Starting phenix.real_space_refine on Thu Nov 14 00:34:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otg_17178/11_2024/8otg_17178.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otg_17178/11_2024/8otg_17178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otg_17178/11_2024/8otg_17178.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otg_17178/11_2024/8otg_17178.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otg_17178/11_2024/8otg_17178.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otg_17178/11_2024/8otg_17178.cif" } resolution = 2.1 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= 0.002 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 5 5.16 5 C 1800 2.51 5 N 530 2.21 5 O 535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 2870 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Restraints were copied for chains: C, B, E, D Time building chain proxies: 2.52, per 1000 atoms: 0.88 Number of scatterers: 2870 At special positions: 0 Unit cell: (123.9, 121.422, 33.04, 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 5 16.00 O 535 8.00 N 530 7.00 C 1800 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: 0.61 Conformation dependent library (CDL) restraints added in 398.9 milliseconds 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 660 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 56.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.542A pdb=" N GLN A 307 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N TYR B 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.606A 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 322 removed outlier: 6.363A pdb=" N VAL A 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N LYS E 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N SER A 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 325 through 330 removed outlier: 6.828A pdb=" N GLY B 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN A 327 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLY A 326 " --> pdb=" O ASN E 327 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N HIS E 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE A 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 337 through 346 removed outlier: 6.566A pdb=" N GLU A 338 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N SER B 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS A 340 " --> pdb=" O SER B 341 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N LYS B 343 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N GLU A 342 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ASP B 345 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N LEU A 344 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU E 344 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASP A 345 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N PHE E 346 " --> pdb=" O ASP A 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 350 through 357 removed outlier: 6.466A pdb=" N GLN A 351 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ILE B 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LYS A 353 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N SER B 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLY A 355 " --> pdb=" O SER B 356 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 360 through 362 removed outlier: 6.316A pdb=" N THR A 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 369 through 378 removed outlier: 6.635A pdb=" N LYS A 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N GLU B 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE A 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N HIS B 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N THR A 373 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LEU B 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS A 375 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N PHE B 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR A 377 " --> pdb=" O PHE B 378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 306 through 310 Processing sheet with id=AB1, first strand: chain 'C' and resid 313 through 314 Processing sheet with id=AB2, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.364A pdb=" N VAL C 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N LYS D 321 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N SER C 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 325 through 330 removed outlier: 6.219A pdb=" N GLY C 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N HIS D 329 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE C 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 337 through 346 removed outlier: 6.861A pdb=" N LEU D 344 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASP C 345 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N PHE D 346 " --> pdb=" O ASP C 345 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 350 through 357 Processing sheet with id=AB6, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.316A pdb=" N THR C 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 369 through 378 64 hydrogen bonds defined for protein. 192 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: 0.59 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 596 1.34 - 1.46: 644 1.46 - 1.58: 1670 1.58 - 1.69: 0 1.69 - 1.81: 5 Bond restraints: 2915 Sorted by residual: bond pdb=" C ARG D 379 " pdb=" O ARG D 379 " ideal model delta sigma weight residual 1.231 1.338 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C ARG E 379 " pdb=" O ARG E 379 " ideal model delta sigma weight residual 1.231 1.338 -0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" C ARG C 379 " pdb=" O ARG C 379 " ideal model delta sigma weight residual 1.231 1.338 -0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" C ARG B 379 " pdb=" O ARG B 379 " ideal model delta sigma weight residual 1.231 1.337 -0.106 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C ARG A 379 " pdb=" O ARG A 379 " ideal model delta sigma weight residual 1.231 1.337 -0.106 2.00e-02 2.50e+03 2.84e+01 ... (remaining 2910 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 2822 1.09 - 2.18: 850 2.18 - 3.27: 171 3.27 - 4.36: 47 4.36 - 5.45: 10 Bond angle restraints: 3900 Sorted by residual: angle pdb=" CA ASP D 348 " pdb=" CB ASP D 348 " pdb=" CG ASP D 348 " ideal model delta sigma weight residual 112.60 116.66 -4.06 1.00e+00 1.00e+00 1.65e+01 angle pdb=" CA ASP A 348 " pdb=" CB ASP A 348 " pdb=" CG ASP A 348 " ideal model delta sigma weight residual 112.60 116.66 -4.06 1.00e+00 1.00e+00 1.64e+01 angle pdb=" CA ASP B 348 " pdb=" CB ASP B 348 " pdb=" CG ASP B 348 " ideal model delta sigma weight residual 112.60 116.66 -4.06 1.00e+00 1.00e+00 1.64e+01 angle pdb=" CA ASP C 348 " pdb=" CB ASP C 348 " pdb=" CG ASP C 348 " ideal model delta sigma weight residual 112.60 116.65 -4.05 1.00e+00 1.00e+00 1.64e+01 angle pdb=" CA ASP E 348 " pdb=" CB ASP E 348 " pdb=" CG ASP E 348 " ideal model delta sigma weight residual 112.60 116.64 -4.04 1.00e+00 1.00e+00 1.63e+01 ... (remaining 3895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.04: 1680 13.04 - 26.08: 50 26.08 - 39.12: 30 39.12 - 52.15: 5 52.15 - 65.19: 15 Dihedral angle restraints: 1780 sinusoidal: 745 harmonic: 1035 Sorted by residual: dihedral pdb=" CA ILE E 360 " pdb=" C ILE E 360 " pdb=" N THR E 361 " pdb=" CA THR E 361 " ideal model delta harmonic sigma weight residual 180.00 163.47 16.53 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ILE C 360 " pdb=" C ILE C 360 " pdb=" N THR C 361 " pdb=" CA THR C 361 " ideal model delta harmonic sigma weight residual 180.00 163.49 16.51 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ILE A 360 " pdb=" C ILE A 360 " pdb=" N THR A 361 " pdb=" CA THR A 361 " ideal model delta harmonic sigma weight residual 180.00 163.51 16.49 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 1777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 138 0.034 - 0.068: 115 0.068 - 0.102: 132 0.102 - 0.136: 35 0.136 - 0.170: 20 Chirality restraints: 440 Sorted by residual: chirality pdb=" CB ILE C 328 " pdb=" CA ILE C 328 " pdb=" CG1 ILE C 328 " pdb=" CG2 ILE C 328 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CB ILE E 328 " pdb=" CA ILE E 328 " pdb=" CG1 ILE E 328 " pdb=" CG2 ILE E 328 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.04e-01 chirality pdb=" CB ILE A 328 " pdb=" CA ILE A 328 " pdb=" CG1 ILE A 328 " pdb=" CG2 ILE A 328 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.03e-01 ... (remaining 437 not shown) Planarity restraints: 495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 363 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.51e+00 pdb=" C VAL B 363 " -0.027 2.00e-02 2.50e+03 pdb=" O VAL B 363 " 0.010 2.00e-02 2.50e+03 pdb=" N PRO B 364 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 363 " 0.008 2.00e-02 2.50e+03 1.58e-02 2.49e+00 pdb=" C VAL E 363 " -0.027 2.00e-02 2.50e+03 pdb=" O VAL E 363 " 0.010 2.00e-02 2.50e+03 pdb=" N PRO E 364 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 363 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.48e+00 pdb=" C VAL D 363 " 0.027 2.00e-02 2.50e+03 pdb=" O VAL D 363 " -0.010 2.00e-02 2.50e+03 pdb=" N PRO D 364 " -0.009 2.00e-02 2.50e+03 ... (remaining 492 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 1130 2.96 - 3.45: 2178 3.45 - 3.93: 4648 3.93 - 4.42: 4399 4.42 - 4.90: 8706 Nonbonded interactions: 21061 Sorted by model distance: nonbonded pdb=" OG1 THR A 361 " pdb=" ND1 HIS E 330 " model vdw 2.479 3.120 nonbonded pdb=" ND1 HIS A 330 " pdb=" OG1 THR B 361 " model vdw 2.479 3.120 nonbonded pdb=" OG1 THR C 361 " pdb=" ND1 HIS D 330 " model vdw 2.480 3.120 nonbonded pdb=" N ASP C 348 " pdb=" O ASP C 348 " model vdw 2.614 2.496 nonbonded pdb=" N ASP A 348 " pdb=" O ASP A 348 " model vdw 2.614 2.496 ... (remaining 21056 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 3.140 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: 0.020 Set scattering table: 0.030 Process input model: 11.560 Find NCS groups from input model: 0.100 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:11.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 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 : 0.009 0.107 2915 Z= 0.593 Angle : 1.122 5.450 3900 Z= 0.735 Chirality : 0.072 0.170 440 Planarity : 0.005 0.027 495 Dihedral : 11.339 65.192 1120 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 1.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.03 % Allowed : 1.52 % Favored : 95.45 % 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: -2.90 (0.33), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.25), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS E 362 PHE 0.010 0.003 PHE C 378 TYR 0.005 0.004 TYR D 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 0.369 Fit side-chains REVERT: A 321 LYS cc_start: 0.8784 (mttt) cc_final: 0.8553 (mttm) REVERT: A 379 ARG cc_start: 0.7216 (ptm160) cc_final: 0.6868 (ptp90) REVERT: B 321 LYS cc_start: 0.8781 (mttt) cc_final: 0.8554 (mttm) REVERT: C 321 LYS cc_start: 0.8778 (mttt) cc_final: 0.8506 (mttm) REVERT: C 340 LYS cc_start: 0.8646 (mtpm) cc_final: 0.8322 (tttp) REVERT: C 375 LYS cc_start: 0.8594 (tttt) cc_final: 0.8361 (ttmm) REVERT: C 379 ARG cc_start: 0.7295 (ptm160) cc_final: 0.6650 (ppt90) REVERT: D 349 ARG cc_start: 0.8600 (mtt180) cc_final: 0.7428 (mmp-170) REVERT: D 375 LYS cc_start: 0.8491 (tttt) cc_final: 0.8187 (ttmm) REVERT: E 349 ARG cc_start: 0.8595 (mtt180) cc_final: 0.7470 (mmp-170) REVERT: E 375 LYS cc_start: 0.8481 (tttt) cc_final: 0.8240 (ttmm) outliers start: 10 outliers final: 0 residues processed: 160 average time/residue: 1.4664 time to fit residues: 238.7923 Evaluate side-chains 83 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 307 GLN B 327 ASN B 351 GLN C 307 GLN C 327 ASN C 330 HIS C 351 GLN D 307 GLN D 351 GLN E 307 GLN E 351 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2915 Z= 0.205 Angle : 0.600 6.184 3900 Z= 0.290 Chirality : 0.049 0.136 440 Planarity : 0.003 0.023 495 Dihedral : 4.767 13.692 385 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.82 % Allowed : 18.79 % Favored : 79.39 % 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: -2.44 (0.34), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.26), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 374 PHE 0.018 0.002 PHE E 378 TYR 0.008 0.002 TYR C 310 ARG 0.004 0.001 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.350 Fit side-chains REVERT: B 379 ARG cc_start: 0.7507 (ptp-110) cc_final: 0.6417 (ptt-90) REVERT: D 349 ARG cc_start: 0.8613 (mtt180) cc_final: 0.7228 (mmp-170) REVERT: E 325 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8331 (tt) REVERT: E 349 ARG cc_start: 0.8639 (mtt180) cc_final: 0.7490 (mmp-170) outliers start: 6 outliers final: 3 residues processed: 88 average time/residue: 1.3618 time to fit residues: 122.3488 Evaluate side-chains 86 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain E residue 325 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 8 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 34 optimal weight: 0.5980 chunk 28 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 25 optimal weight: 0.0870 chunk 23 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 overall best weight: 1.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 351 GLN B 307 GLN B 330 HIS C 307 GLN D 307 GLN D 351 GLN E 307 GLN E 351 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2915 Z= 0.187 Angle : 0.564 5.563 3900 Z= 0.279 Chirality : 0.049 0.133 440 Planarity : 0.003 0.019 495 Dihedral : 4.731 13.391 385 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.82 % Allowed : 17.88 % Favored : 80.30 % 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: -2.28 (0.33), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.25), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.013 0.002 PHE E 378 TYR 0.007 0.002 TYR D 310 ARG 0.004 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.357 Fit side-chains REVERT: B 379 ARG cc_start: 0.7612 (ptp-110) cc_final: 0.6373 (ptt90) REVERT: D 325 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8377 (tt) REVERT: D 349 ARG cc_start: 0.8639 (mtt180) cc_final: 0.7334 (mmp-170) REVERT: E 325 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8415 (tt) REVERT: E 349 ARG cc_start: 0.8649 (mtt180) cc_final: 0.7303 (mmp-170) REVERT: E 379 ARG cc_start: 0.5130 (OUTLIER) cc_final: 0.4240 (mtt-85) outliers start: 6 outliers final: 0 residues processed: 88 average time/residue: 1.3866 time to fit residues: 124.6638 Evaluate side-chains 84 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 31 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 9 optimal weight: 0.0770 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 overall best weight: 3.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 351 GLN B 307 GLN C 307 GLN C 351 GLN D 307 GLN E 307 GLN E 351 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 2915 Z= 0.322 Angle : 0.650 7.680 3900 Z= 0.322 Chirality : 0.051 0.140 440 Planarity : 0.003 0.016 495 Dihedral : 5.113 14.862 385 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.21 % Allowed : 19.09 % Favored : 79.70 % 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: -2.16 (0.33), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.25), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 329 PHE 0.012 0.002 PHE C 378 TYR 0.008 0.002 TYR D 310 ARG 0.003 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.330 Fit side-chains REVERT: B 317 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8477 (mttm) REVERT: B 379 ARG cc_start: 0.7701 (ptp-110) cc_final: 0.6302 (ptt90) REVERT: D 349 ARG cc_start: 0.8635 (mtt180) cc_final: 0.7400 (mmp-170) REVERT: E 325 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8676 (tt) REVERT: E 349 ARG cc_start: 0.8646 (mtt180) cc_final: 0.7469 (mmp-170) REVERT: E 379 ARG cc_start: 0.5052 (OUTLIER) cc_final: 0.4113 (mtt-85) outliers start: 4 outliers final: 1 residues processed: 86 average time/residue: 1.3926 time to fit residues: 122.2684 Evaluate side-chains 85 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 327 ASN A 351 GLN B 307 GLN C 307 GLN C 351 GLN D 307 GLN D 327 ASN E 307 GLN E 351 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 2915 Z= 0.515 Angle : 0.729 8.388 3900 Z= 0.371 Chirality : 0.055 0.169 440 Planarity : 0.003 0.019 495 Dihedral : 5.443 16.276 385 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.42 % Allowed : 17.27 % Favored : 80.30 % 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: -2.01 (0.33), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.25), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 329 PHE 0.012 0.002 PHE C 378 TYR 0.010 0.003 TYR E 310 ARG 0.002 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.371 Fit side-chains REVERT: B 317 LYS cc_start: 0.8856 (mtmt) cc_final: 0.8514 (mttp) REVERT: B 379 ARG cc_start: 0.7692 (ptp-110) cc_final: 0.6381 (ptt90) REVERT: C 317 LYS cc_start: 0.8806 (mtmt) cc_final: 0.8466 (mttm) REVERT: D 325 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8807 (tt) REVERT: D 342 GLU cc_start: 0.8104 (tt0) cc_final: 0.7662 (mt-10) REVERT: D 349 ARG cc_start: 0.8659 (mtt180) cc_final: 0.7391 (mmp-170) REVERT: D 379 ARG cc_start: 0.5170 (OUTLIER) cc_final: 0.4341 (mtt-85) REVERT: E 349 ARG cc_start: 0.8640 (mtt180) cc_final: 0.7422 (mmp-170) REVERT: E 379 ARG cc_start: 0.5063 (OUTLIER) cc_final: 0.4050 (mtt-85) outliers start: 8 outliers final: 2 residues processed: 92 average time/residue: 1.3662 time to fit residues: 128.3210 Evaluate side-chains 91 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 11 optimal weight: 8.9990 chunk 17 optimal weight: 0.0970 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 28 optimal weight: 0.0070 chunk 18 optimal weight: 0.6980 chunk 33 optimal weight: 0.2980 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 351 GLN B 307 GLN C 307 GLN C 351 GLN D 307 GLN D 351 GLN E 307 GLN E 351 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2915 Z= 0.114 Angle : 0.546 8.766 3900 Z= 0.259 Chirality : 0.049 0.125 440 Planarity : 0.002 0.013 495 Dihedral : 4.516 12.880 385 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.30 % Allowed : 20.00 % Favored : 79.70 % 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: -1.82 (0.34), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.26), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 330 PHE 0.009 0.001 PHE C 378 TYR 0.011 0.003 TYR D 310 ARG 0.002 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.395 Fit side-chains REVERT: B 379 ARG cc_start: 0.7697 (ptp-110) cc_final: 0.7455 (mtp85) REVERT: C 317 LYS cc_start: 0.8722 (mtmt) cc_final: 0.8375 (mttm) REVERT: D 325 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.7927 (tt) REVERT: D 349 ARG cc_start: 0.8592 (mtt180) cc_final: 0.7352 (mmp-170) REVERT: E 349 ARG cc_start: 0.8587 (mtt180) cc_final: 0.7258 (mmp-170) outliers start: 1 outliers final: 0 residues processed: 89 average time/residue: 1.2711 time to fit residues: 115.6255 Evaluate side-chains 83 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 10 optimal weight: 0.0050 chunk 6 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 overall best weight: 1.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 307 GLN C 307 GLN D 307 GLN D 351 GLN E 307 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2915 Z= 0.191 Angle : 0.587 8.631 3900 Z= 0.287 Chirality : 0.049 0.133 440 Planarity : 0.002 0.013 495 Dihedral : 4.737 13.808 385 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.61 % Allowed : 20.91 % Favored : 78.48 % 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: -1.70 (0.34), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.26), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 374 PHE 0.009 0.002 PHE C 378 TYR 0.010 0.002 TYR E 310 ARG 0.002 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 81 time to evaluate : 0.367 Fit side-chains REVERT: B 379 ARG cc_start: 0.7681 (ptp-110) cc_final: 0.7358 (mtp85) REVERT: D 325 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8499 (tt) REVERT: D 349 ARG cc_start: 0.8644 (mtt180) cc_final: 0.7415 (mmp-170) REVERT: E 349 ARG cc_start: 0.8637 (mtt180) cc_final: 0.7306 (mmp-170) outliers start: 2 outliers final: 1 residues processed: 82 average time/residue: 1.3339 time to fit residues: 111.8516 Evaluate side-chains 82 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 32 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 31 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 overall best weight: 3.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 307 GLN C 307 GLN C 351 GLN D 307 GLN D 351 GLN E 307 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2915 Z= 0.306 Angle : 0.670 8.827 3900 Z= 0.329 Chirality : 0.051 0.140 440 Planarity : 0.002 0.014 495 Dihedral : 4.996 15.164 385 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.21 % Allowed : 20.30 % Favored : 78.48 % 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: -1.74 (0.34), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.26), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 329 PHE 0.009 0.002 PHE C 378 TYR 0.010 0.002 TYR E 310 ARG 0.002 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.399 Fit side-chains REVERT: B 317 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8618 (mttp) REVERT: B 379 ARG cc_start: 0.7713 (ptp-110) cc_final: 0.6293 (ptt90) REVERT: C 317 LYS cc_start: 0.8806 (mtmt) cc_final: 0.8464 (mttm) REVERT: D 325 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8695 (tt) REVERT: D 349 ARG cc_start: 0.8631 (mtt180) cc_final: 0.7404 (mmp-170) REVERT: E 349 ARG cc_start: 0.8632 (mtt180) cc_final: 0.7436 (mmp-170) REVERT: E 379 ARG cc_start: 0.4933 (OUTLIER) cc_final: 0.3973 (mtt-85) outliers start: 4 outliers final: 1 residues processed: 82 average time/residue: 1.4213 time to fit residues: 119.0323 Evaluate side-chains 84 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 23 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 17 optimal weight: 0.0570 chunk 22 optimal weight: 0.5980 chunk 29 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 overall best weight: 2.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 307 GLN C 307 GLN C 351 GLN D 307 GLN D 351 GLN E 307 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2915 Z= 0.276 Angle : 0.654 8.911 3900 Z= 0.327 Chirality : 0.050 0.137 440 Planarity : 0.002 0.014 495 Dihedral : 4.972 14.928 385 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.21 % Allowed : 20.00 % Favored : 78.79 % 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: -1.73 (0.35), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.26), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 329 PHE 0.009 0.002 PHE C 378 TYR 0.010 0.002 TYR E 310 ARG 0.002 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.367 Fit side-chains REVERT: B 379 ARG cc_start: 0.7653 (ptp-110) cc_final: 0.7309 (mtp85) REVERT: C 317 LYS cc_start: 0.8803 (mtmt) cc_final: 0.8459 (mttm) REVERT: D 325 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8623 (tt) REVERT: D 349 ARG cc_start: 0.8633 (mtt180) cc_final: 0.7401 (mmp-170) REVERT: E 349 ARG cc_start: 0.8652 (mtt180) cc_final: 0.7465 (mmp-170) REVERT: E 379 ARG cc_start: 0.4922 (OUTLIER) cc_final: 0.3951 (mtt-85) outliers start: 4 outliers final: 1 residues processed: 82 average time/residue: 1.4011 time to fit residues: 117.2812 Evaluate side-chains 83 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 4 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 11 optimal weight: 0.3980 chunk 28 optimal weight: 6.9990 chunk 3 optimal weight: 0.0050 chunk 5 optimal weight: 8.9990 chunk 24 optimal weight: 0.0170 chunk 1 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 overall best weight: 1.6836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 307 GLN C 307 GLN C 351 GLN D 307 GLN D 351 GLN E 307 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2915 Z= 0.199 Angle : 0.646 8.926 3900 Z= 0.316 Chirality : 0.050 0.132 440 Planarity : 0.002 0.014 495 Dihedral : 4.798 14.163 385 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.52 % Allowed : 20.00 % Favored : 78.48 % 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: -1.68 (0.35), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 374 PHE 0.009 0.002 PHE C 378 TYR 0.010 0.002 TYR E 310 ARG 0.002 0.000 ARG D 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.404 Fit side-chains REVERT: B 379 ARG cc_start: 0.7648 (ptp-110) cc_final: 0.7342 (mtp85) REVERT: C 317 LYS cc_start: 0.8762 (mtmt) cc_final: 0.8419 (mttm) REVERT: D 325 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8445 (tt) REVERT: D 349 ARG cc_start: 0.8641 (mtt180) cc_final: 0.7416 (mmp-170) REVERT: E 349 ARG cc_start: 0.8638 (mtt180) cc_final: 0.7460 (mmp-170) REVERT: E 379 ARG cc_start: 0.5284 (OUTLIER) cc_final: 0.4352 (mtt-85) outliers start: 5 outliers final: 2 residues processed: 85 average time/residue: 1.3977 time to fit residues: 121.4558 Evaluate side-chains 84 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 18 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 0.1980 chunk 12 optimal weight: 0.0670 chunk 34 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 overall best weight: 2.2522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 351 GLN B 307 GLN C 307 GLN D 307 GLN D 351 GLN E 307 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.126257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.109784 restraints weight = 3072.924| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.29 r_work: 0.3543 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2915 Z= 0.243 Angle : 0.657 8.863 3900 Z= 0.329 Chirality : 0.050 0.134 440 Planarity : 0.002 0.013 495 Dihedral : 4.870 14.457 385 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.52 % Allowed : 20.00 % Favored : 78.48 % 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: -1.70 (0.35), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 374 PHE 0.009 0.002 PHE C 378 TYR 0.010 0.002 TYR E 310 ARG 0.002 0.000 ARG D 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2520.04 seconds wall clock time: 45 minutes 32.20 seconds (2732.20 seconds total)