Starting phenix.real_space_refine on Sun Mar 10 17:35:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkk_14045/03_2024/7qkk_14045.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkk_14045/03_2024/7qkk_14045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkk_14045/03_2024/7qkk_14045.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkk_14045/03_2024/7qkk_14045.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkk_14045/03_2024/7qkk_14045.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkk_14045/03_2024/7qkk_14045.pdb" } resolution = 2.8 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= 0.001 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: 5 Type Number sf(0) Gaussians S 3 5.16 5 C 1086 2.51 5 N 321 2.21 5 O 324 1.98 5 H 1803 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "C GLU 372": "OE1" <-> "OE2" Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3537 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "C" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "A" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Time building chain proxies: 1.99, per 1000 atoms: 0.56 Number of scatterers: 3537 At special positions: 0 Unit cell: (85.696, 72.512, 37.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 3 16.00 O 324 8.00 N 321 7.00 C 1086 6.00 H 1803 1.00 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 - 3.50 Amino acid : False - 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: 2.75 Conformation dependent library (CDL) restraints added in 365.4 milliseconds 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 396 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 36.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.569A pdb=" N VAL B 306 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N VAL C 309 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE B 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLN B 307 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N TYR A 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL B 309 " --> pdb=" O TYR A 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.963A pdb=" N VAL B 313 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.238A pdb=" N VAL B 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N LYS C 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N SER B 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LYS B 317 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N SER A 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR B 319 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N CYS A 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS B 321 " --> pdb=" O CYS A 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 327 through 330 removed outlier: 6.706A pdb=" N ILE B 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN B 327 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N HIS A 330 " --> pdb=" O ASN B 327 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N HIS B 329 " --> pdb=" O HIS A 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 336 through 340 removed outlier: 6.598A pdb=" N GLN B 336 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N VAL A 339 " --> pdb=" O GLN B 336 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU B 338 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 343 through 346 removed outlier: 6.472A pdb=" N LYS B 343 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N PHE A 346 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASP B 345 " --> pdb=" O PHE A 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 351 through 353 removed outlier: 6.635A pdb=" N SER B 352 " --> pdb=" O LYS C 353 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 356 through 361 removed outlier: 6.758A pdb=" N SER B 356 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ASN A 359 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP B 358 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N THR A 361 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE B 360 " --> pdb=" O THR A 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 374 through 375 16 hydrogen bonds defined for protein. 48 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: 1.06 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 1800 1.12 - 1.29: 289 1.29 - 1.46: 513 1.46 - 1.64: 959 1.64 - 1.81: 3 Bond restraints: 3564 Sorted by residual: bond pdb=" ND2 ASN B 368 " pdb="HD21 ASN B 368 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" ND2 ASN A 368 " pdb="HD21 ASN A 368 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N LYS A 375 " pdb=" H LYS A 375 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" ND2 ASN B 368 " pdb="HD22 ASN B 368 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N LYS A 369 " pdb=" H LYS A 369 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 3559 not shown) Histogram of bond angle deviations from ideal: 96.91 - 103.27: 26 103.27 - 109.62: 2854 109.62 - 115.98: 1733 115.98 - 122.33: 1511 122.33 - 128.69: 368 Bond angle restraints: 6492 Sorted by residual: angle pdb=" CA HIS C 374 " pdb=" CB HIS C 374 " pdb=" CG HIS C 374 " ideal model delta sigma weight residual 113.80 123.66 -9.86 1.00e+00 1.00e+00 9.73e+01 angle pdb=" CA HIS A 374 " pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 113.80 122.99 -9.19 1.00e+00 1.00e+00 8.45e+01 angle pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " pdb=" CD2 HIS A 374 " ideal model delta sigma weight residual 131.20 120.20 11.00 1.30e+00 5.92e-01 7.16e+01 angle pdb=" CB HIS C 374 " pdb=" CG HIS C 374 " pdb=" CD2 HIS C 374 " ideal model delta sigma weight residual 131.20 121.33 9.87 1.30e+00 5.92e-01 5.76e+01 angle pdb=" CA ASP A 358 " pdb=" CB ASP A 358 " pdb=" CG ASP A 358 " ideal model delta sigma weight residual 112.60 119.26 -6.66 1.00e+00 1.00e+00 4.44e+01 ... (remaining 6487 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 14.05: 1377 14.05 - 28.10: 136 28.10 - 42.15: 54 42.15 - 56.20: 34 56.20 - 70.25: 40 Dihedral angle restraints: 1641 sinusoidal: 939 harmonic: 702 Sorted by residual: dihedral pdb=" CA LYS B 375 " pdb=" C LYS B 375 " pdb=" N LEU B 376 " pdb=" CA LEU B 376 " ideal model delta harmonic sigma weight residual 180.00 149.29 30.71 0 5.00e+00 4.00e-02 3.77e+01 dihedral pdb=" C VAL A 363 " pdb=" N VAL A 363 " pdb=" CA VAL A 363 " pdb=" CB VAL A 363 " ideal model delta harmonic sigma weight residual -122.00 -136.61 14.61 0 2.50e+00 1.60e-01 3.42e+01 dihedral pdb=" CA LYS C 375 " pdb=" C LYS C 375 " pdb=" N LEU C 376 " pdb=" CA LEU C 376 " ideal model delta harmonic sigma weight residual 180.00 150.95 29.05 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 1638 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 155 0.091 - 0.182: 80 0.182 - 0.274: 20 0.274 - 0.365: 7 0.365 - 0.456: 2 Chirality restraints: 264 Sorted by residual: chirality pdb=" CA PRO B 364 " pdb=" N PRO B 364 " pdb=" C PRO B 364 " pdb=" CB PRO B 364 " both_signs ideal model delta sigma weight residual False 2.72 2.26 0.46 2.00e-01 2.50e+01 5.20e+00 chirality pdb=" CA VAL B 363 " pdb=" N VAL B 363 " pdb=" C VAL B 363 " pdb=" CB VAL B 363 " both_signs ideal model delta sigma weight residual False 2.44 2.08 0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CA VAL A 363 " pdb=" N VAL A 363 " pdb=" C VAL A 363 " pdb=" CB VAL A 363 " both_signs ideal model delta sigma weight residual False 2.44 2.08 0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 261 not shown) Planarity restraints: 516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 374 " -0.321 2.00e-02 2.50e+03 1.68e-01 6.35e+02 pdb=" CG HIS A 374 " 0.219 2.00e-02 2.50e+03 pdb=" ND1 HIS A 374 " 0.162 2.00e-02 2.50e+03 pdb=" CD2 HIS A 374 " 0.167 2.00e-02 2.50e+03 pdb=" CE1 HIS A 374 " 0.022 2.00e-02 2.50e+03 pdb=" NE2 HIS A 374 " 0.056 2.00e-02 2.50e+03 pdb=" HD2 HIS A 374 " -0.005 2.00e-02 2.50e+03 pdb=" HE1 HIS A 374 " -0.147 2.00e-02 2.50e+03 pdb=" HE2 HIS A 374 " -0.153 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 374 " -0.249 2.00e-02 2.50e+03 1.30e-01 3.83e+02 pdb=" CG HIS C 374 " 0.181 2.00e-02 2.50e+03 pdb=" ND1 HIS C 374 " 0.124 2.00e-02 2.50e+03 pdb=" CD2 HIS C 374 " 0.129 2.00e-02 2.50e+03 pdb=" CE1 HIS C 374 " 0.008 2.00e-02 2.50e+03 pdb=" NE2 HIS C 374 " 0.039 2.00e-02 2.50e+03 pdb=" HD2 HIS C 374 " -0.008 2.00e-02 2.50e+03 pdb=" HE1 HIS C 374 " -0.113 2.00e-02 2.50e+03 pdb=" HE2 HIS C 374 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 374 " 0.151 2.00e-02 2.50e+03 8.51e-02 1.63e+02 pdb=" CG HIS B 374 " -0.120 2.00e-02 2.50e+03 pdb=" ND1 HIS B 374 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 HIS B 374 " -0.078 2.00e-02 2.50e+03 pdb=" CE1 HIS B 374 " -0.026 2.00e-02 2.50e+03 pdb=" NE2 HIS B 374 " -0.040 2.00e-02 2.50e+03 pdb=" HD2 HIS B 374 " 0.027 2.00e-02 2.50e+03 pdb=" HE1 HIS B 374 " 0.094 2.00e-02 2.50e+03 pdb=" HE2 HIS B 374 " 0.066 2.00e-02 2.50e+03 ... (remaining 513 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 185 2.14 - 2.76: 5632 2.76 - 3.37: 9537 3.37 - 3.99: 12229 3.99 - 4.60: 17889 Nonbonded interactions: 45472 Sorted by model distance: nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.525 1.850 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.571 1.850 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.642 1.850 nonbonded pdb=" OD2 ASP B 314 " pdb=" HZ1 LYS B 370 " model vdw 1.674 1.850 nonbonded pdb=" OD2 ASP A 314 " pdb=" HZ2 LYS A 370 " model vdw 1.693 1.850 ... (remaining 45467 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 2.670 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: 0.050 Extract box with map and model: 11.370 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 16.120 Find NCS groups from input model: 0.150 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:11.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 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 : 0.012 0.086 1761 Z= 0.799 Angle : 2.170 11.001 2355 Z= 1.448 Chirality : 0.118 0.456 264 Planarity : 0.017 0.155 300 Dihedral : 13.175 70.250 675 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Cbeta Deviations : 2.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.46 % 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: -3.44 (0.40), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.30), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.004 HIS A 374 PHE 0.021 0.006 PHE C 346 TYR 0.113 0.039 TYR A 310 ARG 0.003 0.001 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 317 LYS cc_start: 0.7438 (ptmt) cc_final: 0.6826 (ptpt) REVERT: B 321 LYS cc_start: 0.8183 (mtpt) cc_final: 0.7606 (mttp) REVERT: B 379 ARG cc_start: 0.7076 (ttt180) cc_final: 0.6286 (mmm-85) REVERT: C 311 LYS cc_start: 0.8273 (pttt) cc_final: 0.6798 (tppt) REVERT: C 317 LYS cc_start: 0.7407 (ptmt) cc_final: 0.7175 (ptpt) REVERT: C 321 LYS cc_start: 0.8264 (mtpt) cc_final: 0.7745 (mttp) REVERT: C 349 ARG cc_start: 0.8292 (ttp-170) cc_final: 0.7184 (mmp-170) REVERT: C 377 THR cc_start: 0.8204 (t) cc_final: 0.7915 (p) REVERT: A 321 LYS cc_start: 0.8617 (mtpt) cc_final: 0.8277 (mttp) REVERT: A 349 ARG cc_start: 0.8001 (ttp-170) cc_final: 0.7274 (ptt-90) REVERT: A 379 ARG cc_start: 0.7143 (ttt180) cc_final: 0.6646 (mmp-170) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 2.2054 time to fit residues: 159.1814 Evaluate side-chains 35 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 1761 Z= 0.254 Angle : 0.804 7.895 2355 Z= 0.429 Chirality : 0.052 0.131 264 Planarity : 0.004 0.040 300 Dihedral : 8.136 28.734 234 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 5.56 % Allowed : 21.72 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.42), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.32), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS A 374 PHE 0.002 0.001 PHE B 346 TYR 0.015 0.003 TYR B 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 39 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 305 SER cc_start: 0.7101 (OUTLIER) cc_final: 0.6885 (p) REVERT: B 306 VAL cc_start: 0.8118 (OUTLIER) cc_final: 0.7848 (p) REVERT: B 379 ARG cc_start: 0.7027 (ttt180) cc_final: 0.6379 (mmm-85) REVERT: C 315 LEU cc_start: 0.8241 (tt) cc_final: 0.7960 (mp) REVERT: C 379 ARG cc_start: 0.7112 (ttt180) cc_final: 0.6221 (ttp-170) REVERT: A 306 VAL cc_start: 0.8217 (OUTLIER) cc_final: 0.7896 (p) REVERT: A 321 LYS cc_start: 0.8527 (mtpt) cc_final: 0.8217 (mttp) REVERT: A 343 LYS cc_start: 0.8003 (tttt) cc_final: 0.7733 (mtmm) REVERT: A 372 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7543 (tt0) outliers start: 11 outliers final: 6 residues processed: 47 average time/residue: 1.4668 time to fit residues: 70.8553 Evaluate side-chains 35 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 26 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 377 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 6 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.5541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1761 Z= 0.192 Angle : 0.690 5.737 2355 Z= 0.366 Chirality : 0.051 0.129 264 Planarity : 0.004 0.047 300 Dihedral : 6.843 22.759 234 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 6.06 % Allowed : 24.75 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.42), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.32), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.002 HIS B 374 PHE 0.003 0.001 PHE C 378 TYR 0.011 0.003 TYR C 310 ARG 0.001 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 29 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: B 306 VAL cc_start: 0.8102 (OUTLIER) cc_final: 0.7871 (p) REVERT: B 379 ARG cc_start: 0.7003 (ttt180) cc_final: 0.6695 (mmm160) REVERT: C 315 LEU cc_start: 0.8355 (tt) cc_final: 0.8018 (mp) REVERT: C 376 LEU cc_start: 0.8037 (mt) cc_final: 0.7743 (tt) REVERT: C 379 ARG cc_start: 0.6962 (ttt180) cc_final: 0.6160 (ttp-170) REVERT: A 306 VAL cc_start: 0.8299 (OUTLIER) cc_final: 0.7983 (p) REVERT: A 321 LYS cc_start: 0.8519 (mtpt) cc_final: 0.8246 (mttp) REVERT: A 343 LYS cc_start: 0.8099 (tttt) cc_final: 0.7804 (mtmm) outliers start: 12 outliers final: 2 residues processed: 37 average time/residue: 1.9146 time to fit residues: 72.5029 Evaluate side-chains 27 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 23 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 377 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 0.0870 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.5763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1761 Z= 0.205 Angle : 0.668 5.083 2355 Z= 0.357 Chirality : 0.050 0.126 264 Planarity : 0.004 0.050 300 Dihedral : 6.392 23.462 234 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.26 % Favored : 88.74 % Rotamer: Outliers : 4.55 % Allowed : 26.26 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.43), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.32), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS B 374 PHE 0.005 0.001 PHE C 378 TYR 0.009 0.002 TYR B 310 ARG 0.002 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 27 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: B 306 VAL cc_start: 0.8090 (OUTLIER) cc_final: 0.7852 (p) REVERT: B 349 ARG cc_start: 0.7788 (ttp-170) cc_final: 0.7500 (ttm110) REVERT: B 379 ARG cc_start: 0.7075 (ttt180) cc_final: 0.6606 (mmm160) REVERT: C 315 LEU cc_start: 0.8365 (tt) cc_final: 0.8102 (mp) REVERT: C 379 ARG cc_start: 0.6959 (ttt180) cc_final: 0.6148 (ttp-170) REVERT: A 306 VAL cc_start: 0.8295 (OUTLIER) cc_final: 0.7998 (p) REVERT: A 321 LYS cc_start: 0.8515 (mtpt) cc_final: 0.8231 (mttp) REVERT: A 379 ARG cc_start: 0.5275 (mmp-170) cc_final: 0.5000 (mmp80) outliers start: 9 outliers final: 4 residues processed: 32 average time/residue: 2.1622 time to fit residues: 70.6439 Evaluate side-chains 26 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 20 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 377 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 18 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.6145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1761 Z= 0.162 Angle : 0.627 5.382 2355 Z= 0.327 Chirality : 0.049 0.125 264 Planarity : 0.004 0.045 300 Dihedral : 5.990 20.023 234 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 3.03 % Allowed : 29.29 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.42), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.32), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 374 PHE 0.002 0.001 PHE B 346 TYR 0.004 0.001 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) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 24 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: B 306 VAL cc_start: 0.8095 (OUTLIER) cc_final: 0.7862 (p) REVERT: B 349 ARG cc_start: 0.7731 (ttp-170) cc_final: 0.7530 (ttm110) REVERT: B 379 ARG cc_start: 0.7091 (ttt180) cc_final: 0.6600 (mmm160) REVERT: C 315 LEU cc_start: 0.8399 (tt) cc_final: 0.8121 (mp) REVERT: C 379 ARG cc_start: 0.6939 (ttt180) cc_final: 0.6085 (ttp-170) REVERT: A 306 VAL cc_start: 0.8294 (OUTLIER) cc_final: 0.8004 (p) REVERT: A 379 ARG cc_start: 0.5161 (mmp-170) cc_final: 0.4881 (mmp80) outliers start: 6 outliers final: 1 residues processed: 25 average time/residue: 2.0444 time to fit residues: 52.3501 Evaluate side-chains 22 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 19 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain A residue 306 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 2 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.6307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1761 Z= 0.147 Angle : 0.592 4.025 2355 Z= 0.310 Chirality : 0.049 0.126 264 Planarity : 0.004 0.040 300 Dihedral : 5.595 21.109 234 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 2.02 % Allowed : 28.79 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.42), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.32), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 374 PHE 0.005 0.001 PHE A 378 TYR 0.014 0.002 TYR C 310 ARG 0.001 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 21 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: B 306 VAL cc_start: 0.8064 (OUTLIER) cc_final: 0.7828 (p) REVERT: B 349 ARG cc_start: 0.7601 (ttp-170) cc_final: 0.7400 (ttm110) REVERT: B 379 ARG cc_start: 0.6972 (ttt180) cc_final: 0.6559 (mmm160) REVERT: C 315 LEU cc_start: 0.8394 (tt) cc_final: 0.8172 (mp) REVERT: C 379 ARG cc_start: 0.6885 (ttt180) cc_final: 0.6116 (ttp-170) REVERT: A 306 VAL cc_start: 0.8280 (OUTLIER) cc_final: 0.7982 (p) REVERT: A 379 ARG cc_start: 0.5136 (mmp-170) cc_final: 0.4812 (mmp80) outliers start: 4 outliers final: 2 residues processed: 22 average time/residue: 2.2253 time to fit residues: 50.0959 Evaluate side-chains 23 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 19 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain A residue 306 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 10 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.6381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1761 Z= 0.169 Angle : 0.584 3.813 2355 Z= 0.308 Chirality : 0.049 0.121 264 Planarity : 0.004 0.041 300 Dihedral : 5.598 18.918 234 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 3.03 % Allowed : 27.78 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.42), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.32), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 374 PHE 0.002 0.001 PHE A 378 TYR 0.008 0.002 TYR C 310 ARG 0.002 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 21 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: B 306 VAL cc_start: 0.8110 (OUTLIER) cc_final: 0.7886 (p) REVERT: B 379 ARG cc_start: 0.6959 (ttt180) cc_final: 0.6524 (mmm160) REVERT: C 315 LEU cc_start: 0.8392 (tt) cc_final: 0.8157 (mp) REVERT: C 379 ARG cc_start: 0.6896 (ttt180) cc_final: 0.6035 (ttp-170) REVERT: A 306 VAL cc_start: 0.8258 (OUTLIER) cc_final: 0.7962 (p) REVERT: A 379 ARG cc_start: 0.5152 (mmp-170) cc_final: 0.4806 (mmp80) outliers start: 6 outliers final: 3 residues processed: 23 average time/residue: 2.3656 time to fit residues: 55.6150 Evaluate side-chains 24 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 19 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 320 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 19 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 16 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.6551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1761 Z= 0.154 Angle : 0.578 4.070 2355 Z= 0.302 Chirality : 0.049 0.122 264 Planarity : 0.004 0.038 300 Dihedral : 5.440 19.698 234 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.54 % Allowed : 27.27 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.43), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.32), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 374 PHE 0.002 0.001 PHE A 378 TYR 0.006 0.001 TYR C 310 ARG 0.003 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 22 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: B 306 VAL cc_start: 0.8112 (OUTLIER) cc_final: 0.7886 (p) REVERT: B 379 ARG cc_start: 0.6941 (ttt180) cc_final: 0.6516 (mmm160) REVERT: C 379 ARG cc_start: 0.6921 (ttt180) cc_final: 0.6023 (ttp-110) REVERT: A 306 VAL cc_start: 0.8236 (OUTLIER) cc_final: 0.7942 (p) REVERT: A 379 ARG cc_start: 0.5311 (mmp-170) cc_final: 0.4944 (mmp80) outliers start: 7 outliers final: 3 residues processed: 25 average time/residue: 1.9227 time to fit residues: 49.3761 Evaluate side-chains 25 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 20 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 320 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 2 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.6605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 1761 Z= 0.144 Angle : 0.557 4.941 2355 Z= 0.290 Chirality : 0.049 0.123 264 Planarity : 0.005 0.056 300 Dihedral : 5.327 18.675 234 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.03 % Allowed : 27.78 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.43), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 374 PHE 0.002 0.001 PHE B 346 TYR 0.006 0.001 TYR C 310 ARG 0.011 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 20 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: B 379 ARG cc_start: 0.6896 (ttt180) cc_final: 0.6594 (mpt90) REVERT: C 349 ARG cc_start: 0.7888 (ttm170) cc_final: 0.7612 (ttm110) REVERT: C 379 ARG cc_start: 0.6824 (ttt180) cc_final: 0.5976 (ttp-110) REVERT: A 306 VAL cc_start: 0.8253 (OUTLIER) cc_final: 0.7963 (p) REVERT: A 379 ARG cc_start: 0.5238 (mmp-170) cc_final: 0.4931 (mmp80) outliers start: 6 outliers final: 3 residues processed: 23 average time/residue: 2.1000 time to fit residues: 49.4970 Evaluate side-chains 23 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 19 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 320 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 14 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.6617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1761 Z= 0.175 Angle : 0.571 3.477 2355 Z= 0.302 Chirality : 0.049 0.122 264 Planarity : 0.004 0.040 300 Dihedral : 5.412 19.783 234 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 2.02 % Allowed : 28.28 % Favored : 69.70 % 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: -3.55 (0.43), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 374 PHE 0.002 0.001 PHE B 378 TYR 0.009 0.002 TYR C 310 ARG 0.004 0.001 ARG B 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 19 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: B 379 ARG cc_start: 0.6872 (ttt180) cc_final: 0.6383 (mmm160) REVERT: C 379 ARG cc_start: 0.6832 (ttt180) cc_final: 0.5948 (ttp-110) REVERT: A 306 VAL cc_start: 0.8322 (OUTLIER) cc_final: 0.8083 (p) REVERT: A 379 ARG cc_start: 0.5221 (mmp-170) cc_final: 0.4880 (mmp80) outliers start: 4 outliers final: 3 residues processed: 22 average time/residue: 2.0926 time to fit residues: 47.4161 Evaluate side-chains 23 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 19 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 320 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 19 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.131466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.116554 restraints weight = 7116.335| |-----------------------------------------------------------------------------| r_work (start): 0.4437 rms_B_bonded: 2.67 r_work: 0.4352 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.4256 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.4256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.6625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1761 Z= 0.186 Angle : 0.590 5.019 2355 Z= 0.310 Chirality : 0.049 0.126 264 Planarity : 0.005 0.062 300 Dihedral : 5.529 19.204 234 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 2.02 % Allowed : 28.28 % Favored : 69.70 % 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: -3.55 (0.44), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 374 PHE 0.003 0.001 PHE B 378 TYR 0.009 0.002 TYR C 310 ARG 0.013 0.001 ARG B 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2900.58 seconds wall clock time: 51 minutes 25.86 seconds (3085.86 seconds total)