Starting phenix.real_space_refine on Sun Apr 27 04:05:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k18_36788/04_2025/8k18_36788.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k18_36788/04_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_36788/04_2025/8k18_36788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k18_36788/04_2025/8k18_36788.map" model { file = "/net/cci-nas-00/data/ceres_data/8k18_36788/04_2025/8k18_36788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k18_36788/04_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-5669/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: 3.26, 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: 0.83 Conformation dependent library (CDL) restraints added in 429.8 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: 0.42 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: 0.84 Time building geometry restraints manager: 1.00 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: 2.270 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.050 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.520 ------------------------------------------------------------------------------- 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 3330 Z= 0.814 Angle : 1.855 9.208 4522 Z= 1.236 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 Details of bonding type rmsd hydrogen bonds : bond 0.26754 ( 92) hydrogen bonds : angle 11.25427 ( 231) SS BOND : bond 0.01694 ( 4) SS BOND : angle 2.10352 ( 8) covalent geometry : bond 0.01403 ( 3326) covalent geometry : angle 1.85463 ( 4514) *********************** 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 : 0.369 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: 0.3070 time to fit residues: 11.6050 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 : 0.399 ------------------------------------------------------------------------------- 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 3330 Z= 0.267 Angle : 0.776 9.320 4522 Z= 0.417 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 Details of bonding type rmsd hydrogen bonds : bond 0.04327 ( 92) hydrogen bonds : angle 8.31828 ( 231) SS BOND : bond 0.00827 ( 4) SS BOND : angle 1.17175 ( 8) covalent geometry : bond 0.00556 ( 3326) covalent geometry : angle 0.77514 ( 4514) *********************** 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 : 0.960 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: 0.3679 time to fit residues: 11.2141 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 : 0.552 ------------------------------------------------------------------------------- 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 3330 Z= 0.163 Angle : 0.651 8.591 4522 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 Details of bonding type rmsd hydrogen bonds : bond 0.03466 ( 92) hydrogen bonds : angle 7.60302 ( 231) SS BOND : bond 0.00489 ( 4) SS BOND : angle 0.65626 ( 8) covalent geometry : bond 0.00345 ( 3326) covalent geometry : angle 0.65072 ( 4514) *********************** 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 : 0.460 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: 0.3151 time to fit residues: 7.1970 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: 2.9990 overall best weight: 4.4166 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.036907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.031566 restraints weight = 45103.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.031294 restraints weight = 122468.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.031036 restraints weight = 130846.938| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.5920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3330 Z= 0.146 Angle : 0.616 8.662 4522 Z= 0.324 Chirality : 0.044 0.187 482 Planarity : 0.005 0.032 586 Dihedral : 4.973 18.039 455 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % 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: -1.21 (0.42), residues: 406 helix: -2.16 (1.41), residues: 12 sheet: -1.27 (0.46), residues: 115 loop : -0.48 (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 0.017 0.001 PHE E 392 TYR 0.011 0.001 TYR E 501 ARG 0.004 0.001 ARG C 38 Details of bonding type rmsd hydrogen bonds : bond 0.03031 ( 92) hydrogen bonds : angle 7.09129 ( 231) SS BOND : bond 0.00292 ( 4) SS BOND : angle 0.61741 ( 8) covalent geometry : bond 0.00311 ( 3326) covalent geometry : angle 0.61602 ( 4514) *********************** 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 18 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 10 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 MET cc_start: 0.3048 (ttt) cc_final: 0.1453 (tpp) outliers start: 8 outliers final: 5 residues processed: 18 average time/residue: 0.2081 time to fit residues: 4.8231 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 : 0.391 ------------------------------------------------------------------------------- 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 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: 8.9990 chunk 15 optimal weight: 40.0000 chunk 5 optimal weight: 7.9990 chunk 14 optimal weight: 50.0000 chunk 19 optimal weight: 0.1980 chunk 8 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 37 optimal weight: 40.0000 chunk 36 optimal weight: 6.9990 overall best weight: 6.2388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.036622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.031722 restraints weight = 44025.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.031568 restraints weight = 110128.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.031302 restraints weight = 112002.048| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.7045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3330 Z= 0.183 Angle : 0.671 9.556 4522 Z= 0.354 Chirality : 0.044 0.163 482 Planarity : 0.005 0.033 586 Dihedral : 5.198 17.569 455 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 25.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % 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: -1.38 (0.42), residues: 406 helix: -2.88 (0.91), residues: 24 sheet: -1.28 (0.46), residues: 115 loop : -0.48 (0.40), residues: 267 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 0.023 0.002 PHE E 392 TYR 0.016 0.002 TYR E 501 ARG 0.004 0.001 ARG C 38 Details of bonding type rmsd hydrogen bonds : bond 0.03525 ( 92) hydrogen bonds : angle 7.11334 ( 231) SS BOND : bond 0.00500 ( 4) SS BOND : angle 0.92119 ( 8) covalent geometry : bond 0.00383 ( 3326) covalent geometry : angle 0.67055 ( 4514) *********************** 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 22 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 12 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 MET cc_start: 0.3921 (ttt) cc_final: 0.2032 (tpt) outliers start: 10 outliers final: 6 residues processed: 22 average time/residue: 0.2397 time to fit residues: 6.6797 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 : 0.432 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 50.0000 chunk 22 optimal weight: 0.0970 chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 1 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 overall best weight: 3.1582 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.036676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.028450 restraints weight = 42778.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.026581 restraints weight = 103627.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.026288 restraints weight = 127254.279| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.7056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3330 Z= 0.123 Angle : 0.604 9.502 4522 Z= 0.322 Chirality : 0.044 0.168 482 Planarity : 0.004 0.030 586 Dihedral : 4.864 17.390 455 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.54 % Allowed : 18.31 % 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: -1.19 (0.43), residues: 406 helix: -2.04 (1.28), residues: 18 sheet: -1.53 (0.45), residues: 118 loop : -0.26 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 35 HIS 0.003 0.001 HIS D 70 PHE 0.015 0.001 PHE E 392 TYR 0.017 0.002 TYR C 79 ARG 0.004 0.001 ARG C 38 Details of bonding type rmsd hydrogen bonds : bond 0.02898 ( 92) hydrogen bonds : angle 6.73981 ( 231) SS BOND : bond 0.00278 ( 4) SS BOND : angle 0.54507 ( 8) covalent geometry : bond 0.00259 ( 3326) covalent geometry : angle 0.60360 ( 4514) *********************** 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: 9 poor density : 11 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 MET cc_start: 0.5572 (ttt) cc_final: 0.3560 (tpt) outliers start: 9 outliers final: 5 residues processed: 20 average time/residue: 0.2732 time to fit residues: 6.8828 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 : 0.662 ------------------------------------------------------------------------------- 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: 10.0000 chunk 8 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 20 optimal weight: 40.0000 chunk 26 optimal weight: 8.9990 chunk 29 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.035943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.030071 restraints weight = 50970.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.026242 restraints weight = 119655.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.025659 restraints weight = 164078.065| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.8221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3330 Z= 0.237 Angle : 0.754 8.805 4522 Z= 0.394 Chirality : 0.046 0.131 482 Planarity : 0.005 0.036 586 Dihedral : 5.435 18.008 455 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 32.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % 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: -1.42 (0.43), residues: 406 helix: -2.49 (1.07), residues: 25 sheet: -1.48 (0.48), residues: 114 loop : -0.46 (0.40), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 35 HIS 0.003 0.001 HIS E 505 PHE 0.026 0.003 PHE E 392 TYR 0.025 0.003 TYR C 79 ARG 0.005 0.001 ARG E 454 Details of bonding type rmsd hydrogen bonds : bond 0.03976 ( 92) hydrogen bonds : angle 7.25130 ( 231) SS BOND : bond 0.00699 ( 4) SS BOND : angle 1.16401 ( 8) covalent geometry : bond 0.00492 ( 3326) covalent geometry : angle 0.75318 ( 4514) *********************** 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 19 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 11 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 4 MET cc_start: 0.7217 (ttt) cc_final: 0.5827 (tpt) outliers start: 8 outliers final: 7 residues processed: 19 average time/residue: 0.4699 time to fit residues: 10.6768 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 : 1.062 ------------------------------------------------------------------------------- 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 6 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 21 optimal weight: 50.0000 chunk 10 optimal weight: 9.9990 chunk 34 optimal weight: 0.2980 chunk 26 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 28 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.035761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.028820 restraints weight = 45687.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 87)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.024536 restraints weight = 111854.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.023913 restraints weight = 150682.743| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.8175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3330 Z= 0.146 Angle : 0.680 11.539 4522 Z= 0.350 Chirality : 0.045 0.156 482 Planarity : 0.005 0.035 586 Dihedral : 5.151 17.296 455 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 24.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.82 % Allowed : 18.87 % 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: -1.30 (0.43), residues: 406 helix: -2.33 (1.10), residues: 24 sheet: -1.56 (0.45), residues: 124 loop : -0.24 (0.42), residues: 258 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 0.014 0.002 PHE E 392 TYR 0.018 0.002 TYR C 79 ARG 0.003 0.001 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.03147 ( 92) hydrogen bonds : angle 7.08161 ( 231) SS BOND : bond 0.00337 ( 4) SS BOND : angle 0.71884 ( 8) covalent geometry : bond 0.00311 ( 3326) covalent geometry : angle 0.67969 ( 4514) *********************** 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 20 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 10 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 MET cc_start: 0.7158 (ttt) cc_final: 0.5861 (tpt) outliers start: 10 outliers final: 8 residues processed: 20 average time/residue: 0.3022 time to fit residues: 7.4732 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 : 0.383 ------------------------------------------------------------------------------- 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 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: 8.9990 chunk 21 optimal weight: 30.0000 chunk 8 optimal weight: 30.0000 chunk 15 optimal weight: 40.0000 chunk 1 optimal weight: 0.0970 chunk 13 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 30.0000 chunk 19 optimal weight: 6.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.035515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 148)---------------| | r_work = 0.3588 r_free = 0.3588 target = 0.025092 restraints weight = 45821.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.024371 restraints weight = 82528.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.024151 restraints weight = 103574.546| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.8269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3330 Z= 0.134 Angle : 0.671 10.830 4522 Z= 0.346 Chirality : 0.045 0.196 482 Planarity : 0.004 0.029 586 Dihedral : 5.046 23.198 455 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 21.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % 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: -1.23 (0.44), residues: 406 helix: -2.09 (1.16), residues: 24 sheet: -1.51 (0.45), residues: 125 loop : -0.20 (0.42), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 35 HIS 0.003 0.001 HIS D 70 PHE 0.018 0.001 PHE E 392 TYR 0.015 0.002 TYR C 79 ARG 0.003 0.000 ARG C 38 Details of bonding type rmsd hydrogen bonds : bond 0.03097 ( 92) hydrogen bonds : angle 6.86178 ( 231) SS BOND : bond 0.00331 ( 4) SS BOND : angle 0.68017 ( 8) covalent geometry : bond 0.00283 ( 3326) covalent geometry : angle 0.67137 ( 4514) *********************** 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 21 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 10 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 MET cc_start: 0.6776 (ttt) cc_final: 0.5087 (tpt) outliers start: 11 outliers final: 9 residues processed: 20 average time/residue: 0.2078 time to fit residues: 5.2279 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 : 0.359 ------------------------------------------------------------------------------- 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 3 GLN 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 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 33 optimal weight: 8.9990 chunk 18 optimal weight: 50.0000 chunk 31 optimal weight: 30.0000 chunk 32 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 3 optimal weight: 0.1980 chunk 21 optimal weight: 30.0000 chunk 6 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 overall best weight: 7.2388 ------------------------------------------------------------------------------- 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 ** D 93 HIS ** 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 = 0.3726 r_free = 0.3726 target = 0.035010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.027900 restraints weight = 48776.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.025158 restraints weight = 126200.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.025126 restraints weight = 163384.164| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.8849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3330 Z= 0.199 Angle : 0.736 10.262 4522 Z= 0.377 Chirality : 0.046 0.174 482 Planarity : 0.005 0.033 586 Dihedral : 5.372 21.541 455 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 28.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % 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: -1.21 (0.44), residues: 406 helix: -2.15 (1.14), residues: 24 sheet: -1.48 (0.46), residues: 124 loop : -0.19 (0.43), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 35 HIS 0.003 0.001 HIS D 70 PHE 0.035 0.002 PHE E 392 TYR 0.017 0.002 TYR C 79 ARG 0.004 0.001 ARG E 454 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 92) hydrogen bonds : angle 6.94939 ( 231) SS BOND : bond 0.00564 ( 4) SS BOND : angle 1.23959 ( 8) covalent geometry : bond 0.00425 ( 3326) covalent geometry : angle 0.73508 ( 4514) ********************** 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 22 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 12 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 347 PHE cc_start: 0.7644 (OUTLIER) cc_final: 0.6315 (m-80) REVERT: D 4 MET cc_start: 0.6737 (ttt) cc_final: 0.5092 (tpt) outliers start: 10 outliers final: 8 residues processed: 22 average time/residue: 0.2349 time to fit residues: 6.5640 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 : 0.410 ------------------------------------------------------------------------------- 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 26 SER 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: 0.6980 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 12 optimal weight: 30.0000 chunk 36 optimal weight: 7.9990 chunk 22 optimal weight: 30.0000 chunk 34 optimal weight: 40.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.034749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.028053 restraints weight = 47540.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 84)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.024276 restraints weight = 118539.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.023943 restraints weight = 151822.231| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.8887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3330 Z= 0.152 Angle : 0.680 10.467 4522 Z= 0.350 Chirality : 0.045 0.166 482 Planarity : 0.004 0.033 586 Dihedral : 5.212 24.170 455 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 24.23 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: -1.20 (0.44), residues: 406 helix: -2.16 (1.13), residues: 24 sheet: -1.46 (0.46), residues: 124 loop : -0.19 (0.43), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 35 HIS 0.003 0.001 HIS D 70 PHE 0.026 0.002 PHE E 392 TYR 0.020 0.002 TYR E 501 ARG 0.003 0.000 ARG E 454 Details of bonding type rmsd hydrogen bonds : bond 0.03204 ( 92) hydrogen bonds : angle 6.93271 ( 231) SS BOND : bond 0.00443 ( 4) SS BOND : angle 0.95377 ( 8) covalent geometry : bond 0.00325 ( 3326) covalent geometry : angle 0.67920 ( 4514) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1803.80 seconds wall clock time: 32 minutes 50.66 seconds (1970.66 seconds total)