Starting phenix.real_space_refine on Sun Apr 27 04:33:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k7b_62147/04_2025/9k7b_62147.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k7b_62147/04_2025/9k7b_62147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k7b_62147/04_2025/9k7b_62147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k7b_62147/04_2025/9k7b_62147.map" model { file = "/net/cci-nas-00/data/ceres_data/9k7b_62147/04_2025/9k7b_62147.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k7b_62147/04_2025/9k7b_62147.cif" } resolution = 2.75 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= 0.090 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 36 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 3048 2.51 5 N 664 2.21 5 O 772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 4522 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4333 Classifications: {'peptide': 544} Link IDs: {'PTRANS': 27, 'TRANS': 516} Chain: "A" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 189 Unusual residues: {' CL': 1, ' NA': 1, 'CLR': 5, 'TAU': 4} Classifications: {'undetermined': 11, 'water': 19} Link IDs: {None: 29} Time building chain proxies: 3.54, per 1000 atoms: 0.78 Number of scatterers: 4522 At special positions: 0 Unit cell: (82.49, 65.7, 87.6, 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) Cl 1 17.00 S 36 16.00 Na 1 11.00 O 772 8.00 N 664 7.00 C 3048 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 501.6 milliseconds 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 992 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 1 sheets defined 82.7% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 46 through 55 removed outlier: 3.522A pdb=" N LEU A 52 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A 53 " --> pdb=" O ASP A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.971A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 90 removed outlier: 4.019A pdb=" N PHE A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE A 81 " --> pdb=" O GLY A 77 " (cutoff:3.500A) Proline residue: A 82 - end of helix Processing helix chain 'A' and resid 90 through 106 Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.765A pdb=" N GLU A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 121 through 153 removed outlier: 3.516A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.631A pdb=" N HIS A 161 " --> pdb=" O PRO A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 removed outlier: 3.862A pdb=" N LYS A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 217 through 238 Processing helix chain 'A' and resid 245 through 266 Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 269 through 279 Processing helix chain 'A' and resid 281 through 286 removed outlier: 3.993A pdb=" N LEU A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU A 286 " --> pdb=" O ILE A 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 286' Processing helix chain 'A' and resid 287 through 303 removed outlier: 4.153A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.500A pdb=" N SER A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 356 removed outlier: 3.853A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 363 removed outlier: 4.538A pdb=" N ALA A 363 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 381 Proline residue: A 375 - end of helix Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.509A pdb=" N TRP A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 423 Processing helix chain 'A' and resid 424 through 447 removed outlier: 4.046A pdb=" N GLU A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N MET A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.773A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 Processing helix chain 'A' and resid 484 through 497 Processing helix chain 'A' and resid 502 through 510 Processing helix chain 'A' and resid 510 through 526 Processing helix chain 'A' and resid 533 through 535 No H-bonds generated for 'chain 'A' and resid 533 through 535' Processing helix chain 'A' and resid 539 through 568 removed outlier: 4.072A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS A 556 " --> pdb=" O SER A 552 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL A 557 " --> pdb=" O SER A 553 " (cutoff:3.500A) Proline residue: A 558 - end of helix Processing helix chain 'A' and resid 571 through 581 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 287 hydrogen bonds defined for protein. 855 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: 1.20 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 643 1.32 - 1.44: 1388 1.44 - 1.57: 2574 1.57 - 1.69: 0 1.69 - 1.82: 50 Bond restraints: 4655 Sorted by residual: bond pdb=" C PRO A 118 " pdb=" O PRO A 118 " ideal model delta sigma weight residual 1.237 1.192 0.045 1.26e-02 6.30e+03 1.29e+01 bond pdb=" CA MET A 381 " pdb=" C MET A 381 " ideal model delta sigma weight residual 1.527 1.558 -0.030 1.02e-02 9.61e+03 8.87e+00 bond pdb=" CA SER A 365 " pdb=" C SER A 365 " ideal model delta sigma weight residual 1.530 1.496 0.034 1.14e-02 7.69e+03 8.73e+00 bond pdb=" C CYS A 71 " pdb=" O CYS A 71 " ideal model delta sigma weight residual 1.236 1.203 0.033 1.15e-02 7.56e+03 8.21e+00 bond pdb=" CA GLY A 295 " pdb=" C GLY A 295 " ideal model delta sigma weight residual 1.517 1.484 0.032 1.14e-02 7.69e+03 8.06e+00 ... (remaining 4650 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.49: 6264 4.49 - 8.98: 103 8.98 - 13.47: 10 13.47 - 17.95: 1 17.95 - 22.44: 1 Bond angle restraints: 6379 Sorted by residual: angle pdb=" N ALA A 462 " pdb=" CA ALA A 462 " pdb=" C ALA A 462 " ideal model delta sigma weight residual 111.07 119.90 -8.83 1.07e+00 8.73e-01 6.82e+01 angle pdb=" O1 TAU A 701 " pdb=" S TAU A 701 " pdb=" O2 TAU A 701 " ideal model delta sigma weight residual 113.04 90.60 22.44 3.00e+00 1.11e-01 5.60e+01 angle pdb=" N LEU A 278 " pdb=" CA LEU A 278 " pdb=" C LEU A 278 " ideal model delta sigma weight residual 111.36 119.10 -7.74 1.09e+00 8.42e-01 5.05e+01 angle pdb=" N VAL A 510 " pdb=" CA VAL A 510 " pdb=" C VAL A 510 " ideal model delta sigma weight residual 111.62 116.99 -5.37 7.90e-01 1.60e+00 4.63e+01 angle pdb=" N VAL A 64 " pdb=" CA VAL A 64 " pdb=" C VAL A 64 " ideal model delta sigma weight residual 110.72 117.17 -6.45 1.01e+00 9.80e-01 4.07e+01 ... (remaining 6374 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.78: 2710 23.78 - 47.56: 114 47.56 - 71.34: 29 71.34 - 95.11: 3 95.11 - 118.89: 5 Dihedral angle restraints: 2861 sinusoidal: 1293 harmonic: 1568 Sorted by residual: dihedral pdb=" CB CYS A 162 " pdb=" SG CYS A 162 " pdb=" SG CYS A 171 " pdb=" CB CYS A 171 " ideal model delta sinusoidal sigma weight residual 93.00 179.49 -86.49 1 1.00e+01 1.00e-02 9.01e+01 dihedral pdb=" C1 CLR A 707 " pdb=" C2 CLR A 707 " pdb=" C3 CLR A 707 " pdb=" O1 CLR A 707 " ideal model delta sinusoidal sigma weight residual 180.04 61.15 118.89 1 3.00e+01 1.11e-03 1.58e+01 dihedral pdb=" C10 CLR A 707 " pdb=" C1 CLR A 707 " pdb=" C2 CLR A 707 " pdb=" C3 CLR A 707 " ideal model delta sinusoidal sigma weight residual -56.83 61.06 -117.89 1 3.00e+01 1.11e-03 1.57e+01 ... (remaining 2858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 455 0.078 - 0.155: 168 0.155 - 0.233: 61 0.233 - 0.310: 27 0.310 - 0.388: 3 Chirality restraints: 714 Sorted by residual: chirality pdb=" CA LEU A 278 " pdb=" N LEU A 278 " pdb=" C LEU A 278 " pdb=" CB LEU A 278 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CA PHE A 474 " pdb=" N PHE A 474 " pdb=" C PHE A 474 " pdb=" CB PHE A 474 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CA TYR A 137 " pdb=" N TYR A 137 " pdb=" C TYR A 137 " pdb=" CB TYR A 137 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 711 not shown) Planarity restraints: 743 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 374 " 0.049 5.00e-02 4.00e+02 7.38e-02 8.72e+00 pdb=" N PRO A 375 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 92 " -0.040 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO A 93 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 512 " 0.040 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO A 513 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 513 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 513 " 0.034 5.00e-02 4.00e+02 ... (remaining 740 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 14 2.41 - 3.03: 2947 3.03 - 3.65: 6947 3.65 - 4.28: 11641 4.28 - 4.90: 18703 Nonbonded interactions: 40252 Sorted by model distance: nonbonded pdb=" O PHE A 392 " pdb=" CD1 LEU A 396 " model vdw 1.784 3.460 nonbonded pdb=" NH1 ARG A 66 " pdb=" OD1 ASP A 459 " model vdw 2.030 3.120 nonbonded pdb=" N1 TAU A 703 " pdb=" O1 TAU A 704 " model vdw 2.175 3.120 nonbonded pdb=" CG1 VAL A 182 " pdb=" CE3 TRP A 183 " model vdw 2.195 3.760 nonbonded pdb=" CG LEU A 52 " pdb=" CE1 PHE A 58 " model vdw 2.229 3.770 ... (remaining 40247 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.360 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.140 Find NCS groups from input model: 0.040 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:11.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 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 : 0.013 0.664 4657 Z= 1.152 Angle : 1.403 22.442 6381 Z= 0.871 Chirality : 0.102 0.388 714 Planarity : 0.008 0.074 743 Dihedral : 14.676 118.892 1866 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.71 % Allowed : 6.42 % Favored : 91.86 % 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: 1.92 (0.35), residues: 542 helix: 2.20 (0.25), residues: 386 sheet: None (None), residues: 0 loop : -1.16 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 113 HIS 0.003 0.001 HIS A 164 PHE 0.018 0.002 PHE A 392 TYR 0.018 0.002 TYR A 69 ARG 0.005 0.001 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.18057 ( 287) hydrogen bonds : angle 6.40464 ( 855) SS BOND : bond 0.00413 ( 1) SS BOND : angle 3.33827 ( 2) covalent geometry : bond 0.00845 ( 4655) covalent geometry : angle 1.40188 ( 6379) Misc. bond : bond 0.66383 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.467 Fit side-chains REVERT: A 113 TRP cc_start: 0.6943 (m100) cc_final: 0.6594 (m100) REVERT: A 161 HIS cc_start: 0.8358 (m-70) cc_final: 0.8103 (m-70) REVERT: A 197 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6596 (mt-10) REVERT: A 200 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6699 (mt-10) REVERT: A 275 LYS cc_start: 0.5752 (ttmt) cc_final: 0.5227 (mttp) REVERT: A 289 GLN cc_start: 0.7225 (pt0) cc_final: 0.6458 (mt0) REVERT: A 309 MET cc_start: 0.7636 (mmt) cc_final: 0.7325 (mmt) REVERT: A 325 ASP cc_start: 0.6862 (m-30) cc_final: 0.6566 (m-30) REVERT: A 402 SER cc_start: 0.7277 (m) cc_final: 0.6799 (p) REVERT: A 494 ASP cc_start: 0.7647 (t0) cc_final: 0.7407 (t0) REVERT: A 504 MET cc_start: 0.7071 (mmt) cc_final: 0.6418 (mmt) outliers start: 8 outliers final: 2 residues processed: 102 average time/residue: 0.8203 time to fit residues: 88.6818 Evaluate side-chains 62 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 375 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 5.9990 chunk 40 optimal weight: 0.2980 chunk 22 optimal weight: 0.0980 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 0.0470 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 154 GLN A 161 HIS A 333 ASN A 355 GLN A 567 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.158188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.119682 restraints weight = 4774.206| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.78 r_work: 0.3230 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4657 Z= 0.153 Angle : 0.698 10.293 6381 Z= 0.340 Chirality : 0.046 0.208 714 Planarity : 0.005 0.041 743 Dihedral : 10.916 73.859 929 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.14 % Allowed : 11.99 % Favored : 85.87 % 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: 1.82 (0.35), residues: 542 helix: 1.96 (0.25), residues: 389 sheet: None (None), residues: 0 loop : -0.75 (0.50), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 470 HIS 0.008 0.002 HIS A 161 PHE 0.030 0.002 PHE A 58 TYR 0.019 0.001 TYR A 69 ARG 0.002 0.000 ARG A 423 Details of bonding type rmsd hydrogen bonds : bond 0.05358 ( 287) hydrogen bonds : angle 4.96441 ( 855) SS BOND : bond 0.00714 ( 1) SS BOND : angle 8.29189 ( 2) covalent geometry : bond 0.00329 ( 4655) covalent geometry : angle 0.68266 ( 6379) Misc. bond : bond 0.00550 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.439 Fit side-chains REVERT: A 176 MET cc_start: 0.6723 (mmm) cc_final: 0.6366 (mmm) REVERT: A 200 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8176 (mt-10) REVERT: A 275 LYS cc_start: 0.7532 (ttmt) cc_final: 0.6931 (mtmt) REVERT: A 402 SER cc_start: 0.8618 (m) cc_final: 0.8378 (t) REVERT: A 504 MET cc_start: 0.8250 (mmt) cc_final: 0.7849 (mmt) REVERT: A 506 TYR cc_start: 0.6922 (m-10) cc_final: 0.5870 (t80) outliers start: 10 outliers final: 3 residues processed: 73 average time/residue: 1.0265 time to fit residues: 78.4625 Evaluate side-chains 58 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 486 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 0.0060 chunk 47 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 HIS A 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.159846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.120856 restraints weight = 4777.104| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.82 r_work: 0.3147 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4657 Z= 0.145 Angle : 0.640 15.812 6381 Z= 0.304 Chirality : 0.045 0.255 714 Planarity : 0.004 0.036 743 Dihedral : 9.223 57.425 926 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.57 % Allowed : 13.92 % Favored : 83.51 % 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: 1.60 (0.36), residues: 542 helix: 1.78 (0.26), residues: 397 sheet: None (None), residues: 0 loop : -0.94 (0.50), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 113 HIS 0.005 0.002 HIS A 164 PHE 0.020 0.002 PHE A 191 TYR 0.019 0.001 TYR A 69 ARG 0.006 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04782 ( 287) hydrogen bonds : angle 4.73779 ( 855) SS BOND : bond 0.01821 ( 1) SS BOND : angle 4.30772 ( 2) covalent geometry : bond 0.00325 ( 4655) covalent geometry : angle 0.63552 ( 6379) Misc. bond : bond 0.00087 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.476 Fit side-chains REVERT: A 200 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8296 (mt-10) REVERT: A 275 LYS cc_start: 0.7646 (ttmt) cc_final: 0.7049 (mtmt) REVERT: A 284 ARG cc_start: 0.7740 (mmt180) cc_final: 0.7034 (tmt170) REVERT: A 289 GLN cc_start: 0.8267 (pt0) cc_final: 0.7629 (tt0) REVERT: A 402 SER cc_start: 0.8638 (m) cc_final: 0.8409 (t) REVERT: A 504 MET cc_start: 0.8289 (mmt) cc_final: 0.7871 (mmt) REVERT: A 506 TYR cc_start: 0.6978 (m-10) cc_final: 0.5971 (t80) REVERT: A 534 LYS cc_start: 0.8659 (mtpt) cc_final: 0.8310 (mtmm) outliers start: 12 outliers final: 4 residues processed: 72 average time/residue: 1.0988 time to fit residues: 83.1081 Evaluate side-chains 63 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 322 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 33 optimal weight: 0.4980 chunk 27 optimal weight: 0.0670 chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 0.0980 chunk 20 optimal weight: 0.3980 chunk 25 optimal weight: 0.6980 chunk 3 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 567 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.160402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.122844 restraints weight = 4600.769| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.72 r_work: 0.3222 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4657 Z= 0.117 Angle : 0.554 7.942 6381 Z= 0.268 Chirality : 0.043 0.375 714 Planarity : 0.004 0.033 743 Dihedral : 8.519 55.040 926 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.36 % Allowed : 14.99 % Favored : 82.66 % 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: 1.72 (0.36), residues: 542 helix: 1.86 (0.26), residues: 398 sheet: None (None), residues: 0 loop : -0.90 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 470 HIS 0.001 0.000 HIS A 164 PHE 0.016 0.001 PHE A 191 TYR 0.018 0.001 TYR A 69 ARG 0.006 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04150 ( 287) hydrogen bonds : angle 4.54802 ( 855) SS BOND : bond 0.00042 ( 1) SS BOND : angle 2.81366 ( 2) covalent geometry : bond 0.00244 ( 4655) covalent geometry : angle 0.55189 ( 6379) Misc. bond : bond 0.00764 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.480 Fit side-chains REVERT: A 275 LYS cc_start: 0.7695 (ttmt) cc_final: 0.7126 (mtmt) REVERT: A 284 ARG cc_start: 0.7723 (mmt180) cc_final: 0.7066 (tmt170) REVERT: A 289 GLN cc_start: 0.8335 (pt0) cc_final: 0.7744 (tt0) REVERT: A 402 SER cc_start: 0.8646 (m) cc_final: 0.8402 (t) REVERT: A 504 MET cc_start: 0.8281 (mmt) cc_final: 0.7852 (mmt) REVERT: A 506 TYR cc_start: 0.6947 (m-10) cc_final: 0.6032 (t80) REVERT: A 534 LYS cc_start: 0.8630 (mtpt) cc_final: 0.8338 (mtmm) outliers start: 11 outliers final: 2 residues processed: 72 average time/residue: 0.9588 time to fit residues: 72.5101 Evaluate side-chains 60 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 304 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 30 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 16 optimal weight: 0.0970 chunk 42 optimal weight: 2.9990 chunk 22 optimal weight: 0.0270 chunk 23 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 567 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.159371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.121472 restraints weight = 4675.080| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.74 r_work: 0.3187 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4657 Z= 0.114 Angle : 0.545 10.342 6381 Z= 0.262 Chirality : 0.040 0.218 714 Planarity : 0.004 0.032 743 Dihedral : 7.752 52.953 926 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.43 % Allowed : 14.13 % Favored : 82.44 % 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: 1.75 (0.37), residues: 542 helix: 1.89 (0.26), residues: 399 sheet: None (None), residues: 0 loop : -0.91 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 PHE 0.012 0.001 PHE A 392 TYR 0.019 0.001 TYR A 69 ARG 0.007 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04054 ( 287) hydrogen bonds : angle 4.48739 ( 855) SS BOND : bond 0.00014 ( 1) SS BOND : angle 2.45635 ( 2) covalent geometry : bond 0.00248 ( 4655) covalent geometry : angle 0.54308 ( 6379) Misc. bond : bond 0.00240 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: A 275 LYS cc_start: 0.7698 (ttmt) cc_final: 0.7067 (mtmt) REVERT: A 284 ARG cc_start: 0.7690 (mmt180) cc_final: 0.7019 (tmt170) REVERT: A 289 GLN cc_start: 0.8314 (pt0) cc_final: 0.7671 (tt0) REVERT: A 402 SER cc_start: 0.8622 (m) cc_final: 0.8372 (t) REVERT: A 504 MET cc_start: 0.8304 (mmt) cc_final: 0.7893 (mmt) REVERT: A 506 TYR cc_start: 0.6979 (m-10) cc_final: 0.6057 (t80) REVERT: A 534 LYS cc_start: 0.8622 (mtpt) cc_final: 0.8360 (mtmm) REVERT: A 577 LYS cc_start: 0.6487 (mttp) cc_final: 0.6138 (pptt) outliers start: 16 outliers final: 7 residues processed: 72 average time/residue: 0.9266 time to fit residues: 70.1470 Evaluate side-chains 68 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 429 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.157799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.118286 restraints weight = 4654.621| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.80 r_work: 0.3162 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4657 Z= 0.138 Angle : 0.569 9.698 6381 Z= 0.273 Chirality : 0.042 0.262 714 Planarity : 0.004 0.034 743 Dihedral : 7.539 52.420 926 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.36 % Allowed : 15.42 % Favored : 82.23 % 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: 1.57 (0.37), residues: 542 helix: 1.77 (0.26), residues: 400 sheet: None (None), residues: 0 loop : -1.07 (0.52), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 PHE 0.016 0.002 PHE A 392 TYR 0.018 0.001 TYR A 69 ARG 0.006 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04237 ( 287) hydrogen bonds : angle 4.54967 ( 855) SS BOND : bond 0.00034 ( 1) SS BOND : angle 2.31187 ( 2) covalent geometry : bond 0.00315 ( 4655) covalent geometry : angle 0.56733 ( 6379) Misc. bond : bond 0.00354 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 275 LYS cc_start: 0.7721 (ttmt) cc_final: 0.7065 (mtmt) REVERT: A 284 ARG cc_start: 0.7737 (mmt180) cc_final: 0.7032 (tmt170) REVERT: A 289 GLN cc_start: 0.8347 (pt0) cc_final: 0.7672 (tt0) REVERT: A 320 TYR cc_start: 0.8397 (t80) cc_final: 0.8163 (t80) REVERT: A 402 SER cc_start: 0.8598 (m) cc_final: 0.8352 (t) REVERT: A 504 MET cc_start: 0.8332 (mmt) cc_final: 0.7967 (mmt) REVERT: A 506 TYR cc_start: 0.6988 (m-10) cc_final: 0.6055 (t80) REVERT: A 534 LYS cc_start: 0.8641 (mtpt) cc_final: 0.8359 (mtmm) REVERT: A 577 LYS cc_start: 0.6484 (mttp) cc_final: 0.6140 (pptt) outliers start: 11 outliers final: 7 residues processed: 69 average time/residue: 0.8650 time to fit residues: 62.9776 Evaluate side-chains 66 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 429 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 33 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 HIS A 567 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.156473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.116938 restraints weight = 4614.934| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.79 r_work: 0.3132 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4657 Z= 0.141 Angle : 0.564 13.429 6381 Z= 0.271 Chirality : 0.041 0.168 714 Planarity : 0.004 0.035 743 Dihedral : 7.359 52.744 926 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.14 % Allowed : 15.42 % Favored : 82.44 % 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: 1.51 (0.37), residues: 542 helix: 1.74 (0.26), residues: 399 sheet: None (None), residues: 0 loop : -1.12 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 PHE 0.016 0.002 PHE A 392 TYR 0.018 0.001 TYR A 69 ARG 0.006 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04264 ( 287) hydrogen bonds : angle 4.57047 ( 855) SS BOND : bond 0.00052 ( 1) SS BOND : angle 2.23430 ( 2) covalent geometry : bond 0.00330 ( 4655) covalent geometry : angle 0.56256 ( 6379) Misc. bond : bond 0.00479 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 275 LYS cc_start: 0.7732 (ttmt) cc_final: 0.7085 (mttt) REVERT: A 284 ARG cc_start: 0.7739 (mmt180) cc_final: 0.7046 (tmt170) REVERT: A 289 GLN cc_start: 0.8338 (pt0) cc_final: 0.7645 (tt0) REVERT: A 320 TYR cc_start: 0.8409 (t80) cc_final: 0.8161 (t80) REVERT: A 402 SER cc_start: 0.8626 (m) cc_final: 0.8410 (t) REVERT: A 504 MET cc_start: 0.8332 (mmt) cc_final: 0.7972 (mmt) REVERT: A 506 TYR cc_start: 0.6982 (m-10) cc_final: 0.6056 (t80) REVERT: A 577 LYS cc_start: 0.6450 (mttp) cc_final: 0.6105 (pptt) outliers start: 10 outliers final: 7 residues processed: 66 average time/residue: 0.9016 time to fit residues: 62.7360 Evaluate side-chains 66 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 429 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 34 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 13 optimal weight: 0.2980 chunk 3 optimal weight: 0.0570 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN A 567 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.158360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.119080 restraints weight = 4666.291| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.79 r_work: 0.3174 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4657 Z= 0.116 Angle : 0.538 12.455 6381 Z= 0.259 Chirality : 0.040 0.154 714 Planarity : 0.004 0.036 743 Dihedral : 7.267 53.103 926 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.71 % Allowed : 16.06 % Favored : 82.23 % 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: 1.68 (0.37), residues: 542 helix: 1.86 (0.26), residues: 399 sheet: None (None), residues: 0 loop : -1.04 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 PHE 0.012 0.001 PHE A 392 TYR 0.018 0.001 TYR A 69 ARG 0.007 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.03984 ( 287) hydrogen bonds : angle 4.47342 ( 855) SS BOND : bond 0.00119 ( 1) SS BOND : angle 1.71452 ( 2) covalent geometry : bond 0.00259 ( 4655) covalent geometry : angle 0.53690 ( 6379) Misc. bond : bond 0.00249 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: A 275 LYS cc_start: 0.7740 (ttmt) cc_final: 0.7065 (mttt) REVERT: A 284 ARG cc_start: 0.7743 (mmt180) cc_final: 0.7072 (tmt170) REVERT: A 289 GLN cc_start: 0.8318 (pt0) cc_final: 0.7634 (tt0) REVERT: A 401 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7597 (t70) REVERT: A 402 SER cc_start: 0.8613 (m) cc_final: 0.8403 (t) REVERT: A 504 MET cc_start: 0.8332 (mmt) cc_final: 0.7928 (mmt) REVERT: A 506 TYR cc_start: 0.6958 (m-10) cc_final: 0.6034 (t80) REVERT: A 577 LYS cc_start: 0.6472 (mttp) cc_final: 0.6131 (pptt) outliers start: 8 outliers final: 6 residues processed: 69 average time/residue: 0.9654 time to fit residues: 70.2394 Evaluate side-chains 66 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 429 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 31 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 567 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.156322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.118327 restraints weight = 4641.786| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.72 r_work: 0.3188 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4657 Z= 0.134 Angle : 0.557 12.507 6381 Z= 0.268 Chirality : 0.040 0.157 714 Planarity : 0.004 0.036 743 Dihedral : 7.236 52.557 926 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.71 % Allowed : 16.49 % 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: 1.57 (0.37), residues: 542 helix: 1.78 (0.26), residues: 400 sheet: None (None), residues: 0 loop : -1.12 (0.53), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 470 HIS 0.002 0.001 HIS A 164 PHE 0.015 0.001 PHE A 392 TYR 0.018 0.001 TYR A 69 ARG 0.006 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04157 ( 287) hydrogen bonds : angle 4.50372 ( 855) SS BOND : bond 0.00053 ( 1) SS BOND : angle 2.01056 ( 2) covalent geometry : bond 0.00310 ( 4655) covalent geometry : angle 0.55610 ( 6379) Misc. bond : bond 0.00234 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 275 LYS cc_start: 0.7733 (ttmt) cc_final: 0.7069 (mttt) REVERT: A 284 ARG cc_start: 0.7725 (mmt180) cc_final: 0.7060 (tmt170) REVERT: A 289 GLN cc_start: 0.8319 (pt0) cc_final: 0.7638 (tt0) REVERT: A 401 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7606 (t70) REVERT: A 402 SER cc_start: 0.8612 (m) cc_final: 0.8411 (t) REVERT: A 504 MET cc_start: 0.8341 (mmt) cc_final: 0.7960 (mmt) REVERT: A 506 TYR cc_start: 0.6991 (m-10) cc_final: 0.6075 (t80) REVERT: A 577 LYS cc_start: 0.6551 (mttp) cc_final: 0.6190 (pptt) outliers start: 8 outliers final: 5 residues processed: 68 average time/residue: 0.9049 time to fit residues: 64.9691 Evaluate side-chains 66 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 429 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 27 optimal weight: 0.0170 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 567 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.157765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.118600 restraints weight = 4611.220| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.78 r_work: 0.3155 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4657 Z= 0.124 Angle : 0.546 12.203 6381 Z= 0.264 Chirality : 0.040 0.153 714 Planarity : 0.004 0.037 743 Dihedral : 7.182 52.966 926 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.71 % Allowed : 16.27 % Favored : 82.01 % 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: 1.59 (0.37), residues: 542 helix: 1.80 (0.26), residues: 400 sheet: None (None), residues: 0 loop : -1.13 (0.53), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 470 HIS 0.002 0.001 HIS A 170 PHE 0.013 0.001 PHE A 392 TYR 0.018 0.001 TYR A 69 ARG 0.006 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04046 ( 287) hydrogen bonds : angle 4.48262 ( 855) SS BOND : bond 0.00051 ( 1) SS BOND : angle 1.77794 ( 2) covalent geometry : bond 0.00282 ( 4655) covalent geometry : angle 0.54553 ( 6379) Misc. bond : bond 0.00217 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 275 LYS cc_start: 0.7737 (ttmt) cc_final: 0.7057 (mttt) REVERT: A 284 ARG cc_start: 0.7680 (mmt180) cc_final: 0.7024 (tmt170) REVERT: A 289 GLN cc_start: 0.8320 (pt0) cc_final: 0.7630 (tt0) REVERT: A 401 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7599 (t70) REVERT: A 504 MET cc_start: 0.8339 (mmt) cc_final: 0.7764 (mmt) REVERT: A 506 TYR cc_start: 0.6979 (m-10) cc_final: 0.6055 (t80) REVERT: A 577 LYS cc_start: 0.6542 (mttp) cc_final: 0.6163 (pptt) outliers start: 8 outliers final: 5 residues processed: 69 average time/residue: 0.8885 time to fit residues: 64.7258 Evaluate side-chains 65 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 429 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 11 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 22 optimal weight: 0.0060 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 567 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.156777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.118705 restraints weight = 4601.379| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.73 r_work: 0.3160 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4657 Z= 0.124 Angle : 0.545 12.074 6381 Z= 0.263 Chirality : 0.040 0.151 714 Planarity : 0.004 0.037 743 Dihedral : 7.141 56.920 926 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.86 % Allowed : 17.34 % 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: 1.60 (0.37), residues: 542 helix: 1.83 (0.26), residues: 399 sheet: None (None), residues: 0 loop : -1.16 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 PHE 0.013 0.001 PHE A 392 TYR 0.018 0.001 TYR A 69 ARG 0.009 0.001 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04035 ( 287) hydrogen bonds : angle 4.48224 ( 855) SS BOND : bond 0.00003 ( 1) SS BOND : angle 1.89873 ( 2) covalent geometry : bond 0.00286 ( 4655) covalent geometry : angle 0.54382 ( 6379) Misc. bond : bond 0.00208 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3894.38 seconds wall clock time: 67 minutes 55.84 seconds (4075.84 seconds total)