Starting phenix.real_space_refine on Thu Mar 6 01:54:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k18_36788/03_2025/8k18_36788.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k18_36788/03_2025/8k18_36788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k18_36788/03_2025/8k18_36788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k18_36788/03_2025/8k18_36788.map" model { file = "/net/cci-nas-00/data/ceres_data/8k18_36788/03_2025/8k18_36788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k18_36788/03_2025/8k18_36788.cif" } resolution = 3.68 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= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1444 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 2063 2.51 5 N 541 2.21 5 O 626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3246 Number of models: 1 Model: "" Number of chains: 3 Chain: "E" Number of atoms: 1505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1505 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 10, 'TRANS': 177} Chain breaks: 1 Chain: "C" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 931 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 113} Chain: "D" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Time building chain proxies: 3.25, per 1000 atoms: 1.00 Number of scatterers: 3246 At special positions: 0 Unit cell: (64.66, 64.66, 92.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 626 8.00 N 541 7.00 C 2063 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.01 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.05 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 353.9 milliseconds 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 754 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 9 sheets defined 12.1% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.891A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 368 Processing helix chain 'E' and resid 405 through 410 Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'C' and resid 28 through 32 removed outlier: 4.042A pdb=" N ARG C 31 " --> pdb=" O ILE C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.747A pdb=" N ILE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.932A pdb=" N GLU E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER E 399 " --> pdb=" O GLU E 354 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS E 356 " --> pdb=" O ALA E 397 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE E 392 " --> pdb=" O VAL E 524 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL E 524 " --> pdb=" O PHE E 392 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.932A pdb=" N GLU E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER E 399 " --> pdb=" O GLU E 354 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS E 356 " --> pdb=" O ALA E 397 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 452 through 454 removed outlier: 3.577A pdb=" N TYR E 453 " --> pdb=" O GLN E 493 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.800A pdb=" N THR C 113 " --> pdb=" O TYR C 93 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR C 93 " --> pdb=" O THR C 113 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N THR C 92 " --> pdb=" O GLN C 39 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET C 34 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ILE C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 17 through 20 removed outlier: 3.511A pdb=" N LEU C 20 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU C 80 " --> pdb=" O LEU C 20 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.701A pdb=" N VAL D 19 " --> pdb=" O ILE D 75 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.500A pdb=" N GLU D 105 " --> pdb=" O LEU D 11 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.646A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) 95 hydrogen bonds defined for protein. 231 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.83 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 627 1.32 - 1.45: 880 1.45 - 1.57: 1799 1.57 - 1.70: 0 1.70 - 1.82: 20 Bond restraints: 3326 Sorted by residual: bond pdb=" N GLY C 91 " pdb=" CA GLY C 91 " ideal model delta sigma weight residual 1.444 1.478 -0.034 9.10e-03 1.21e+04 1.38e+01 bond pdb=" CZ ARG C 38 " pdb=" NH2 ARG C 38 " ideal model delta sigma weight residual 1.330 1.283 0.047 1.30e-02 5.92e+03 1.30e+01 bond pdb=" CZ ARG C 71 " pdb=" NH1 ARG C 71 " ideal model delta sigma weight residual 1.323 1.278 0.045 1.40e-02 5.10e+03 1.02e+01 bond pdb=" N VAL E 483 " pdb=" CA VAL E 483 " ideal model delta sigma weight residual 1.456 1.494 -0.039 1.23e-02 6.61e+03 9.87e+00 bond pdb=" CA PHE E 515 " pdb=" C PHE E 515 " ideal model delta sigma weight residual 1.524 1.562 -0.038 1.25e-02 6.40e+03 9.48e+00 ... (remaining 3321 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 3178 1.84 - 3.68: 1098 3.68 - 5.53: 200 5.53 - 7.37: 33 7.37 - 9.21: 5 Bond angle restraints: 4514 Sorted by residual: angle pdb=" NE ARG C 71 " pdb=" CZ ARG C 71 " pdb=" NH2 ARG C 71 " ideal model delta sigma weight residual 119.20 126.52 -7.32 9.00e-01 1.23e+00 6.62e+01 angle pdb=" CA GLY C 91 " pdb=" C GLY C 91 " pdb=" N THR C 92 " ideal model delta sigma weight residual 114.50 122.53 -8.03 1.19e+00 7.06e-01 4.56e+01 angle pdb=" O GLY C 91 " pdb=" C GLY C 91 " pdb=" N THR C 92 " ideal model delta sigma weight residual 123.59 117.81 5.78 8.70e-01 1.32e+00 4.41e+01 angle pdb=" OE1 GLN D 27 " pdb=" CD GLN D 27 " pdb=" NE2 GLN D 27 " ideal model delta sigma weight residual 122.60 116.03 6.57 1.00e+00 1.00e+00 4.32e+01 angle pdb=" CA PHE E 515 " pdb=" CB PHE E 515 " pdb=" CG PHE E 515 " ideal model delta sigma weight residual 113.80 119.75 -5.95 1.00e+00 1.00e+00 3.54e+01 ... (remaining 4509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.82: 1737 15.82 - 31.64: 152 31.64 - 47.46: 47 47.46 - 63.28: 11 63.28 - 79.10: 4 Dihedral angle restraints: 1951 sinusoidal: 761 harmonic: 1190 Sorted by residual: dihedral pdb=" CD ARG E 457 " pdb=" NE ARG E 457 " pdb=" CZ ARG E 457 " pdb=" NH1 ARG E 457 " ideal model delta sinusoidal sigma weight residual 0.00 67.40 -67.40 1 1.00e+01 1.00e-02 5.91e+01 dihedral pdb=" CD ARG C 103 " pdb=" NE ARG C 103 " pdb=" CZ ARG C 103 " pdb=" NH1 ARG C 103 " ideal model delta sinusoidal sigma weight residual 0.00 -39.95 39.95 1 1.00e+01 1.00e-02 2.24e+01 dihedral pdb=" CB CYS E 336 " pdb=" SG CYS E 336 " pdb=" SG CYS E 361 " pdb=" CB CYS E 361 " ideal model delta sinusoidal sigma weight residual -86.00 -123.61 37.61 1 1.00e+01 1.00e-02 1.99e+01 ... (remaining 1948 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 234 0.059 - 0.117: 159 0.117 - 0.175: 65 0.175 - 0.233: 20 0.233 - 0.291: 4 Chirality restraints: 482 Sorted by residual: chirality pdb=" CA THR C 92 " pdb=" N THR C 92 " pdb=" C THR C 92 " pdb=" CB THR C 92 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CB VAL C 29 " pdb=" CA VAL C 29 " pdb=" CG1 VAL C 29 " pdb=" CG2 VAL C 29 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA ASP E 427 " pdb=" N ASP E 427 " pdb=" C ASP E 427 " pdb=" CB ASP E 427 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 479 not shown) Planarity restraints: 586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 109 " -0.150 2.00e-02 2.50e+03 8.15e-02 1.66e+02 pdb=" CG TRP C 109 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP C 109 " 0.117 2.00e-02 2.50e+03 pdb=" CD2 TRP C 109 " 0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP C 109 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 TRP C 109 " -0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP C 109 " 0.071 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 109 " -0.115 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 109 " 0.081 2.00e-02 2.50e+03 pdb=" CH2 TRP C 109 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 457 " -1.003 9.50e-02 1.11e+02 4.50e-01 1.22e+02 pdb=" NE ARG E 457 " 0.061 2.00e-02 2.50e+03 pdb=" CZ ARG E 457 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG E 457 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG E 457 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 449 " 0.110 2.00e-02 2.50e+03 7.74e-02 1.20e+02 pdb=" CG TYR E 449 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR E 449 " -0.043 2.00e-02 2.50e+03 pdb=" CD2 TYR E 449 " -0.053 2.00e-02 2.50e+03 pdb=" CE1 TYR E 449 " -0.071 2.00e-02 2.50e+03 pdb=" CE2 TYR E 449 " -0.063 2.00e-02 2.50e+03 pdb=" CZ TYR E 449 " -0.030 2.00e-02 2.50e+03 pdb=" OH TYR E 449 " 0.145 2.00e-02 2.50e+03 ... (remaining 583 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 9 2.58 - 3.16: 2495 3.16 - 3.74: 5033 3.74 - 4.32: 7191 4.32 - 4.90: 11493 Nonbonded interactions: 26221 Sorted by model distance: nonbonded pdb=" CG ARG E 355 " pdb=" OD1 ASP E 398 " model vdw 1.995 3.440 nonbonded pdb=" OD1 ASN E 417 " pdb=" CE2 TYR C 52 " model vdw 1.999 3.340 nonbonded pdb=" OD2 ASP E 420 " pdb=" OG SER C 56 " model vdw 2.093 3.040 nonbonded pdb=" CG2 VAL C 24 " pdb=" CG2 VAL C 29 " model vdw 2.424 3.880 nonbonded pdb=" ND2 ASN E 481 " pdb=" CG2 VAL E 483 " model vdw 2.433 3.540 ... (remaining 26216 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.600 Find NCS groups from input model: 0.030 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3435 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 : 0.014 0.047 3326 Z= 0.918 Angle : 1.855 9.208 4514 Z= 1.237 Chirality : 0.089 0.291 482 Planarity : 0.034 0.450 586 Dihedral : 13.981 79.096 1185 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.85 % Allowed : 8.73 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % 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: -1.91 (0.40), residues: 406 helix: -4.07 (0.61), residues: 24 sheet: -1.36 (0.48), residues: 89 loop : -1.00 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.150 0.027 TRP C 109 HIS 0.025 0.008 HIS D 93 PHE 0.069 0.014 PHE E 497 TYR 0.145 0.026 TYR E 449 ARG 0.015 0.003 ARG C 31 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 33 average time/residue: 0.3093 time to fit residues: 11.7148 Evaluate side-chains 13 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 457 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 20.0000 chunk 29 optimal weight: 8.9990 chunk 16 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 30 optimal weight: 50.0000 chunk 11 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 GLN ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.037546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.026566 restraints weight = 485223.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.026520 restraints weight = 558220.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.026350 restraints weight = 518102.596| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 3326 Z= 0.356 Angle : 0.775 9.320 4514 Z= 0.416 Chirality : 0.048 0.262 482 Planarity : 0.006 0.050 586 Dihedral : 6.223 44.723 459 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 21.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.10 % Allowed : 12.11 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % 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 (0.41), residues: 406 helix: -3.42 (1.09), residues: 12 sheet: -1.63 (0.44), residues: 112 loop : -0.55 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP D 35 HIS 0.003 0.001 HIS D 93 PHE 0.020 0.002 PHE E 371 TYR 0.017 0.002 TYR E 365 ARG 0.006 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 14 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 347 PHE cc_start: 0.7291 (OUTLIER) cc_final: 0.6045 (m-80) REVERT: E 449 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.7851 (m-80) outliers start: 11 outliers final: 6 residues processed: 24 average time/residue: 0.2925 time to fit residues: 8.3087 Evaluate side-chains 20 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 12 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain E residue 449 TYR Chi-restraints excluded: chain E residue 457 ARG Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 106 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 35 optimal weight: 50.0000 chunk 38 optimal weight: 30.0000 chunk 31 optimal weight: 40.0000 chunk 12 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.036938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.036388 restraints weight = 48676.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.036292 restraints weight = 121337.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.036228 restraints weight = 140571.554| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.5439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3326 Z= 0.221 Angle : 0.651 8.591 4514 Z= 0.342 Chirality : 0.044 0.196 482 Planarity : 0.005 0.034 586 Dihedral : 5.568 33.269 459 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.25 % Allowed : 15.77 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % 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: -1.38 (0.41), residues: 406 helix: -2.66 (1.27), residues: 12 sheet: -1.42 (0.44), residues: 115 loop : -0.56 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 35 HIS 0.002 0.001 HIS D 70 PHE 0.027 0.002 PHE E 392 TYR 0.015 0.002 TYR E 501 ARG 0.004 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 13 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 449 TYR cc_start: 0.8482 (OUTLIER) cc_final: 0.8101 (m-80) outliers start: 8 outliers final: 5 residues processed: 19 average time/residue: 0.2996 time to fit residues: 6.8298 Evaluate side-chains 17 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 11 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain E residue 449 TYR Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 14 optimal weight: 0.0870 chunk 3 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 30.0000 chunk 34 optimal weight: 30.0000 chunk 7 optimal weight: 20.0000 chunk 8 optimal weight: 8.9990 chunk 23 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 11 optimal weight: 6.9990 chunk 5 optimal weight: 0.4980 overall best weight: 3.9164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.037044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.031528 restraints weight = 44811.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.030874 restraints weight = 141589.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.030638 restraints weight = 172740.190| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.5790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3326 Z= 0.182 Angle : 0.609 8.820 4514 Z= 0.319 Chirality : 0.043 0.188 482 Planarity : 0.004 0.032 586 Dihedral : 4.910 18.137 455 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.25 % Allowed : 16.34 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % 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: -1.19 (0.42), residues: 406 helix: -2.11 (1.44), residues: 12 sheet: -1.27 (0.45), residues: 115 loop : -0.46 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 35 HIS 0.002 0.001 HIS D 70 PHE 0.016 0.001 PHE E 392 TYR 0.011 0.001 TYR E 501 ARG 0.004 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 11 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 MET cc_start: 0.3013 (ttt) cc_final: 0.1524 (tpp) outliers start: 8 outliers final: 5 residues processed: 19 average time/residue: 0.1970 time to fit residues: 4.8840 Evaluate side-chains 16 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 11 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 30 optimal weight: 20.0000 chunk 15 optimal weight: 40.0000 chunk 5 optimal weight: 0.3980 chunk 14 optimal weight: 30.0000 chunk 19 optimal weight: 9.9990 chunk 8 optimal weight: 30.0000 chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 6 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.036427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.033969 restraints weight = 47505.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.033908 restraints weight = 128669.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.033688 restraints weight = 133605.386| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.6351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3326 Z= 0.184 Angle : 0.599 9.318 4514 Z= 0.318 Chirality : 0.043 0.174 482 Planarity : 0.004 0.029 586 Dihedral : 4.801 16.881 455 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.54 % Allowed : 18.03 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % 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: -1.13 (0.42), residues: 406 helix: -2.11 (1.43), residues: 12 sheet: -1.19 (0.46), residues: 116 loop : -0.43 (0.40), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 35 HIS 0.002 0.001 HIS D 70 PHE 0.028 0.002 PHE E 392 TYR 0.013 0.001 TYR E 501 ARG 0.004 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 10 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 MET cc_start: 0.2433 (ttt) cc_final: 0.0923 (tpt) outliers start: 9 outliers final: 5 residues processed: 19 average time/residue: 0.1911 time to fit residues: 4.7570 Evaluate side-chains 15 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 10 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 50.0000 chunk 22 optimal weight: 50.0000 chunk 7 optimal weight: 0.5980 chunk 14 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 30 optimal weight: 50.0000 chunk 15 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 30.0000 chunk 17 optimal weight: 5.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 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 = 0.036405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.030943 restraints weight = 46135.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.030379 restraints weight = 124502.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.030260 restraints weight = 150608.953| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.6430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3326 Z= 0.149 Angle : 0.590 9.804 4514 Z= 0.311 Chirality : 0.043 0.180 482 Planarity : 0.004 0.028 586 Dihedral : 4.624 17.152 455 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.97 % Allowed : 18.87 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.43), residues: 406 helix: -1.74 (1.55), residues: 12 sheet: -1.38 (0.45), residues: 118 loop : -0.22 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 35 HIS 0.002 0.001 HIS D 70 PHE 0.015 0.001 PHE E 392 TYR 0.011 0.001 TYR E 501 ARG 0.004 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 10 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 MET cc_start: 0.2925 (ttt) cc_final: 0.1302 (tpt) outliers start: 7 outliers final: 5 residues processed: 17 average time/residue: 0.2040 time to fit residues: 4.4520 Evaluate side-chains 15 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 10 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 30.0000 chunk 17 optimal weight: 20.0000 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 0.3980 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 38 optimal weight: 40.0000 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.036255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.031160 restraints weight = 48224.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.030382 restraints weight = 133774.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.030301 restraints weight = 176986.316| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.6509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3326 Z= 0.138 Angle : 0.563 9.404 4514 Z= 0.298 Chirality : 0.043 0.210 482 Planarity : 0.004 0.028 586 Dihedral : 4.412 17.290 455 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.10 % Allowed : 18.03 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % 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: -0.84 (0.44), residues: 406 helix: -1.42 (1.67), residues: 12 sheet: -1.17 (0.46), residues: 118 loop : -0.14 (0.41), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 35 HIS 0.002 0.001 HIS D 70 PHE 0.018 0.001 PHE E 392 TYR 0.009 0.001 TYR E 489 ARG 0.003 0.000 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 10 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 347 PHE cc_start: 0.7422 (OUTLIER) cc_final: 0.5966 (m-80) REVERT: D 4 MET cc_start: 0.2893 (ttt) cc_final: 0.1163 (tpt) outliers start: 11 outliers final: 8 residues processed: 21 average time/residue: 0.2535 time to fit residues: 6.5034 Evaluate side-chains 18 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 9 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 403 LYS Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain E residue 457 ARG Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 88 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 6 optimal weight: 20.0000 chunk 9 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 34 optimal weight: 30.0000 chunk 26 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 28 optimal weight: 40.0000 chunk 32 optimal weight: 30.0000 chunk 35 optimal weight: 50.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.036524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.029808 restraints weight = 45056.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.027763 restraints weight = 117379.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.027166 restraints weight = 191212.031| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.7129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3326 Z= 0.195 Angle : 0.602 9.059 4514 Z= 0.315 Chirality : 0.043 0.174 482 Planarity : 0.004 0.029 586 Dihedral : 4.617 17.662 455 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 21.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.54 % Allowed : 18.87 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % 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: -0.96 (0.44), residues: 406 helix: -2.37 (1.08), residues: 24 sheet: -1.20 (0.47), residues: 117 loop : -0.08 (0.42), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 35 HIS 0.002 0.001 HIS D 70 PHE 0.018 0.001 PHE E 392 TYR 0.022 0.002 TYR C 79 ARG 0.003 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 9 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 347 PHE cc_start: 0.7772 (OUTLIER) cc_final: 0.6184 (m-80) REVERT: D 4 MET cc_start: 0.4833 (ttt) cc_final: 0.2874 (tpt) outliers start: 9 outliers final: 7 residues processed: 18 average time/residue: 0.2425 time to fit residues: 5.4587 Evaluate side-chains 17 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 9 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain E residue 457 ARG Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 88 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 27 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 15 optimal weight: 30.0000 chunk 1 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 40.0000 chunk 10 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.036095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.029212 restraints weight = 46587.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.028247 restraints weight = 101836.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.027944 restraints weight = 128877.721| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.7659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3326 Z= 0.215 Angle : 0.630 8.953 4514 Z= 0.331 Chirality : 0.044 0.183 482 Planarity : 0.004 0.033 586 Dihedral : 4.729 16.981 455 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 23.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.54 % Allowed : 18.87 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % 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: -1.08 (0.44), residues: 406 helix: -2.39 (1.10), residues: 24 sheet: -1.35 (0.46), residues: 117 loop : -0.14 (0.42), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 35 HIS 0.002 0.001 HIS D 70 PHE 0.018 0.002 PHE E 392 TYR 0.018 0.002 TYR C 79 ARG 0.004 0.001 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 11 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 MET cc_start: 0.4900 (ttt) cc_final: 0.3007 (tpt) outliers start: 9 outliers final: 7 residues processed: 20 average time/residue: 0.2008 time to fit residues: 5.1261 Evaluate side-chains 18 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 11 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain E residue 457 ARG Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 88 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.0570 chunk 18 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 15 optimal weight: 30.0000 chunk 3 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 10 optimal weight: 20.0000 chunk 35 optimal weight: 40.0000 overall best weight: 4.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.036103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.029226 restraints weight = 43916.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.025756 restraints weight = 91936.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.025546 restraints weight = 150808.896| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.7844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3326 Z= 0.188 Angle : 0.623 9.068 4514 Z= 0.330 Chirality : 0.044 0.197 482 Planarity : 0.004 0.028 586 Dihedral : 4.725 20.158 455 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 21.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.97 % Allowed : 18.87 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % 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: -1.14 (0.44), residues: 406 helix: -2.33 (1.10), residues: 24 sheet: -1.41 (0.46), residues: 117 loop : -0.18 (0.42), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 35 HIS 0.003 0.001 HIS D 70 PHE 0.026 0.002 PHE E 392 TYR 0.016 0.002 TYR C 79 ARG 0.003 0.000 ARG E 454 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 11 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 MET cc_start: 0.6072 (ttt) cc_final: 0.4475 (tpt) outliers start: 7 outliers final: 7 residues processed: 18 average time/residue: 0.2707 time to fit residues: 5.9126 Evaluate side-chains 17 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 10 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain E residue 457 ARG Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 88 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 21 optimal weight: 50.0000 chunk 12 optimal weight: 40.0000 chunk 36 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 overall best weight: 7.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.035686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.029082 restraints weight = 46435.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.027957 restraints weight = 114607.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.024815 restraints weight = 144875.932| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.8724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3326 Z= 0.271 Angle : 0.700 8.762 4514 Z= 0.369 Chirality : 0.045 0.163 482 Planarity : 0.005 0.032 586 Dihedral : 5.186 20.451 455 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 29.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.69 % Allowed : 19.72 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % 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: -1.36 (0.43), residues: 406 helix: -2.53 (1.04), residues: 24 sheet: -1.56 (0.46), residues: 115 loop : -0.34 (0.42), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP D 35 HIS 0.002 0.001 HIS D 70 PHE 0.027 0.002 PHE E 392 TYR 0.021 0.002 TYR E 501 ARG 0.005 0.001 ARG E 454 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1403.63 seconds wall clock time: 25 minutes 27.53 seconds (1527.53 seconds total)