : 0.547 9.191 6697 Z= 0.278 Chirality : 0.041 0.151 778 Planarity : 0.004 0.041 818 Dihedral : 4.969 40.096 718 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % 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: 2.37 (0.35), residues: 609 helix: 2.25 (0.24), residues: 456 sheet: None (None), residues: 0 loop : -0.54 (0.54), residues: 153 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 0.010 0.001 TYR A 528 ARG 0.001 0.000 ARG A 267 Details of bonding type rmsd hydrogen bonds : bond 0.03720 ( 345) hydrogen bonds : angle 5.14811 ( 1029) SS BOND : bond 0.00362 ( 4) SS BOND : angle 1.22585 ( 8) covalent geometry : bond 0.00287 ( 4903) covalent geometry : angle 0.54579 ( 6689) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2623.63 seconds wall clock time: 45 minutes 41.75 seconds (2741.75 seconds total)