Starting phenix.real_space_refine on Mon Feb 10 23:15:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ql3_14062/02_2025/7ql3_14062.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ql3_14062/02_2025/7ql3_14062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ql3_14062/02_2025/7ql3_14062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ql3_14062/02_2025/7ql3_14062.map" model { file = "/net/cci-nas-00/data/ceres_data/7ql3_14062/02_2025/7ql3_14062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ql3_14062/02_2025/7ql3_14062.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 6 5.16 5 C 2046 2.51 5 N 588 2.21 5 O 606 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-5592/modules/chem_data/mon_lib" Total number of atoms: 3246 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 541 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "B" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 541 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "C" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 541 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "D" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 541 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "E" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 541 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "F" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 541 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Time building chain proxies: 2.61, per 1000 atoms: 0.80 Number of scatterers: 3246 At special positions: 0 Unit cell: (95.79, 111.6, 35.34, 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 6 16.00 O 606 8.00 N 588 7.00 C 2046 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: 0.73 Conformation dependent library (CDL) restraints added in 375.5 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 33.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 309 through 310 removed outlier: 6.734A pdb=" N VAL A 309 " --> pdb=" O TYR B 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.758A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 325 removed outlier: 3.525A pdb=" N LEU A 325 " --> pdb=" O SER B 324 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N SER A 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N GLY C 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N CYS A 322 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU C 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N SER A 324 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.623A pdb=" N HIS A 329 " --> pdb=" O HIS C 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 336 through 339 removed outlier: 6.521A pdb=" N GLN A 336 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N VAL B 339 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU A 338 " --> pdb=" O VAL B 339 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 345 through 346 removed outlier: 6.682A pdb=" N ASP A 345 " --> pdb=" O PHE B 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 359 through 361 removed outlier: 6.581A pdb=" N ASN A 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 368 through 371 Processing sheet with id=AA9, first strand: chain 'B' and resid 374 through 377 removed outlier: 6.599A pdb=" N HIS A 374 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N THR C 377 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU A 376 " --> pdb=" O THR C 377 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 309 through 310 removed outlier: 6.609A pdb=" N VAL D 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.707A pdb=" N VAL D 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 317 through 325 removed outlier: 3.582A pdb=" N LEU D 325 " --> pdb=" O SER E 324 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 328 through 330 removed outlier: 6.694A pdb=" N HIS D 329 " --> pdb=" O HIS F 330 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 336 through 339 removed outlier: 6.528A pdb=" N GLN D 336 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N VAL E 339 " --> pdb=" O GLN D 336 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLU D 338 " --> pdb=" O VAL E 339 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 345 through 346 removed outlier: 6.591A pdb=" N ASP D 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 359 through 361 removed outlier: 6.580A pdb=" N ASN D 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 368 through 371 removed outlier: 6.623A pdb=" N ASN D 368 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N ILE F 371 " --> pdb=" O ASN D 368 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LYS D 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 374 through 377 removed outlier: 6.658A pdb=" N HIS D 374 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N THR F 377 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU D 376 " --> pdb=" O THR F 377 " (cutoff:3.500A) 57 hydrogen bonds defined for protein. 171 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: 0.73 Time building geometry restraints manager: 0.86 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: 879 1.33 - 1.45: 446 1.45 - 1.57: 1969 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3300 Sorted by residual: bond pdb=" CA LYS C 331 " pdb=" C LYS C 331 " ideal model delta sigma weight residual 1.532 1.550 -0.018 6.50e-03 2.37e+04 7.90e+00 bond pdb=" CZ ARG A 349 " pdb=" NH2 ARG A 349 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.30e+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 6.68e+00 bond pdb=" CZ ARG F 349 " pdb=" NH2 ARG F 349 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.30e+00 bond pdb=" CZ ARG C 349 " pdb=" NH2 ARG C 349 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.30e-02 5.92e+03 6.21e+00 ... (remaining 3295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 3767 2.85 - 5.70: 618 5.70 - 8.55: 26 8.55 - 11.40: 4 11.40 - 14.25: 1 Bond angle restraints: 4416 Sorted by residual: angle pdb=" N GLY A 323 " pdb=" CA GLY A 323 " pdb=" C GLY A 323 " ideal model delta sigma weight residual 111.14 125.39 -14.25 1.80e+00 3.09e-01 6.27e+01 angle pdb=" N SER D 356 " pdb=" CA SER D 356 " pdb=" C SER D 356 " ideal model delta sigma weight residual 111.03 117.92 -6.89 1.11e+00 8.12e-01 3.85e+01 angle pdb=" N SER A 356 " pdb=" CA SER A 356 " pdb=" C SER A 356 " ideal model delta sigma weight residual 111.03 117.88 -6.85 1.11e+00 8.12e-01 3.81e+01 angle pdb=" N SER A 324 " pdb=" CA SER A 324 " pdb=" C SER A 324 " ideal model delta sigma weight residual 108.02 97.08 10.94 1.78e+00 3.16e-01 3.78e+01 angle pdb=" N GLY D 323 " pdb=" CA GLY D 323 " pdb=" C GLY D 323 " ideal model delta sigma weight residual 110.56 120.42 -9.86 1.66e+00 3.63e-01 3.53e+01 ... (remaining 4411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.12: 1791 14.12 - 28.25: 167 28.25 - 42.37: 34 42.37 - 56.50: 6 56.50 - 70.62: 6 Dihedral angle restraints: 2004 sinusoidal: 834 harmonic: 1170 Sorted by residual: dihedral pdb=" CA GLY A 323 " pdb=" C GLY A 323 " pdb=" N SER A 324 " pdb=" CA SER A 324 " ideal model delta harmonic sigma weight residual 180.00 149.74 30.26 0 5.00e+00 4.00e-02 3.66e+01 dihedral pdb=" CA CYS A 322 " pdb=" C CYS A 322 " pdb=" N GLY A 323 " pdb=" CA GLY A 323 " ideal model delta harmonic sigma weight residual -180.00 -150.36 -29.64 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA CYS C 322 " pdb=" C CYS C 322 " pdb=" N GLY C 323 " pdb=" CA GLY C 323 " ideal model delta harmonic sigma weight residual 180.00 -150.77 -29.23 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 2001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 275 0.080 - 0.160: 166 0.160 - 0.240: 36 0.240 - 0.320: 11 0.320 - 0.400: 10 Chirality restraints: 498 Sorted by residual: chirality pdb=" CA GLN A 351 " pdb=" N GLN A 351 " pdb=" C GLN A 351 " pdb=" CB GLN A 351 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CA GLN D 351 " pdb=" N GLN D 351 " pdb=" C GLN D 351 " pdb=" CB GLN D 351 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CA HIS E 362 " pdb=" N HIS E 362 " pdb=" C HIS E 362 " pdb=" CB HIS E 362 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.45e+00 ... (remaining 495 not shown) Planarity restraints: 558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " 0.129 2.00e-02 2.50e+03 6.75e-02 9.11e+01 pdb=" CG TYR C 310 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " -0.063 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " -0.026 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " 0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " -0.122 2.00e-02 2.50e+03 6.55e-02 8.59e+01 pdb=" CG TYR F 310 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " 0.058 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " 0.037 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " 0.029 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " -0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 310 " -0.105 2.00e-02 2.50e+03 5.57e-02 6.20e+01 pdb=" CG TYR D 310 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR D 310 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR D 310 " 0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR D 310 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR D 310 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR D 310 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 310 " -0.080 2.00e-02 2.50e+03 ... (remaining 555 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 1389 2.97 - 3.45: 2648 3.45 - 3.94: 4714 3.94 - 4.42: 4640 4.42 - 4.90: 9852 Nonbonded interactions: 23243 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.489 3.040 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.502 3.040 nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.524 3.040 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.526 3.040 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.530 3.040 ... (remaining 23238 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.280 Find NCS groups from input model: 0.120 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 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 0.035 3300 Z= 0.765 Angle : 2.010 14.251 4416 Z= 1.337 Chirality : 0.111 0.400 498 Planarity : 0.011 0.067 558 Dihedral : 12.269 70.619 1260 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Cbeta Deviations : 2.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -3.47 (0.31), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.24), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS F 362 PHE 0.037 0.011 PHE B 346 TYR 0.129 0.041 TYR C 310 ARG 0.003 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.404 Fit side-chains REVERT: B 352 SER cc_start: 0.9293 (t) cc_final: 0.8913 (m) REVERT: E 352 SER cc_start: 0.9144 (t) cc_final: 0.8810 (m) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.2317 time to fit residues: 20.0624 Evaluate side-chains 50 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS B 330 HIS B 374 HIS C 374 HIS ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS E 330 HIS E 374 HIS F 374 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.142781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.133265 restraints weight = 3676.609| |-----------------------------------------------------------------------------| r_work (start): 0.4264 rms_B_bonded: 2.00 r_work: 0.4121 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.4005 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3300 Z= 0.243 Angle : 0.851 8.456 4416 Z= 0.419 Chirality : 0.054 0.175 498 Planarity : 0.004 0.036 558 Dihedral : 6.925 20.548 432 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.08 % Allowed : 9.14 % Favored : 89.78 % 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: -2.76 (0.34), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS D 330 PHE 0.010 0.002 PHE F 346 TYR 0.017 0.004 TYR C 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.400 Fit side-chains REVERT: B 352 SER cc_start: 0.9069 (t) cc_final: 0.8590 (m) REVERT: C 343 LYS cc_start: 0.8475 (tttt) cc_final: 0.8254 (mttp) REVERT: D 343 LYS cc_start: 0.8588 (mtpp) cc_final: 0.8315 (mtmm) REVERT: D 348 ASP cc_start: 0.8623 (t0) cc_final: 0.8378 (t0) REVERT: E 343 LYS cc_start: 0.8543 (mtmm) cc_final: 0.8300 (mtpt) REVERT: F 343 LYS cc_start: 0.8420 (tttt) cc_final: 0.8144 (mtmt) outliers start: 4 outliers final: 3 residues processed: 53 average time/residue: 0.2598 time to fit residues: 15.7420 Evaluate side-chains 46 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain C residue 320 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 ASN D 330 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.138240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.128828 restraints weight = 3732.168| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 1.99 r_work: 0.4069 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3947 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3300 Z= 0.305 Angle : 0.767 7.134 4416 Z= 0.388 Chirality : 0.053 0.162 498 Planarity : 0.006 0.051 558 Dihedral : 6.368 18.577 432 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.69 % Allowed : 9.68 % Favored : 87.63 % 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: -2.66 (0.35), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS E 362 PHE 0.013 0.002 PHE F 346 TYR 0.022 0.005 TYR C 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.418 Fit side-chains REVERT: B 352 SER cc_start: 0.9039 (t) cc_final: 0.8679 (m) REVERT: C 352 SER cc_start: 0.9173 (t) cc_final: 0.8827 (m) REVERT: D 343 LYS cc_start: 0.8640 (mtpp) cc_final: 0.8245 (mtmt) REVERT: E 343 LYS cc_start: 0.8683 (mtmm) cc_final: 0.8253 (mttp) REVERT: E 375 LYS cc_start: 0.8422 (mttt) cc_final: 0.8089 (tttp) REVERT: F 352 SER cc_start: 0.9118 (t) cc_final: 0.8778 (m) outliers start: 10 outliers final: 4 residues processed: 46 average time/residue: 0.2558 time to fit residues: 13.6197 Evaluate side-chains 44 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 39 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.139916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.130760 restraints weight = 3784.229| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 1.98 r_work: 0.4086 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3967 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3300 Z= 0.236 Angle : 0.672 7.495 4416 Z= 0.334 Chirality : 0.050 0.132 498 Planarity : 0.006 0.049 558 Dihedral : 5.853 16.685 432 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.15 % Allowed : 11.02 % Favored : 86.83 % 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: -2.67 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 362 PHE 0.007 0.001 PHE C 346 TYR 0.016 0.004 TYR C 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.378 Fit side-chains REVERT: B 352 SER cc_start: 0.8940 (t) cc_final: 0.8618 (m) REVERT: C 352 SER cc_start: 0.9109 (t) cc_final: 0.8850 (m) REVERT: D 343 LYS cc_start: 0.8638 (mtpp) cc_final: 0.8292 (mtmt) REVERT: E 343 LYS cc_start: 0.8746 (mtmm) cc_final: 0.8422 (mttp) REVERT: E 375 LYS cc_start: 0.8418 (mttt) cc_final: 0.8075 (tttp) REVERT: F 352 SER cc_start: 0.9046 (t) cc_final: 0.8800 (m) REVERT: F 369 LYS cc_start: 0.8606 (tttt) cc_final: 0.8400 (tttp) outliers start: 8 outliers final: 3 residues processed: 47 average time/residue: 0.2153 time to fit residues: 11.9215 Evaluate side-chains 47 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain E residue 315 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 5 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS B 327 ASN C 329 HIS D 327 ASN D 329 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.137361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.128564 restraints weight = 3841.637| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 1.87 r_work: 0.4055 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3938 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3300 Z= 0.285 Angle : 0.686 7.231 4416 Z= 0.346 Chirality : 0.051 0.138 498 Planarity : 0.006 0.051 558 Dihedral : 5.746 16.076 432 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.69 % Allowed : 13.44 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.37), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS E 362 PHE 0.009 0.002 PHE F 346 TYR 0.019 0.004 TYR C 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.382 Fit side-chains REVERT: B 352 SER cc_start: 0.8999 (t) cc_final: 0.8716 (m) REVERT: C 375 LYS cc_start: 0.8160 (mttt) cc_final: 0.7860 (tttm) REVERT: D 343 LYS cc_start: 0.8687 (mtpp) cc_final: 0.8354 (mtmt) REVERT: D 352 SER cc_start: 0.9033 (t) cc_final: 0.8785 (m) REVERT: E 375 LYS cc_start: 0.8436 (mttt) cc_final: 0.8183 (tttp) REVERT: F 375 LYS cc_start: 0.8096 (mttt) cc_final: 0.7719 (tttm) outliers start: 10 outliers final: 4 residues processed: 52 average time/residue: 0.2096 time to fit residues: 12.9319 Evaluate side-chains 49 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 10 optimal weight: 0.0470 chunk 18 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 overall best weight: 3.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 327 ASN F 329 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.136460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.127296 restraints weight = 3915.460| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 2.00 r_work: 0.4036 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3919 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3300 Z= 0.284 Angle : 0.677 8.740 4416 Z= 0.341 Chirality : 0.050 0.139 498 Planarity : 0.006 0.051 558 Dihedral : 5.659 15.631 432 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.61 % Allowed : 15.86 % Favored : 82.53 % 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: -2.60 (0.37), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS E 362 PHE 0.009 0.002 PHE F 346 TYR 0.018 0.004 TYR C 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.362 Fit side-chains REVERT: B 352 SER cc_start: 0.8938 (t) cc_final: 0.8674 (m) REVERT: C 375 LYS cc_start: 0.8166 (mttt) cc_final: 0.7832 (tttp) REVERT: D 343 LYS cc_start: 0.8654 (mtpp) cc_final: 0.8099 (mttp) REVERT: D 352 SER cc_start: 0.8954 (t) cc_final: 0.8736 (m) REVERT: E 375 LYS cc_start: 0.8434 (mttt) cc_final: 0.8179 (tttp) REVERT: F 375 LYS cc_start: 0.8140 (mttt) cc_final: 0.7794 (tttm) outliers start: 6 outliers final: 3 residues processed: 50 average time/residue: 0.2262 time to fit residues: 13.3234 Evaluate side-chains 49 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain C residue 320 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 7 optimal weight: 0.0040 chunk 11 optimal weight: 0.0370 overall best weight: 3.2076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.137479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.128407 restraints weight = 3813.659| |-----------------------------------------------------------------------------| r_work (start): 0.4188 rms_B_bonded: 1.96 r_work: 0.4048 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3930 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3300 Z= 0.240 Angle : 0.671 8.109 4416 Z= 0.332 Chirality : 0.049 0.136 498 Planarity : 0.006 0.050 558 Dihedral : 5.451 15.090 432 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.88 % Allowed : 15.32 % Favored : 82.80 % 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: -2.64 (0.37), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 362 PHE 0.008 0.002 PHE F 346 TYR 0.014 0.003 TYR C 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.412 Fit side-chains REVERT: B 352 SER cc_start: 0.8910 (t) cc_final: 0.8647 (m) REVERT: C 375 LYS cc_start: 0.8295 (mttt) cc_final: 0.7866 (tttp) REVERT: D 343 LYS cc_start: 0.8638 (mtpp) cc_final: 0.8123 (mttp) REVERT: D 352 SER cc_start: 0.8921 (t) cc_final: 0.8710 (m) REVERT: E 375 LYS cc_start: 0.8502 (mttt) cc_final: 0.8176 (tttp) REVERT: F 375 LYS cc_start: 0.8150 (mttt) cc_final: 0.7809 (tttm) outliers start: 7 outliers final: 5 residues processed: 50 average time/residue: 0.2172 time to fit residues: 12.7364 Evaluate side-chains 49 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.0040 chunk 5 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 14 optimal weight: 0.1980 chunk 29 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.141849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.132557 restraints weight = 3758.636| |-----------------------------------------------------------------------------| r_work (start): 0.4236 rms_B_bonded: 1.99 r_work: 0.4096 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3979 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3300 Z= 0.158 Angle : 0.641 7.696 4416 Z= 0.307 Chirality : 0.048 0.129 498 Planarity : 0.006 0.054 558 Dihedral : 4.997 13.942 432 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.34 % Allowed : 15.59 % Favored : 83.06 % 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: -2.60 (0.37), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 362 PHE 0.005 0.001 PHE A 378 TYR 0.008 0.002 TYR A 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.399 Fit side-chains REVERT: B 352 SER cc_start: 0.8830 (t) cc_final: 0.8567 (m) REVERT: C 375 LYS cc_start: 0.8275 (mttt) cc_final: 0.7867 (tttp) REVERT: D 343 LYS cc_start: 0.8591 (mtpp) cc_final: 0.8087 (mttp) REVERT: D 352 SER cc_start: 0.8821 (t) cc_final: 0.8607 (m) REVERT: E 375 LYS cc_start: 0.8520 (mttt) cc_final: 0.8166 (tttp) REVERT: F 375 LYS cc_start: 0.8147 (mttt) cc_final: 0.7767 (tttm) outliers start: 5 outliers final: 4 residues processed: 49 average time/residue: 0.2092 time to fit residues: 12.1578 Evaluate side-chains 48 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 33 optimal weight: 0.2980 chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 overall best weight: 6.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.131172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.122127 restraints weight = 3992.470| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 2.02 r_work: 0.3969 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3849 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 3300 Z= 0.429 Angle : 0.774 9.035 4416 Z= 0.392 Chirality : 0.054 0.165 498 Planarity : 0.007 0.062 558 Dihedral : 5.841 16.561 432 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.61 % Allowed : 15.32 % Favored : 83.06 % 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: -2.69 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS E 362 PHE 0.015 0.003 PHE F 346 TYR 0.024 0.006 TYR C 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.492 Fit side-chains REVERT: B 352 SER cc_start: 0.8982 (t) cc_final: 0.8763 (m) REVERT: C 375 LYS cc_start: 0.8313 (mttt) cc_final: 0.7992 (tttp) REVERT: D 343 LYS cc_start: 0.8604 (mtpp) cc_final: 0.8074 (mttp) REVERT: E 375 LYS cc_start: 0.8575 (mttt) cc_final: 0.8227 (tttp) REVERT: F 375 LYS cc_start: 0.8234 (mttt) cc_final: 0.7907 (tttm) outliers start: 6 outliers final: 5 residues processed: 52 average time/residue: 0.2134 time to fit residues: 13.0954 Evaluate side-chains 47 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 361 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 0.1980 chunk 36 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 25 optimal weight: 0.4980 chunk 23 optimal weight: 10.0000 overall best weight: 5.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.131097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.121540 restraints weight = 3913.246| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 2.17 r_work: 0.3954 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3833 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3300 Z= 0.364 Angle : 0.772 9.590 4416 Z= 0.391 Chirality : 0.053 0.143 498 Planarity : 0.007 0.064 558 Dihedral : 5.803 16.291 432 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.61 % Allowed : 15.59 % Favored : 82.80 % 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: -2.83 (0.35), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS E 362 PHE 0.010 0.002 PHE F 346 TYR 0.020 0.005 TYR C 310 ARG 0.001 0.000 ARG D 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.425 Fit side-chains REVERT: B 352 SER cc_start: 0.8868 (t) cc_final: 0.8646 (m) REVERT: C 375 LYS cc_start: 0.8269 (mttt) cc_final: 0.7938 (tttp) REVERT: D 343 LYS cc_start: 0.8592 (mtpp) cc_final: 0.8059 (mttp) REVERT: E 375 LYS cc_start: 0.8534 (mttt) cc_final: 0.8195 (tttp) REVERT: F 375 LYS cc_start: 0.8226 (mttt) cc_final: 0.7836 (tttm) outliers start: 6 outliers final: 6 residues processed: 47 average time/residue: 0.1674 time to fit residues: 9.5231 Evaluate side-chains 46 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 361 THR Chi-restraints excluded: chain E residue 361 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 16 optimal weight: 0.0020 chunk 25 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 overall best weight: 4.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.132353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.123152 restraints weight = 3894.350| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 2.03 r_work: 0.3980 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3861 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3300 Z= 0.312 Angle : 0.771 9.320 4416 Z= 0.385 Chirality : 0.052 0.142 498 Planarity : 0.007 0.063 558 Dihedral : 5.656 15.658 432 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.34 % Allowed : 16.67 % Favored : 81.99 % 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: -2.84 (0.35), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 362 PHE 0.008 0.002 PHE F 346 TYR 0.018 0.004 TYR C 310 ARG 0.001 0.000 ARG D 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1732.82 seconds wall clock time: 31 minutes 47.26 seconds (1907.26 seconds total)