Starting phenix.real_space_refine on Thu Nov 14 06:24:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k18_36788/11_2024/8k18_36788.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k18_36788/11_2024/8k18_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k18_36788/11_2024/8k18_36788.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k18_36788/11_2024/8k18_36788.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k18_36788/11_2024/8k18_36788.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k18_36788/11_2024/8k18_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-5513/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: 3.06, per 1000 atoms: 0.94 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: 0.78 Conformation dependent library (CDL) restraints added in 396.2 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: 0.45 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: 0.85 Time building geometry restraints manager: 0.92 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: 1.980 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: 0.020 Set scattering table: 0.040 Process input model: 13.210 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.340 ------------------------------------------------------------------------------- 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 : 0.400 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: 0.3267 time to fit residues: 12.2938 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 : 0.353 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3935 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 : 0.354 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: 0.5071 (OUTLIER) cc_final: 0.4623 (m-80) outliers start: 11 outliers final: 6 residues processed: 24 average time/residue: 0.2758 time to fit residues: 7.8953 Evaluate side-chains 20 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 13 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 10 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 35 optimal weight: 50.0000 chunk 38 optimal weight: 30.0000 chunk 31 optimal weight: 30.0000 chunk 12 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3933 moved from start: 0.5430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3326 Z= 0.213 Angle : 0.647 8.532 4514 Z= 0.340 Chirality : 0.043 0.194 482 Planarity : 0.005 0.034 586 Dihedral : 5.540 33.131 459 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.97 % Allowed : 15.77 % Favored : 82.25 % 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: -1.37 (0.41), residues: 406 helix: -2.63 (1.28), residues: 12 sheet: -1.40 (0.44), residues: 115 loop : -0.56 (0.38), 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 0.014 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 20 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 13 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 ILE cc_start: 0.0287 (OUTLIER) cc_final: 0.0054 (mt) REVERT: C 65 ASP cc_start: 0.4734 (p0) cc_final: 0.4516 (p0) outliers start: 7 outliers final: 5 residues processed: 18 average time/residue: 0.3130 time to fit residues: 6.8360 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 : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 28 ILE 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 18 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 21 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 overall best weight: 5.7788 ------------------------------------------------------------------------------- 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** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4022 moved from start: 0.6276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3326 Z= 0.233 Angle : 0.646 8.280 4514 Z= 0.338 Chirality : 0.044 0.182 482 Planarity : 0.005 0.031 586 Dihedral : 5.171 18.327 455 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 21.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.82 % Allowed : 15.77 % 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: -1.33 (0.42), residues: 406 helix: -2.40 (1.33), residues: 12 sheet: -1.26 (0.46), residues: 112 loop : -0.62 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 35 HIS 0.002 0.001 HIS D 70 PHE 0.020 0.002 PHE E 392 TYR 0.014 0.002 TYR E 489 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 20 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 10 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 20 average time/residue: 0.2410 time to fit residues: 6.2251 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 : 0.507 ------------------------------------------------------------------------------- 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 28 optimal weight: 0.4980 chunk 15 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 12 optimal weight: 30.0000 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 overall best weight: 4.2986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3997 moved from start: 0.6512 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= 0.183 Angle : 0.604 8.422 4514 Z= 0.320 Chirality : 0.043 0.173 482 Planarity : 0.004 0.029 586 Dihedral : 4.971 17.481 455 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % 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: -1.27 (0.42), residues: 406 helix: -2.71 (1.04), residues: 18 sheet: -1.28 (0.45), residues: 116 loop : -0.43 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 35 HIS 0.003 0.001 HIS D 70 PHE 0.021 0.002 PHE E 392 TYR 0.016 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 : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 19 average time/residue: 0.1980 time to fit residues: 4.8950 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 : 0.409 ------------------------------------------------------------------------------- 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 9 optimal weight: 4.9990 chunk 37 optimal weight: 20.0000 chunk 31 optimal weight: 30.0000 chunk 17 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 21 optimal weight: 40.0000 chunk 27 optimal weight: 30.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4231 moved from start: 0.8056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3326 Z= 0.316 Angle : 0.742 8.772 4514 Z= 0.391 Chirality : 0.045 0.146 482 Planarity : 0.005 0.037 586 Dihedral : 5.640 18.422 455 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 32.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.25 % Allowed : 19.72 % Favored : 78.03 % 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: -1.51 (0.43), residues: 406 helix: -2.56 (1.08), residues: 25 sheet: -1.55 (0.48), residues: 112 loop : -0.52 (0.40), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 35 HIS 0.003 0.001 HIS D 70 PHE 0.023 0.003 PHE E 392 TYR 0.027 0.002 TYR E 501 ARG 0.005 0.001 ARG E 454 *********************** 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 20 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 12 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 MET cc_start: 0.2355 (ttt) cc_final: 0.1261 (tpt) outliers start: 8 outliers final: 6 residues processed: 20 average time/residue: 0.1977 time to fit residues: 5.1416 Evaluate side-chains 18 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 12 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 26 SER 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 21 optimal weight: 50.0000 chunk 31 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 18 optimal weight: 50.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4172 moved from start: 0.8198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3326 Z= 0.233 Angle : 0.702 10.100 4514 Z= 0.362 Chirality : 0.045 0.133 482 Planarity : 0.005 0.032 586 Dihedral : 5.364 18.061 455 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 27.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.82 % Allowed : 18.31 % 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: -1.50 (0.43), residues: 406 helix: -2.55 (1.04), residues: 24 sheet: -1.61 (0.46), residues: 114 loop : -0.48 (0.40), residues: 268 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 0.017 0.002 PHE E 392 TYR 0.016 0.002 TYR E 501 ARG 0.004 0.001 ARG E 454 *********************** 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 22 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 12 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 MET cc_start: 0.2033 (ttt) cc_final: 0.1514 (ttt) outliers start: 10 outliers final: 7 residues processed: 21 average time/residue: 0.3096 time to fit residues: 7.7116 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 : 0.393 ------------------------------------------------------------------------------- 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 26 SER Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 32 optimal weight: 30.0000 chunk 35 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 15 optimal weight: 40.0000 chunk 27 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 31 optimal weight: 30.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- 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 ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4276 moved from start: 0.9023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3326 Z= 0.302 Angle : 0.773 9.928 4514 Z= 0.401 Chirality : 0.046 0.133 482 Planarity : 0.005 0.036 586 Dihedral : 5.654 18.615 455 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 33.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % 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: -1.61 (0.43), residues: 406 helix: -2.61 (1.01), residues: 25 sheet: -1.83 (0.46), residues: 111 loop : -0.50 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 35 HIS 0.003 0.001 HIS D 70 PHE 0.023 0.002 PHE E 392 TYR 0.022 0.002 TYR E 501 ARG 0.005 0.001 ARG E 454 *********************** 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 21 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 12 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 MET cc_start: 0.2441 (ttt) cc_final: 0.1919 (ttt) outliers start: 9 outliers final: 7 residues processed: 21 average time/residue: 0.2980 time to fit residues: 7.4710 Evaluate side-chains 16 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 9 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 26 SER Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 40.0000 chunk 22 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 25 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4227 moved from start: 0.9121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3326 Z= 0.243 Angle : 0.722 10.026 4514 Z= 0.377 Chirality : 0.046 0.165 482 Planarity : 0.005 0.036 586 Dihedral : 5.519 24.499 455 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 30.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % 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: -1.49 (0.44), residues: 406 helix: -2.55 (1.02), residues: 24 sheet: -1.76 (0.45), residues: 122 loop : -0.33 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 35 HIS 0.002 0.001 HIS D 70 PHE 0.023 0.002 PHE E 392 TYR 0.016 0.002 TYR E 501 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 : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 MET cc_start: 0.2300 (ttt) cc_final: 0.1877 (ttt) REVERT: D 35 TRP cc_start: 0.4036 (OUTLIER) cc_final: 0.3272 (t60) outliers start: 9 outliers final: 8 residues processed: 20 average time/residue: 0.2575 time to fit residues: 6.3774 Evaluate side-chains 17 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 8 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 26 SER Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 20.0000 chunk 18 optimal weight: 50.0000 chunk 24 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 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** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4203 moved from start: 0.9272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3326 Z= 0.224 Angle : 0.713 9.994 4514 Z= 0.369 Chirality : 0.046 0.228 482 Planarity : 0.005 0.037 586 Dihedral : 5.441 25.893 455 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 29.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.54 % Allowed : 19.15 % Favored : 78.31 % 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: -1.35 (0.44), residues: 406 helix: -2.06 (1.16), residues: 24 sheet: -1.64 (0.45), residues: 122 loop : -0.29 (0.43), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 35 HIS 0.003 0.001 HIS D 70 PHE 0.029 0.002 PHE E 392 TYR 0.026 0.002 TYR C 79 ARG 0.003 0.001 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 19 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 10 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 4 MET cc_start: 0.2556 (ttt) cc_final: 0.1446 (tpt) REVERT: D 35 TRP cc_start: 0.3976 (OUTLIER) cc_final: 0.3209 (t60) outliers start: 9 outliers final: 8 residues processed: 19 average time/residue: 0.2307 time to fit residues: 5.5435 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 : 0.365 ------------------------------------------------------------------------------- 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 26 SER Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 1 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 35 optimal weight: 50.0000 chunk 20 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 23 optimal weight: 30.0000 chunk 15 optimal weight: 50.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- 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 ** 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 = 0.3701 r_free = 0.3701 target = 0.034122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.028459 restraints weight = 56061.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.028459 restraints weight = 135859.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.028459 restraints weight = 135850.585| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 1.0037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3326 Z= 0.287 Angle : 0.767 9.679 4514 Z= 0.395 Chirality : 0.047 0.136 482 Planarity : 0.005 0.043 586 Dihedral : 5.690 27.367 455 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 33.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.54 % Allowed : 19.44 % Favored : 78.03 % 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: -1.56 (0.44), residues: 406 helix: -2.16 (1.12), residues: 24 sheet: -1.66 (0.46), residues: 122 loop : -0.52 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 35 HIS 0.003 0.001 HIS D 70 PHE 0.029 0.002 PHE E 392 TYR 0.027 0.002 TYR C 79 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: 1020.09 seconds wall clock time: 19 minutes 34.93 seconds (1174.93 seconds total)