Starting phenix.real_space_refine on Sat May 10 01:17:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k7b_62147/05_2025/9k7b_62147.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k7b_62147/05_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_62147/05_2025/9k7b_62147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k7b_62147/05_2025/9k7b_62147.map" model { file = "/net/cci-nas-00/data/ceres_data/9k7b_62147/05_2025/9k7b_62147.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k7b_62147/05_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-5687/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: 3.62, per 1000 atoms: 0.80 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: 1.32 Conformation dependent library (CDL) restraints added in 474.8 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: 0.42 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: 1.21 Time building geometry restraints manager: 1.47 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: 1.810 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.990 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.320 ------------------------------------------------------------------------------- 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 : 0.499 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: 0.7590 time to fit residues: 82.5395 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 : 0.435 ------------------------------------------------------------------------------- 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 = 43)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.119661 restraints weight = 4774.205| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.78 r_work: 0.3227 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 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 : 0.441 Fit side-chains REVERT: A 176 MET cc_start: 0.6742 (mmm) cc_final: 0.6384 (mmm) REVERT: A 200 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8180 (mt-10) REVERT: A 275 LYS cc_start: 0.7538 (ttmt) cc_final: 0.6938 (mtmt) REVERT: A 402 SER cc_start: 0.8618 (m) cc_final: 0.8376 (t) REVERT: A 504 MET cc_start: 0.8252 (mmt) cc_final: 0.7851 (mmt) REVERT: A 506 TYR cc_start: 0.6927 (m-10) cc_final: 0.5872 (t80) outliers start: 10 outliers final: 3 residues processed: 73 average time/residue: 1.0067 time to fit residues: 76.8949 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 : 0.481 ------------------------------------------------------------------------------- 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: 2.9990 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: 0.5980 chunk 41 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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 = 0.3799 r_free = 0.3799 target = 0.159066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.120140 restraints weight = 4784.129| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.81 r_work: 0.3146 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4657 Z= 0.141 Angle : 0.639 16.477 6381 Z= 0.303 Chirality : 0.045 0.257 714 Planarity : 0.005 0.038 743 Dihedral : 9.269 57.576 926 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.36 % Allowed : 13.70 % Favored : 83.94 % 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: 1.62 (0.36), residues: 542 helix: 1.79 (0.26), residues: 396 sheet: None (None), residues: 0 loop : -0.90 (0.50), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 113 HIS 0.005 0.001 HIS A 164 PHE 0.021 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 0.04796 ( 287) hydrogen bonds : angle 4.75373 ( 855) SS BOND : bond 0.00801 ( 1) SS BOND : angle 4.26532 ( 2) covalent geometry : bond 0.00315 ( 4655) covalent geometry : angle 0.63480 ( 6379) Misc. bond : bond 0.00073 ( 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 73 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.476 Fit side-chains REVERT: A 200 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8240 (mt-10) REVERT: A 275 LYS cc_start: 0.7565 (ttmt) cc_final: 0.6958 (mtmt) REVERT: A 284 ARG cc_start: 0.7691 (mmt180) cc_final: 0.6956 (tmt170) REVERT: A 289 GLN cc_start: 0.8216 (pt0) cc_final: 0.7555 (tt0) REVERT: A 402 SER cc_start: 0.8608 (m) cc_final: 0.8366 (t) REVERT: A 504 MET cc_start: 0.8239 (mmt) cc_final: 0.7815 (mmt) REVERT: A 506 TYR cc_start: 0.6909 (m-10) cc_final: 0.5882 (t80) REVERT: A 534 LYS cc_start: 0.8642 (mtpt) cc_final: 0.8287 (mtmm) outliers start: 11 outliers final: 5 residues processed: 70 average time/residue: 0.8588 time to fit residues: 63.4649 Evaluate side-chains 62 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 401 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 0.0020 chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 0.0980 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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 = 0.3809 r_free = 0.3809 target = 0.159259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.121249 restraints weight = 4601.237| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.73 r_work: 0.3203 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4657 Z= 0.121 Angle : 0.554 8.472 6381 Z= 0.269 Chirality : 0.042 0.225 714 Planarity : 0.004 0.034 743 Dihedral : 8.492 54.517 926 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.00 % Allowed : 13.92 % Favored : 83.08 % 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: 1.63 (0.36), residues: 542 helix: 1.79 (0.26), residues: 398 sheet: None (None), residues: 0 loop : -0.93 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 470 HIS 0.002 0.001 HIS A 164 PHE 0.021 0.002 PHE A 191 TYR 0.018 0.001 TYR A 69 ARG 0.007 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04194 ( 287) hydrogen bonds : angle 4.55282 ( 855) SS BOND : bond 0.00010 ( 1) SS BOND : angle 2.78687 ( 2) covalent geometry : bond 0.00265 ( 4655) covalent geometry : angle 0.55212 ( 6379) Misc. bond : bond 0.00428 ( 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 75 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.452 Fit side-chains REVERT: A 275 LYS cc_start: 0.7703 (ttmt) cc_final: 0.7137 (mtmt) REVERT: A 284 ARG cc_start: 0.7733 (mmt180) cc_final: 0.7071 (tmt170) REVERT: A 289 GLN cc_start: 0.8342 (pt0) cc_final: 0.7745 (tt0) REVERT: A 402 SER cc_start: 0.8638 (m) cc_final: 0.8397 (t) REVERT: A 504 MET cc_start: 0.8286 (mmt) cc_final: 0.7894 (mmt) REVERT: A 506 TYR cc_start: 0.6962 (m-10) cc_final: 0.6048 (t80) REVERT: A 534 LYS cc_start: 0.8639 (mtpt) cc_final: 0.8337 (mtmm) REVERT: A 577 LYS cc_start: 0.6441 (mttp) cc_final: 0.6104 (pptt) outliers start: 14 outliers final: 3 residues processed: 72 average time/residue: 0.8861 time to fit residues: 67.1895 Evaluate side-chains 61 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 322 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 30 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 chunk 46 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.158351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.118862 restraints weight = 4670.302| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.80 r_work: 0.3158 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4657 Z= 0.131 Angle : 0.563 10.241 6381 Z= 0.270 Chirality : 0.042 0.227 714 Planarity : 0.004 0.034 743 Dihedral : 7.921 55.207 926 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % 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: 1.59 (0.36), residues: 542 helix: 1.76 (0.26), residues: 400 sheet: None (None), residues: 0 loop : -0.98 (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 0.015 0.002 PHE A 392 TYR 0.019 0.001 TYR A 69 ARG 0.006 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04258 ( 287) hydrogen bonds : angle 4.56938 ( 855) SS BOND : bond 0.00079 ( 1) SS BOND : angle 2.50643 ( 2) covalent geometry : bond 0.00299 ( 4655) covalent geometry : angle 0.56161 ( 6379) Misc. bond : bond 0.00236 ( 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 73 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.509 Fit side-chains REVERT: A 275 LYS cc_start: 0.7695 (ttmt) cc_final: 0.7054 (mtmt) REVERT: A 284 ARG cc_start: 0.7724 (mmt180) cc_final: 0.7012 (tmt170) REVERT: A 289 GLN cc_start: 0.8357 (pt0) cc_final: 0.7696 (tt0) REVERT: A 320 TYR cc_start: 0.8372 (t80) cc_final: 0.8119 (t80) REVERT: A 402 SER cc_start: 0.8611 (m) cc_final: 0.8364 (t) REVERT: A 504 MET cc_start: 0.8322 (mmt) cc_final: 0.7988 (mmt) REVERT: A 506 TYR cc_start: 0.6974 (m-10) cc_final: 0.6048 (t80) REVERT: A 534 LYS cc_start: 0.8662 (mtpt) cc_final: 0.8361 (mtmm) REVERT: A 577 LYS cc_start: 0.6492 (mttp) cc_final: 0.6148 (pptt) outliers start: 11 outliers final: 5 residues processed: 70 average time/residue: 0.9702 time to fit residues: 71.3573 Evaluate side-chains 65 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 304 ILE Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 401 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 chunk 45 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.158358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.118897 restraints weight = 4648.159| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.80 r_work: 0.3171 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4657 Z= 0.126 Angle : 0.551 10.546 6381 Z= 0.265 Chirality : 0.041 0.280 714 Planarity : 0.004 0.035 743 Dihedral : 7.558 53.042 926 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.57 % Allowed : 15.20 % 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: 1.60 (0.37), residues: 542 helix: 1.79 (0.26), residues: 400 sheet: None (None), residues: 0 loop : -1.06 (0.52), 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 161 PHE 0.013 0.002 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 0.04111 ( 287) hydrogen bonds : angle 4.52042 ( 855) SS BOND : bond 0.00049 ( 1) SS BOND : angle 2.22447 ( 2) covalent geometry : bond 0.00284 ( 4655) covalent geometry : angle 0.54994 ( 6379) Misc. bond : bond 0.00286 ( 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 75 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.446 Fit side-chains REVERT: A 275 LYS cc_start: 0.7716 (ttmt) cc_final: 0.7076 (mttt) REVERT: A 284 ARG cc_start: 0.7725 (mmt180) cc_final: 0.7020 (tmt170) REVERT: A 289 GLN cc_start: 0.8339 (pt0) cc_final: 0.7658 (tt0) REVERT: A 320 TYR cc_start: 0.8402 (t80) cc_final: 0.8169 (t80) REVERT: A 402 SER cc_start: 0.8598 (m) cc_final: 0.8366 (t) REVERT: A 504 MET cc_start: 0.8336 (mmt) cc_final: 0.7939 (mmt) REVERT: A 506 TYR cc_start: 0.6961 (m-10) cc_final: 0.6041 (t80) REVERT: A 534 LYS cc_start: 0.8669 (mtpt) cc_final: 0.8370 (mtmm) REVERT: A 577 LYS cc_start: 0.6492 (mttp) cc_final: 0.6147 (pptt) outliers start: 12 outliers final: 5 residues processed: 72 average time/residue: 0.8437 time to fit residues: 64.2379 Evaluate side-chains 65 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 304 ILE Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 401 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 33 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.156546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.117197 restraints weight = 4617.684| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.78 r_work: 0.3138 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4657 Z= 0.145 Angle : 0.560 7.889 6381 Z= 0.273 Chirality : 0.042 0.265 714 Planarity : 0.004 0.035 743 Dihedral : 7.447 52.668 926 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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: 1.52 (0.36), residues: 542 helix: 1.72 (0.26), residues: 399 sheet: None (None), residues: 0 loop : -1.04 (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 0.04292 ( 287) hydrogen bonds : angle 4.61056 ( 855) SS BOND : bond 0.00035 ( 1) SS BOND : angle 2.25853 ( 2) covalent geometry : bond 0.00339 ( 4655) covalent geometry : angle 0.55897 ( 6379) Misc. bond : bond 0.00441 ( 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 68 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.479 Fit side-chains REVERT: A 275 LYS cc_start: 0.7732 (ttmt) cc_final: 0.7059 (mttt) REVERT: A 284 ARG cc_start: 0.7744 (mmt180) cc_final: 0.7054 (tmt170) REVERT: A 289 GLN cc_start: 0.8333 (pt0) cc_final: 0.7641 (tt0) REVERT: A 320 TYR cc_start: 0.8402 (t80) cc_final: 0.8157 (t80) REVERT: A 402 SER cc_start: 0.8620 (m) cc_final: 0.8408 (t) REVERT: A 504 MET cc_start: 0.8335 (mmt) cc_final: 0.8007 (mmt) REVERT: A 506 TYR cc_start: 0.6986 (m-10) cc_final: 0.6058 (t80) REVERT: A 534 LYS cc_start: 0.8686 (mtpt) cc_final: 0.8366 (mtmm) REVERT: A 577 LYS cc_start: 0.6461 (mttp) cc_final: 0.6104 (pptt) outliers start: 8 outliers final: 5 residues processed: 67 average time/residue: 0.8876 time to fit residues: 62.6635 Evaluate side-chains 64 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 34 optimal weight: 0.8980 chunk 50 optimal weight: 0.0470 chunk 13 optimal weight: 0.0670 chunk 3 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.157271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.119058 restraints weight = 4686.206| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.75 r_work: 0.3171 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4657 Z= 0.114 Angle : 0.536 11.692 6381 Z= 0.259 Chirality : 0.040 0.152 714 Planarity : 0.004 0.035 743 Dihedral : 7.273 53.187 926 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.50 % Allowed : 16.27 % 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: 1.67 (0.37), residues: 542 helix: 1.85 (0.26), residues: 399 sheet: None (None), residues: 0 loop : -1.04 (0.52), 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 300 TYR 0.018 0.001 TYR A 69 ARG 0.006 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 287) hydrogen bonds : angle 4.50901 ( 855) SS BOND : bond 0.00097 ( 1) SS BOND : angle 1.81743 ( 2) covalent geometry : bond 0.00255 ( 4655) covalent geometry : angle 0.53496 ( 6379) Misc. bond : bond 0.00133 ( 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 66 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.479 Fit side-chains REVERT: A 275 LYS cc_start: 0.7738 (ttmt) cc_final: 0.7067 (mttt) REVERT: A 284 ARG cc_start: 0.7751 (mmt180) cc_final: 0.7079 (tmt170) REVERT: A 289 GLN cc_start: 0.8314 (pt0) cc_final: 0.7624 (tt0) REVERT: A 401 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7598 (t70) REVERT: A 402 SER cc_start: 0.8615 (m) cc_final: 0.8400 (t) REVERT: A 504 MET cc_start: 0.8345 (mmt) cc_final: 0.7934 (mmt) REVERT: A 506 TYR cc_start: 0.6967 (m-10) cc_final: 0.6054 (t80) REVERT: A 534 LYS cc_start: 0.8658 (mtpt) cc_final: 0.8366 (mtmm) REVERT: A 577 LYS cc_start: 0.6495 (mttp) cc_final: 0.6145 (pptt) outliers start: 7 outliers final: 5 residues processed: 64 average time/residue: 0.9703 time to fit residues: 65.2012 Evaluate side-chains 64 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 139 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 31 optimal weight: 0.0170 chunk 29 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 overall best weight: 0.6218 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.157385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.117798 restraints weight = 4628.914| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.80 r_work: 0.3155 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3431 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= 0.122 Angle : 0.541 11.991 6381 Z= 0.261 Chirality : 0.040 0.152 714 Planarity : 0.004 0.035 743 Dihedral : 7.226 52.967 926 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.50 % Allowed : 16.27 % 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: 1.63 (0.37), residues: 542 helix: 1.82 (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 0.012 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 0.007 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 287) hydrogen bonds : angle 4.50837 ( 855) SS BOND : bond 0.00029 ( 1) SS BOND : angle 1.88751 ( 2) covalent geometry : bond 0.00279 ( 4655) covalent geometry : angle 0.54042 ( 6379) Misc. bond : bond 0.00227 ( 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 68 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.471 Fit side-chains REVERT: A 275 LYS cc_start: 0.7725 (ttmt) cc_final: 0.7047 (mttt) REVERT: A 284 ARG cc_start: 0.7709 (mmt180) cc_final: 0.7040 (tmt170) REVERT: A 289 GLN cc_start: 0.8334 (pt0) cc_final: 0.7641 (tt0) REVERT: A 401 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7594 (t70) REVERT: A 402 SER cc_start: 0.8603 (m) cc_final: 0.8401 (t) REVERT: A 504 MET cc_start: 0.8346 (mmt) cc_final: 0.7929 (mmt) REVERT: A 506 TYR cc_start: 0.6974 (m-10) cc_final: 0.6055 (t80) outliers start: 7 outliers final: 4 residues processed: 66 average time/residue: 0.8892 time to fit residues: 62.1135 Evaluate side-chains 65 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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 292 ILE Chi-restraints excluded: chain A residue 401 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 3 optimal weight: 0.9990 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: 0.6980 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.156255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.116963 restraints weight = 4615.861| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.78 r_work: 0.3128 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4657 Z= 0.143 Angle : 0.562 12.137 6381 Z= 0.271 Chirality : 0.041 0.160 714 Planarity : 0.004 0.036 743 Dihedral : 7.237 52.577 926 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.28 % Allowed : 16.27 % 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: 1.53 (0.37), residues: 542 helix: 1.75 (0.26), residues: 400 sheet: None (None), residues: 0 loop : -1.10 (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 170 PHE 0.016 0.002 PHE A 392 TYR 0.017 0.001 TYR A 69 ARG 0.006 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04210 ( 287) hydrogen bonds : angle 4.56236 ( 855) SS BOND : bond 0.00111 ( 1) SS BOND : angle 1.80476 ( 2) covalent geometry : bond 0.00337 ( 4655) covalent geometry : angle 0.56070 ( 6379) Misc. bond : bond 0.00230 ( 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 68 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.509 Fit side-chains REVERT: A 275 LYS cc_start: 0.7704 (ttmt) cc_final: 0.7045 (mttt) REVERT: A 284 ARG cc_start: 0.7697 (mmt180) cc_final: 0.7027 (tmt170) REVERT: A 289 GLN cc_start: 0.8307 (pt0) cc_final: 0.7634 (tt0) REVERT: A 401 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7603 (t70) REVERT: A 504 MET cc_start: 0.8352 (mmt) cc_final: 0.7957 (mmt) REVERT: A 506 TYR cc_start: 0.6993 (m-10) cc_final: 0.6065 (t80) outliers start: 6 outliers final: 4 residues processed: 64 average time/residue: 0.8889 time to fit residues: 60.0440 Evaluate side-chains 64 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 528 VAL 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: 2.9990 chunk 22 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.156705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.116846 restraints weight = 4594.899| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.80 r_work: 0.3147 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4657 Z= 0.136 Angle : 0.554 12.187 6381 Z= 0.268 Chirality : 0.040 0.157 714 Planarity : 0.004 0.037 743 Dihedral : 7.205 54.579 926 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.86 % Allowed : 16.92 % 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: 1.50 (0.37), residues: 542 helix: 1.73 (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 0.015 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 0.04152 ( 287) hydrogen bonds : angle 4.55853 ( 855) SS BOND : bond 0.00053 ( 1) SS BOND : angle 1.98095 ( 2) covalent geometry : bond 0.00316 ( 4655) covalent geometry : angle 0.55319 ( 6379) Misc. bond : bond 0.00220 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3558.56 seconds wall clock time: 62 minutes 6.21 seconds (3726.21 seconds total)