Starting phenix.real_space_refine on Wed Jun 4 09:58:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ql1_14060/06_2025/7ql1_14060.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ql1_14060/06_2025/7ql1_14060.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ql1_14060/06_2025/7ql1_14060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ql1_14060/06_2025/7ql1_14060.map" model { file = "/net/cci-nas-00/data/ceres_data/7ql1_14060/06_2025/7ql1_14060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ql1_14060/06_2025/7ql1_14060.cif" } resolution = 3.34 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 3 5.16 5 C 1053 2.51 5 N 303 2.21 5 O 312 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 1671 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "C" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "D" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Time building chain proxies: 1.63, per 1000 atoms: 0.98 Number of scatterers: 1671 At special positions: 0 Unit cell: (78.516, 85.786, 39.258, 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 3 16.00 O 312 8.00 N 303 7.00 C 1053 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.34 Conformation dependent library (CDL) restraints added in 188.7 milliseconds 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 384 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 35.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 307 through 310 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.749A pdb=" N VAL C 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 318 removed outlier: 6.543A pdb=" N LYS C 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 330 removed outlier: 5.864A pdb=" N GLY A 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N HIS D 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE A 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLY D 326 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN C 327 " --> pdb=" O GLY D 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 337 through 342 removed outlier: 6.307A pdb=" N GLU C 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N SER D 341 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS C 340 " --> pdb=" O SER D 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 345 through 346 removed outlier: 6.512A pdb=" N ASP C 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.497A pdb=" N LYS C 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 360 through 362 removed outlier: 6.431A pdb=" N THR A 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 371 through 377 removed outlier: 6.964A pdb=" N ILE C 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N HIS D 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR C 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N LEU D 376 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS C 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) 27 hydrogen bonds defined for protein. 81 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: 0.34 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 477 1.33 - 1.45: 204 1.45 - 1.57: 1014 1.57 - 1.68: 0 1.68 - 1.80: 3 Bond restraints: 1698 Sorted by residual: bond pdb=" CZ ARG A 349 " pdb=" NH2 ARG A 349 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.75e+00 bond pdb=" CB THR C 361 " pdb=" OG1 THR C 361 " ideal model delta sigma weight residual 1.433 1.389 0.044 1.60e-02 3.91e+03 7.42e+00 bond pdb=" CB THR A 361 " pdb=" OG1 THR A 361 " ideal model delta sigma weight residual 1.433 1.391 0.042 1.60e-02 3.91e+03 7.01e+00 bond pdb=" CZ ARG C 349 " pdb=" NH2 ARG C 349 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.94e+00 bond pdb=" CZ ARG D 349 " pdb=" NH2 ARG D 349 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.81e+00 ... (remaining 1693 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 1325 1.50 - 2.99: 655 2.99 - 4.49: 215 4.49 - 5.98: 62 5.98 - 7.48: 17 Bond angle restraints: 2274 Sorted by residual: angle pdb=" CA ASP D 314 " pdb=" CB ASP D 314 " pdb=" CG ASP D 314 " ideal model delta sigma weight residual 112.60 119.30 -6.70 1.00e+00 1.00e+00 4.49e+01 angle pdb=" CA ASP C 314 " pdb=" CB ASP C 314 " pdb=" CG ASP C 314 " ideal model delta sigma weight residual 112.60 118.83 -6.23 1.00e+00 1.00e+00 3.88e+01 angle pdb=" CB HIS A 329 " pdb=" CG HIS A 329 " pdb=" CD2 HIS A 329 " ideal model delta sigma weight residual 131.20 124.98 6.22 1.30e+00 5.92e-01 2.29e+01 angle pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " pdb=" CD2 HIS A 374 " ideal model delta sigma weight residual 131.20 125.03 6.17 1.30e+00 5.92e-01 2.25e+01 angle pdb=" C LYS C 311 " pdb=" CA LYS C 311 " pdb=" CB LYS C 311 " ideal model delta sigma weight residual 111.11 117.00 -5.89 1.28e+00 6.10e-01 2.11e+01 ... (remaining 2269 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.53: 798 8.53 - 17.06: 162 17.06 - 25.59: 42 25.59 - 34.12: 21 34.12 - 42.65: 9 Dihedral angle restraints: 1032 sinusoidal: 429 harmonic: 603 Sorted by residual: dihedral pdb=" CA ASP C 314 " pdb=" C ASP C 314 " pdb=" N LEU C 315 " pdb=" CA LEU C 315 " ideal model delta harmonic sigma weight residual 180.00 151.10 28.90 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA GLY A 365 " pdb=" C GLY A 365 " pdb=" N GLY A 366 " pdb=" CA GLY A 366 " ideal model delta harmonic sigma weight residual 180.00 151.69 28.31 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA GLN C 336 " pdb=" C GLN C 336 " pdb=" N VAL C 337 " pdb=" CA VAL C 337 " ideal model delta harmonic sigma weight residual 180.00 151.75 28.25 0 5.00e+00 4.00e-02 3.19e+01 ... (remaining 1029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 96 0.049 - 0.097: 67 0.097 - 0.146: 50 0.146 - 0.194: 30 0.194 - 0.243: 15 Chirality restraints: 258 Sorted by residual: chirality pdb=" CA LYS C 311 " pdb=" N LYS C 311 " pdb=" C LYS C 311 " pdb=" CB LYS C 311 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA LYS C 343 " pdb=" N LYS C 343 " pdb=" C LYS C 343 " pdb=" CB LYS C 343 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA ILE C 328 " pdb=" N ILE C 328 " pdb=" C ILE C 328 " pdb=" CB ILE C 328 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 255 not shown) Planarity restraints: 288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 310 " -0.095 2.00e-02 2.50e+03 5.25e-02 5.51e+01 pdb=" CG TYR D 310 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR D 310 " 0.043 2.00e-02 2.50e+03 pdb=" CD2 TYR D 310 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR D 310 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR D 310 " 0.034 2.00e-02 2.50e+03 pdb=" CZ TYR D 310 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 310 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " -0.073 2.00e-02 2.50e+03 4.12e-02 3.40e+01 pdb=" CG TYR C 310 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " 0.036 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " 0.024 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " -0.058 2.00e-02 2.50e+03 2.98e-02 1.78e+01 pdb=" CG TYR A 310 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " -0.039 2.00e-02 2.50e+03 ... (remaining 285 not shown) Histogram of nonbonded interaction distances: 2.65 - 3.10: 1125 3.10 - 3.55: 1466 3.55 - 4.00: 2463 4.00 - 4.45: 2760 4.45 - 4.90: 4982 Nonbonded interactions: 12796 Sorted by model distance: nonbonded pdb=" N GLY A 366 " pdb=" O GLY A 366 " model vdw 2.654 2.496 nonbonded pdb=" O LEU D 325 " pdb=" CA GLY D 326 " model vdw 2.655 2.752 nonbonded pdb=" N GLY D 366 " pdb=" O GLY D 366 " model vdw 2.656 2.496 nonbonded pdb=" O PRO C 332 " pdb=" OG SER D 356 " model vdw 2.656 3.040 nonbonded pdb=" NZ LYS D 370 " pdb=" OE1 GLU D 372 " model vdw 2.663 3.120 ... (remaining 12791 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.120 Find NCS groups from input model: 0.050 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 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 : 0.011 0.044 1698 Z= 0.698 Angle : 2.010 7.476 2274 Z= 1.340 Chirality : 0.103 0.243 258 Planarity : 0.013 0.056 288 Dihedral : 11.062 42.647 648 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.42), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.32), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS C 362 PHE 0.031 0.012 PHE A 378 TYR 0.095 0.035 TYR D 310 ARG 0.003 0.001 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.08736 ( 27) hydrogen bonds : angle 6.90379 ( 81) covalent geometry : bond 0.01078 ( 1698) covalent geometry : angle 2.01023 ( 2274) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.208 Fit side-chains REVERT: A 347 LYS cc_start: 0.8985 (mttt) cc_final: 0.8328 (pttm) REVERT: A 348 ASP cc_start: 0.8712 (t0) cc_final: 0.7898 (p0) REVERT: A 356 SER cc_start: 0.8863 (p) cc_final: 0.8517 (p) REVERT: C 349 ARG cc_start: 0.8785 (mtt180) cc_final: 0.7848 (mmp-170) REVERT: C 370 LYS cc_start: 0.8476 (tttt) cc_final: 0.8120 (tttt) REVERT: D 321 LYS cc_start: 0.8436 (mttt) cc_final: 0.8173 (mtpt) REVERT: D 347 LYS cc_start: 0.9016 (mttt) cc_final: 0.8763 (mptt) REVERT: D 370 LYS cc_start: 0.8664 (tttt) cc_final: 0.8380 (tttm) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.2480 time to fit residues: 23.4606 Evaluate side-chains 74 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 17 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS C 362 HIS ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.130136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.113230 restraints weight = 2479.451| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.65 r_work: 0.3763 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1698 Z= 0.160 Angle : 0.744 6.314 2274 Z= 0.380 Chirality : 0.051 0.146 258 Planarity : 0.004 0.037 288 Dihedral : 7.302 25.295 222 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.08 % Allowed : 17.19 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.43), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.33), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 330 PHE 0.007 0.002 PHE C 346 TYR 0.008 0.002 TYR D 310 ARG 0.004 0.001 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.02070 ( 27) hydrogen bonds : angle 5.41139 ( 81) covalent geometry : bond 0.00374 ( 1698) covalent geometry : angle 0.74403 ( 2274) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.194 Fit side-chains REVERT: A 336 GLN cc_start: 0.8256 (mp10) cc_final: 0.8049 (mp10) REVERT: A 347 LYS cc_start: 0.9224 (mttt) cc_final: 0.8198 (pttm) REVERT: A 348 ASP cc_start: 0.8607 (t0) cc_final: 0.6911 (p0) REVERT: A 356 SER cc_start: 0.8768 (p) cc_final: 0.8176 (p) REVERT: A 368 ASN cc_start: 0.8933 (m-40) cc_final: 0.8728 (m110) REVERT: A 370 LYS cc_start: 0.8831 (ttmt) cc_final: 0.8631 (tttt) REVERT: C 311 LYS cc_start: 0.8793 (ttmt) cc_final: 0.7588 (mmtm) REVERT: C 336 GLN cc_start: 0.8619 (mp10) cc_final: 0.7772 (mp10) REVERT: C 348 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.7955 (t70) REVERT: C 349 ARG cc_start: 0.7963 (mtt180) cc_final: 0.6606 (mmp-170) REVERT: C 377 THR cc_start: 0.8136 (t) cc_final: 0.7916 (p) REVERT: D 321 LYS cc_start: 0.8118 (mttt) cc_final: 0.7686 (mtpt) REVERT: D 340 LYS cc_start: 0.8589 (mtpp) cc_final: 0.8116 (mppt) REVERT: D 347 LYS cc_start: 0.8832 (mttt) cc_final: 0.8291 (mptt) REVERT: D 349 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7399 (mtp85) outliers start: 4 outliers final: 1 residues processed: 74 average time/residue: 0.2333 time to fit residues: 18.5901 Evaluate side-chains 57 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 375 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 20 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 ASN ** D 362 HIS ** 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 = 0.4045 r_free = 0.4045 target = 0.125651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.108053 restraints weight = 2525.844| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.56 r_work: 0.3740 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 1698 Z= 0.265 Angle : 0.743 6.599 2274 Z= 0.381 Chirality : 0.054 0.142 258 Planarity : 0.004 0.037 288 Dihedral : 6.819 21.151 222 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.08 % Allowed : 16.15 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.41), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.31), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS C 330 PHE 0.007 0.002 PHE C 378 TYR 0.014 0.003 TYR D 310 ARG 0.003 0.001 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.02099 ( 27) hydrogen bonds : angle 4.80222 ( 81) covalent geometry : bond 0.00598 ( 1698) covalent geometry : angle 0.74322 ( 2274) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.188 Fit side-chains REVERT: A 336 GLN cc_start: 0.8416 (mp10) cc_final: 0.8178 (mp10) REVERT: A 348 ASP cc_start: 0.8635 (t0) cc_final: 0.7173 (p0) REVERT: A 356 SER cc_start: 0.8575 (p) cc_final: 0.7929 (p) REVERT: C 311 LYS cc_start: 0.9005 (ttmt) cc_final: 0.7874 (mmtm) REVERT: C 336 GLN cc_start: 0.8300 (mp10) cc_final: 0.7021 (mm110) REVERT: C 349 ARG cc_start: 0.8133 (mtt180) cc_final: 0.6698 (mmm160) REVERT: C 370 LYS cc_start: 0.8506 (tttt) cc_final: 0.8259 (tptm) REVERT: C 377 THR cc_start: 0.8248 (t) cc_final: 0.7943 (p) REVERT: D 349 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7827 (mtp85) outliers start: 4 outliers final: 2 residues processed: 54 average time/residue: 0.1711 time to fit residues: 10.3045 Evaluate side-chains 54 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 375 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 18 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 ASN D 362 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.128954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.111536 restraints weight = 2475.431| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.58 r_work: 0.3780 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3670 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1698 Z= 0.171 Angle : 0.645 5.806 2274 Z= 0.327 Chirality : 0.051 0.139 258 Planarity : 0.004 0.039 288 Dihedral : 6.241 18.196 222 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.65 % Allowed : 16.15 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.42), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.32), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 330 PHE 0.004 0.001 PHE D 346 TYR 0.012 0.002 TYR D 310 ARG 0.002 0.001 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.01499 ( 27) hydrogen bonds : angle 4.59462 ( 81) covalent geometry : bond 0.00380 ( 1698) covalent geometry : angle 0.64451 ( 2274) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.189 Fit side-chains REVERT: A 336 GLN cc_start: 0.8484 (mp10) cc_final: 0.8272 (tt0) REVERT: A 348 ASP cc_start: 0.8627 (t0) cc_final: 0.6925 (p0) REVERT: A 356 SER cc_start: 0.8406 (p) cc_final: 0.7662 (p) REVERT: A 358 ASP cc_start: 0.9091 (m-30) cc_final: 0.8878 (m-30) REVERT: C 311 LYS cc_start: 0.8878 (ttmt) cc_final: 0.7781 (mmtm) REVERT: C 336 GLN cc_start: 0.8393 (mp10) cc_final: 0.7136 (mm110) REVERT: C 348 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7808 (t70) REVERT: C 349 ARG cc_start: 0.8099 (mtt180) cc_final: 0.6615 (mmp-170) REVERT: C 370 LYS cc_start: 0.8506 (tttt) cc_final: 0.8269 (tptp) REVERT: C 378 PHE cc_start: 0.7434 (m-80) cc_final: 0.7138 (m-80) REVERT: D 349 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7623 (mtp85) outliers start: 7 outliers final: 4 residues processed: 58 average time/residue: 0.1732 time to fit residues: 11.1776 Evaluate side-chains 57 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 375 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 16 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.125381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.107847 restraints weight = 2523.651| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.57 r_work: 0.3738 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 1698 Z= 0.239 Angle : 0.685 5.614 2274 Z= 0.350 Chirality : 0.052 0.133 258 Planarity : 0.004 0.038 288 Dihedral : 6.290 18.735 222 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.60 % Allowed : 18.75 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.43), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.33), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 330 PHE 0.007 0.002 PHE C 378 TYR 0.013 0.003 TYR D 310 ARG 0.002 0.001 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.01706 ( 27) hydrogen bonds : angle 4.39277 ( 81) covalent geometry : bond 0.00530 ( 1698) covalent geometry : angle 0.68536 ( 2274) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.480 Fit side-chains REVERT: A 336 GLN cc_start: 0.8536 (mp10) cc_final: 0.8294 (tt0) REVERT: A 348 ASP cc_start: 0.8578 (t0) cc_final: 0.7205 (p0) REVERT: C 311 LYS cc_start: 0.8961 (ttmt) cc_final: 0.7827 (mmtm) REVERT: C 349 ARG cc_start: 0.8274 (mtt180) cc_final: 0.6683 (mmm160) REVERT: C 370 LYS cc_start: 0.8543 (tttt) cc_final: 0.8316 (tptp) REVERT: D 338 GLU cc_start: 0.8112 (mp0) cc_final: 0.7883 (mp0) REVERT: D 349 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7974 (mtp85) REVERT: D 368 ASN cc_start: 0.9242 (m-40) cc_final: 0.8827 (m-40) outliers start: 5 outliers final: 4 residues processed: 56 average time/residue: 0.2593 time to fit residues: 16.3028 Evaluate side-chains 55 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 375 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 11 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 0.0030 chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 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 = 0.4051 r_free = 0.4051 target = 0.126677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.108950 restraints weight = 2543.213| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.61 r_work: 0.3751 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3643 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 1698 Z= 0.198 Angle : 0.651 5.592 2274 Z= 0.332 Chirality : 0.051 0.131 258 Planarity : 0.004 0.040 288 Dihedral : 6.079 18.165 222 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.12 % Allowed : 19.79 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.44), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.33), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 330 PHE 0.005 0.001 PHE C 378 TYR 0.012 0.002 TYR D 310 ARG 0.002 0.001 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.01550 ( 27) hydrogen bonds : angle 4.38687 ( 81) covalent geometry : bond 0.00437 ( 1698) covalent geometry : angle 0.65089 ( 2274) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.202 Fit side-chains REVERT: A 336 GLN cc_start: 0.8501 (mp10) cc_final: 0.8300 (tt0) REVERT: A 348 ASP cc_start: 0.8584 (t0) cc_final: 0.7144 (p0) REVERT: C 311 LYS cc_start: 0.8964 (ttmt) cc_final: 0.7811 (mmtm) REVERT: C 336 GLN cc_start: 0.8594 (mp10) cc_final: 0.7165 (mm110) REVERT: C 348 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7879 (t70) REVERT: C 349 ARG cc_start: 0.8260 (mtt180) cc_final: 0.6806 (mmp-170) REVERT: D 338 GLU cc_start: 0.8128 (mp0) cc_final: 0.7349 (mp0) REVERT: D 349 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7663 (mtp85) REVERT: D 368 ASN cc_start: 0.9249 (m-40) cc_final: 0.8830 (m-40) outliers start: 6 outliers final: 4 residues processed: 55 average time/residue: 0.1759 time to fit residues: 10.8104 Evaluate side-chains 57 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 375 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 10 optimal weight: 0.3980 chunk 0 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 3 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 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 = 0.4028 r_free = 0.4028 target = 0.124924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.107307 restraints weight = 2541.993| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.60 r_work: 0.3736 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 1698 Z= 0.239 Angle : 0.673 5.367 2274 Z= 0.344 Chirality : 0.052 0.135 258 Planarity : 0.004 0.038 288 Dihedral : 6.149 18.350 222 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.12 % Allowed : 20.83 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.44), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.33), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 330 PHE 0.006 0.001 PHE D 346 TYR 0.012 0.002 TYR D 310 ARG 0.003 0.001 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.01688 ( 27) hydrogen bonds : angle 4.34645 ( 81) covalent geometry : bond 0.00526 ( 1698) covalent geometry : angle 0.67286 ( 2274) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.196 Fit side-chains REVERT: A 336 GLN cc_start: 0.8539 (mp10) cc_final: 0.8330 (tt0) REVERT: A 348 ASP cc_start: 0.8566 (t0) cc_final: 0.7158 (p0) REVERT: C 336 GLN cc_start: 0.8713 (mp10) cc_final: 0.8277 (mp10) REVERT: C 349 ARG cc_start: 0.8286 (mtt180) cc_final: 0.6774 (mmp-170) REVERT: D 338 GLU cc_start: 0.8072 (mp0) cc_final: 0.7307 (mp0) REVERT: D 349 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7551 (mtp85) REVERT: D 368 ASN cc_start: 0.9252 (m-40) cc_final: 0.8842 (m-40) outliers start: 6 outliers final: 5 residues processed: 52 average time/residue: 0.1803 time to fit residues: 10.4097 Evaluate side-chains 62 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 375 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 6 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 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 = 0.4082 r_free = 0.4082 target = 0.128718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.110992 restraints weight = 2480.036| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.61 r_work: 0.3793 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3679 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 1698 Z= 0.171 Angle : 0.629 5.529 2274 Z= 0.321 Chirality : 0.050 0.128 258 Planarity : 0.004 0.039 288 Dihedral : 5.882 17.422 222 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.17 % Allowed : 20.83 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.44), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.34), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 330 PHE 0.005 0.001 PHE D 346 TYR 0.010 0.002 TYR D 310 ARG 0.002 0.001 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.01509 ( 27) hydrogen bonds : angle 4.39876 ( 81) covalent geometry : bond 0.00378 ( 1698) covalent geometry : angle 0.62892 ( 2274) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.205 Fit side-chains REVERT: A 343 LYS cc_start: 0.8710 (mtpp) cc_final: 0.8313 (mtpp) REVERT: A 347 LYS cc_start: 0.9055 (mttt) cc_final: 0.8217 (pttm) REVERT: A 348 ASP cc_start: 0.8583 (t0) cc_final: 0.6886 (p0) REVERT: A 353 LYS cc_start: 0.8836 (mttt) cc_final: 0.8602 (mtpt) REVERT: A 359 ASN cc_start: 0.8975 (m110) cc_final: 0.8009 (m110) REVERT: C 311 LYS cc_start: 0.8940 (ttmt) cc_final: 0.7782 (mmtm) REVERT: C 336 GLN cc_start: 0.8682 (mp10) cc_final: 0.8227 (mp10) REVERT: C 348 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.7918 (t70) REVERT: C 349 ARG cc_start: 0.8268 (mtt180) cc_final: 0.6804 (mmp-170) REVERT: D 338 GLU cc_start: 0.7941 (mp0) cc_final: 0.7335 (mp0) REVERT: D 349 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7779 (mtp85) REVERT: D 368 ASN cc_start: 0.9219 (m-40) cc_final: 0.8863 (m-40) outliers start: 8 outliers final: 6 residues processed: 62 average time/residue: 0.2184 time to fit residues: 14.7168 Evaluate side-chains 65 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 375 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 20 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 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 = 0.4031 r_free = 0.4031 target = 0.124892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.106982 restraints weight = 2573.220| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.64 r_work: 0.3724 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 1698 Z= 0.238 Angle : 0.689 5.190 2274 Z= 0.352 Chirality : 0.052 0.136 258 Planarity : 0.004 0.038 288 Dihedral : 6.019 17.911 222 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.17 % Allowed : 22.40 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.45), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.34), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 330 PHE 0.005 0.001 PHE D 346 TYR 0.012 0.003 TYR D 310 ARG 0.003 0.001 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.01631 ( 27) hydrogen bonds : angle 4.34554 ( 81) covalent geometry : bond 0.00529 ( 1698) covalent geometry : angle 0.68938 ( 2274) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.208 Fit side-chains REVERT: A 343 LYS cc_start: 0.8753 (mtpp) cc_final: 0.8407 (mtpp) REVERT: A 347 LYS cc_start: 0.9051 (mttt) cc_final: 0.8223 (pttm) REVERT: A 348 ASP cc_start: 0.8532 (t0) cc_final: 0.7127 (p0) REVERT: A 359 ASN cc_start: 0.8910 (m110) cc_final: 0.7888 (m110) REVERT: C 336 GLN cc_start: 0.8756 (mp10) cc_final: 0.8350 (mp10) REVERT: C 349 ARG cc_start: 0.8252 (mtt180) cc_final: 0.6692 (mmp-170) REVERT: D 338 GLU cc_start: 0.7939 (mp0) cc_final: 0.7340 (mp0) REVERT: D 349 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7817 (mtp85) REVERT: D 368 ASN cc_start: 0.9281 (m-40) cc_final: 0.8887 (m-40) outliers start: 8 outliers final: 7 residues processed: 60 average time/residue: 0.2002 time to fit residues: 13.1319 Evaluate side-chains 63 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 375 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 6 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 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 = 0.4105 r_free = 0.4105 target = 0.128733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.112197 restraints weight = 2634.720| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.74 r_work: 0.3812 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1698 Z= 0.116 Angle : 0.637 5.427 2274 Z= 0.323 Chirality : 0.050 0.126 258 Planarity : 0.004 0.042 288 Dihedral : 5.595 16.132 222 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.60 % Allowed : 24.48 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.44), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.34), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 330 PHE 0.004 0.001 PHE D 346 TYR 0.007 0.002 TYR D 310 ARG 0.002 0.001 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.01369 ( 27) hydrogen bonds : angle 4.43542 ( 81) covalent geometry : bond 0.00263 ( 1698) covalent geometry : angle 0.63736 ( 2274) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.215 Fit side-chains REVERT: A 347 LYS cc_start: 0.9136 (mttt) cc_final: 0.8006 (pttm) REVERT: A 348 ASP cc_start: 0.8651 (t0) cc_final: 0.6859 (p0) REVERT: A 359 ASN cc_start: 0.8810 (m110) cc_final: 0.7686 (m110) REVERT: C 311 LYS cc_start: 0.8710 (ttmt) cc_final: 0.7403 (mmtm) REVERT: C 336 GLN cc_start: 0.8647 (mp10) cc_final: 0.7276 (mm110) REVERT: C 348 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7778 (t70) REVERT: C 349 ARG cc_start: 0.8111 (mtt180) cc_final: 0.6481 (mmm160) REVERT: D 338 GLU cc_start: 0.7631 (mp0) cc_final: 0.7125 (mp0) REVERT: D 349 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7694 (mtp85) REVERT: D 368 ASN cc_start: 0.9157 (m-40) cc_final: 0.8708 (m-40) outliers start: 5 outliers final: 3 residues processed: 57 average time/residue: 0.2085 time to fit residues: 13.1118 Evaluate side-chains 59 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 20 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 7 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 5 optimal weight: 0.0040 chunk 8 optimal weight: 0.0980 chunk 18 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 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 = 0.4122 r_free = 0.4122 target = 0.129587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.113118 restraints weight = 2544.015| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.66 r_work: 0.3829 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3717 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1698 Z= 0.124 Angle : 0.634 5.343 2274 Z= 0.320 Chirality : 0.050 0.127 258 Planarity : 0.004 0.042 288 Dihedral : 5.398 15.508 222 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.12 % Allowed : 23.96 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.45), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.34), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 330 PHE 0.003 0.001 PHE D 346 TYR 0.008 0.002 TYR D 310 ARG 0.002 0.001 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.01357 ( 27) hydrogen bonds : angle 4.27892 ( 81) covalent geometry : bond 0.00287 ( 1698) covalent geometry : angle 0.63442 ( 2274) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1363.12 seconds wall clock time: 24 minutes 19.15 seconds (1459.15 seconds total)