Starting phenix.real_space_refine on Tue Feb 13 06:00:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cax_16535/02_2024/8cax_16535.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cax_16535/02_2024/8cax_16535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cax_16535/02_2024/8cax_16535.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cax_16535/02_2024/8cax_16535.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cax_16535/02_2024/8cax_16535.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cax_16535/02_2024/8cax_16535.pdb" } resolution = 3.7 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: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2160 2.51 5 N 636 2.21 5 O 642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A ARG 379": "NH1" <-> "NH2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 349": "NH1" <-> "NH2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "B ARG 379": "NH1" <-> "NH2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 349": "NH1" <-> "NH2" Residue "C GLU 372": "OE1" <-> "OE2" Residue "C ARG 379": "NH1" <-> "NH2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 349": "NH1" <-> "NH2" Residue "D GLU 372": "OE1" <-> "OE2" Residue "D ARG 379": "NH1" <-> "NH2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 349": "NH1" <-> "NH2" Residue "E GLU 372": "OE1" <-> "OE2" Residue "E ARG 379": "NH1" <-> "NH2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 349": "NH1" <-> "NH2" Residue "F GLU 372": "OE1" <-> "OE2" Residue "F ARG 379": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 3444 Number of models: 1 Model: "" Number of chains: 6 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} Chain: "B" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 2.29, per 1000 atoms: 0.66 Number of scatterers: 3444 At special positions: 0 Unit cell: (130.192, 119.48, 37.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 642 8.00 N 636 7.00 C 2160 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 - 3.50 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: 1.19 Conformation dependent library (CDL) restraints added in 637.9 milliseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 308 removed outlier: 6.833A pdb=" N GLN A 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLN E 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.927A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL E 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 321 through 325 removed outlier: 8.973A pdb=" N CYS A 322 " --> pdb=" O GLY B 323 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU B 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N SER A 324 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER E 324 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU A 325 " --> pdb=" O SER E 324 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER F 324 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU E 325 " --> pdb=" O SER F 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 337 through 339 removed outlier: 6.439A pdb=" N VAL A 337 " --> pdb=" O GLU B 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 342 through 346 removed outlier: 6.125A pdb=" N GLU A 342 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N ASP B 345 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU A 344 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LYS A 343 " --> pdb=" O GLU E 342 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LYS E 343 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 350 through 351 removed outlier: 6.351A pdb=" N VAL A 350 " --> pdb=" O GLN B 351 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 354 through 357 removed outlier: 6.131A pdb=" N ILE A 354 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU B 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SER A 356 " --> pdb=" O LEU B 357 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 306 through 308 removed outlier: 6.833A pdb=" N GLN C 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.927A pdb=" N VAL C 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 321 through 325 removed outlier: 6.728A pdb=" N SER D 324 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU C 325 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 337 through 339 Processing sheet with id=AB3, first strand: chain 'C' and resid 342 through 346 removed outlier: 6.838A pdb=" N LYS C 343 " --> pdb=" O GLU D 342 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 350 through 351 Processing sheet with id=AB5, first strand: chain 'C' and resid 354 through 357 36 hydrogen bonds defined for protein. 108 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: 0.72 Time building geometry restraints manager: 1.31 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: 990 1.34 - 1.46: 739 1.46 - 1.58: 1763 1.58 - 1.70: 0 1.70 - 1.82: 6 Bond restraints: 3498 Sorted by residual: bond pdb=" CG HIS B 330 " pdb=" CD2 HIS B 330 " ideal model delta sigma weight residual 1.354 1.311 0.043 1.10e-02 8.26e+03 1.50e+01 bond pdb=" CG HIS F 330 " pdb=" CD2 HIS F 330 " ideal model delta sigma weight residual 1.354 1.312 0.042 1.10e-02 8.26e+03 1.49e+01 bond pdb=" CG HIS D 330 " pdb=" CD2 HIS D 330 " ideal model delta sigma weight residual 1.354 1.312 0.042 1.10e-02 8.26e+03 1.48e+01 bond pdb=" CG HIS E 330 " pdb=" CD2 HIS E 330 " ideal model delta sigma weight residual 1.354 1.312 0.042 1.10e-02 8.26e+03 1.46e+01 bond pdb=" CG HIS C 330 " pdb=" CD2 HIS C 330 " ideal model delta sigma weight residual 1.354 1.312 0.042 1.10e-02 8.26e+03 1.45e+01 ... (remaining 3493 not shown) Histogram of bond angle deviations from ideal: 101.80 - 108.38: 331 108.38 - 114.96: 1880 114.96 - 121.54: 1602 121.54 - 128.11: 837 128.11 - 134.69: 30 Bond angle restraints: 4680 Sorted by residual: angle pdb=" C HIS C 362 " pdb=" CA HIS C 362 " pdb=" CB HIS C 362 " ideal model delta sigma weight residual 109.84 121.10 -11.26 1.63e+00 3.76e-01 4.77e+01 angle pdb=" C HIS D 362 " pdb=" CA HIS D 362 " pdb=" CB HIS D 362 " ideal model delta sigma weight residual 109.84 121.09 -11.25 1.63e+00 3.76e-01 4.76e+01 angle pdb=" C HIS E 362 " pdb=" CA HIS E 362 " pdb=" CB HIS E 362 " ideal model delta sigma weight residual 109.84 121.09 -11.25 1.63e+00 3.76e-01 4.76e+01 angle pdb=" C HIS B 362 " pdb=" CA HIS B 362 " pdb=" CB HIS B 362 " ideal model delta sigma weight residual 109.84 121.07 -11.23 1.63e+00 3.76e-01 4.75e+01 angle pdb=" C HIS A 362 " pdb=" CA HIS A 362 " pdb=" CB HIS A 362 " ideal model delta sigma weight residual 109.84 121.07 -11.23 1.63e+00 3.76e-01 4.75e+01 ... (remaining 4675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.41: 1619 11.41 - 22.81: 350 22.81 - 34.21: 113 34.21 - 45.62: 42 45.62 - 57.02: 12 Dihedral angle restraints: 2136 sinusoidal: 894 harmonic: 1242 Sorted by residual: dihedral pdb=" CA GLY B 326 " pdb=" C GLY B 326 " pdb=" N ASN B 327 " pdb=" CA ASN B 327 " ideal model delta harmonic sigma weight residual 180.00 143.47 36.53 0 5.00e+00 4.00e-02 5.34e+01 dihedral pdb=" CA GLY E 326 " pdb=" C GLY E 326 " pdb=" N ASN E 327 " pdb=" CA ASN E 327 " ideal model delta harmonic sigma weight residual 180.00 143.49 36.51 0 5.00e+00 4.00e-02 5.33e+01 dihedral pdb=" CA GLY D 326 " pdb=" C GLY D 326 " pdb=" N ASN D 327 " pdb=" CA ASN D 327 " ideal model delta harmonic sigma weight residual 180.00 143.50 36.50 0 5.00e+00 4.00e-02 5.33e+01 ... (remaining 2133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 193 0.045 - 0.089: 137 0.089 - 0.134: 99 0.134 - 0.179: 87 0.179 - 0.223: 12 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA HIS B 362 " pdb=" N HIS B 362 " pdb=" C HIS B 362 " pdb=" CB HIS B 362 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA HIS E 362 " pdb=" N HIS E 362 " pdb=" C HIS E 362 " pdb=" CB HIS E 362 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA HIS D 362 " pdb=" N HIS D 362 " pdb=" C HIS D 362 " pdb=" CB HIS D 362 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 525 not shown) Planarity restraints: 594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " 0.024 2.00e-02 2.50e+03 1.57e-02 4.95e+00 pdb=" CG TYR E 310 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 310 " 0.024 2.00e-02 2.50e+03 1.57e-02 4.91e+00 pdb=" CG TYR B 310 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR B 310 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR B 310 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 310 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 310 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 310 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 310 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " 0.024 2.00e-02 2.50e+03 1.56e-02 4.89e+00 pdb=" CG TYR A 310 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " 0.003 2.00e-02 2.50e+03 ... (remaining 591 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 648 2.80 - 3.32: 3342 3.32 - 3.85: 5056 3.85 - 4.37: 6045 4.37 - 4.90: 11475 Nonbonded interactions: 26566 Sorted by model distance: nonbonded pdb=" OG SER B 316 " pdb=" NZ LYS B 370 " model vdw 2.271 2.520 nonbonded pdb=" OG SER D 316 " pdb=" NZ LYS D 370 " model vdw 2.271 2.520 nonbonded pdb=" OG SER F 316 " pdb=" NZ LYS F 370 " model vdw 2.271 2.520 nonbonded pdb=" OG SER A 316 " pdb=" NZ LYS A 370 " model vdw 2.271 2.520 nonbonded pdb=" OG SER E 316 " pdb=" NZ LYS E 370 " model vdw 2.271 2.520 ... (remaining 26561 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' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.500 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.650 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 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 0.043 3498 Z= 0.598 Angle : 1.646 11.259 4680 Z= 1.069 Chirality : 0.092 0.223 528 Planarity : 0.009 0.040 594 Dihedral : 14.826 57.023 1344 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 4.55 % Allowed : 7.58 % Favored : 87.88 % Cbeta Deviations : 1.52 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.41 % 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: -3.97 (0.25), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.19), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.005 HIS E 330 PHE 0.015 0.003 PHE D 378 TYR 0.036 0.010 TYR E 310 ARG 0.004 0.001 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 183 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 LYS cc_start: 0.9051 (tttt) cc_final: 0.8834 (tttp) REVERT: B 310 TYR cc_start: 0.8145 (t80) cc_final: 0.7858 (t80) REVERT: B 346 PHE cc_start: 0.8797 (m-80) cc_final: 0.7886 (p90) REVERT: B 369 LYS cc_start: 0.8704 (mttt) cc_final: 0.8488 (ttmt) REVERT: C 310 TYR cc_start: 0.8172 (t80) cc_final: 0.7787 (t80) REVERT: C 345 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8053 (t0) REVERT: C 346 PHE cc_start: 0.8834 (m-80) cc_final: 0.8070 (p90) REVERT: D 349 ARG cc_start: 0.8905 (mtt180) cc_final: 0.8204 (pmt-80) REVERT: D 372 GLU cc_start: 0.8531 (tt0) cc_final: 0.8157 (mp0) REVERT: D 375 LYS cc_start: 0.9126 (tttt) cc_final: 0.8838 (tttp) REVERT: E 308 ILE cc_start: 0.9394 (mt) cc_final: 0.9117 (mp) REVERT: E 310 TYR cc_start: 0.8050 (t80) cc_final: 0.7797 (t80) REVERT: E 369 LYS cc_start: 0.8715 (mttt) cc_final: 0.8504 (ttpt) REVERT: E 372 GLU cc_start: 0.8734 (tt0) cc_final: 0.8312 (mp0) REVERT: E 375 LYS cc_start: 0.9018 (tttt) cc_final: 0.8741 (tttm) REVERT: E 378 PHE cc_start: 0.8799 (t80) cc_final: 0.8491 (t80) REVERT: F 343 LYS cc_start: 0.9041 (mttm) cc_final: 0.8508 (tmmt) REVERT: F 349 ARG cc_start: 0.8745 (mtt180) cc_final: 0.7988 (ptt-90) outliers start: 18 outliers final: 6 residues processed: 189 average time/residue: 0.2203 time to fit residues: 47.2810 Evaluate side-chains 110 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 103 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 345 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 HIS ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 HIS D 330 HIS D 336 GLN ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3498 Z= 0.217 Angle : 0.700 6.609 4680 Z= 0.360 Chirality : 0.049 0.137 528 Planarity : 0.006 0.048 594 Dihedral : 7.381 49.170 476 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.79 % Allowed : 19.19 % Favored : 77.02 % 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 (0.27), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.21), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 374 PHE 0.015 0.002 PHE F 346 TYR 0.013 0.002 TYR A 310 ARG 0.002 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 LYS cc_start: 0.9474 (tptm) cc_final: 0.9105 (mmtm) REVERT: B 336 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8415 (tp40) REVERT: B 346 PHE cc_start: 0.8965 (m-80) cc_final: 0.7841 (p90) REVERT: C 310 TYR cc_start: 0.7784 (t80) cc_final: 0.7245 (t80) REVERT: C 336 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8178 (tp40) REVERT: C 346 PHE cc_start: 0.8792 (m-80) cc_final: 0.7822 (p90) REVERT: D 372 GLU cc_start: 0.8497 (tt0) cc_final: 0.8031 (mp0) REVERT: D 376 LEU cc_start: 0.8613 (tp) cc_final: 0.8339 (tt) REVERT: E 310 TYR cc_start: 0.7927 (t80) cc_final: 0.7392 (t80) REVERT: E 369 LYS cc_start: 0.8576 (mttt) cc_final: 0.8361 (ttpt) REVERT: E 372 GLU cc_start: 0.8708 (tt0) cc_final: 0.8362 (mp0) outliers start: 15 outliers final: 11 residues processed: 131 average time/residue: 0.1562 time to fit residues: 24.6545 Evaluate side-chains 106 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 28 optimal weight: 30.0000 chunk 19 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN C 359 ASN D 359 ASN E 336 GLN ** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 HIS F 336 GLN ** F 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3498 Z= 0.204 Angle : 0.724 11.688 4680 Z= 0.341 Chirality : 0.049 0.128 528 Planarity : 0.005 0.045 594 Dihedral : 6.308 51.945 468 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.55 % Allowed : 19.19 % Favored : 76.26 % 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: -3.01 (0.28), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.21), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS C 330 PHE 0.014 0.001 PHE E 378 TYR 0.014 0.003 TYR A 310 ARG 0.002 0.001 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 336 GLN cc_start: 0.8627 (tm-30) cc_final: 0.8377 (tp40) REVERT: B 345 ASP cc_start: 0.8694 (t0) cc_final: 0.8377 (t0) REVERT: B 346 PHE cc_start: 0.9014 (m-80) cc_final: 0.7844 (p90) REVERT: C 310 TYR cc_start: 0.7630 (t80) cc_final: 0.7095 (t80) REVERT: C 346 PHE cc_start: 0.8860 (m-80) cc_final: 0.7864 (p90) REVERT: D 372 GLU cc_start: 0.8581 (tt0) cc_final: 0.8141 (mp0) REVERT: D 376 LEU cc_start: 0.8590 (tp) cc_final: 0.8282 (tt) REVERT: E 372 GLU cc_start: 0.8688 (tt0) cc_final: 0.8253 (mp0) REVERT: F 310 TYR cc_start: 0.7409 (t80) cc_final: 0.7055 (m-80) outliers start: 18 outliers final: 14 residues processed: 114 average time/residue: 0.1106 time to fit residues: 16.1588 Evaluate side-chains 108 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 325 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS D 336 GLN ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 GLN ** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.5727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3498 Z= 0.336 Angle : 0.799 13.499 4680 Z= 0.378 Chirality : 0.050 0.136 528 Planarity : 0.005 0.040 594 Dihedral : 6.724 53.867 468 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 4.04 % Allowed : 22.22 % Favored : 73.74 % 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: -3.06 (0.28), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.21), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS A 330 PHE 0.018 0.002 PHE D 378 TYR 0.020 0.004 TYR A 310 ARG 0.003 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 LEU cc_start: 0.9287 (mp) cc_final: 0.9038 (mt) REVERT: B 310 TYR cc_start: 0.7359 (t80) cc_final: 0.6798 (p90) REVERT: B 336 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8384 (tp40) REVERT: B 345 ASP cc_start: 0.8785 (t0) cc_final: 0.8458 (t0) REVERT: B 346 PHE cc_start: 0.9062 (m-80) cc_final: 0.8023 (p90) REVERT: C 310 TYR cc_start: 0.7657 (t80) cc_final: 0.7229 (t80) REVERT: C 346 PHE cc_start: 0.8850 (m-80) cc_final: 0.8016 (p90) REVERT: D 372 GLU cc_start: 0.8747 (tt0) cc_final: 0.8324 (mp0) REVERT: E 372 GLU cc_start: 0.8802 (tt0) cc_final: 0.8368 (mp0) outliers start: 16 outliers final: 14 residues processed: 104 average time/residue: 0.1116 time to fit residues: 14.9962 Evaluate side-chains 101 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 345 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 36 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 23 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 HIS ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.6108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 3498 Z= 0.326 Angle : 0.806 13.869 4680 Z= 0.380 Chirality : 0.051 0.138 528 Planarity : 0.005 0.039 594 Dihedral : 6.966 58.128 468 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 4.55 % Allowed : 21.97 % Favored : 73.48 % 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: -3.06 (0.28), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.21), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS A 330 PHE 0.020 0.002 PHE E 378 TYR 0.016 0.004 TYR A 310 ARG 0.004 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: B 310 TYR cc_start: 0.7430 (t80) cc_final: 0.6910 (p90) REVERT: B 336 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8332 (tp40) REVERT: B 345 ASP cc_start: 0.8890 (t0) cc_final: 0.8519 (t0) REVERT: B 346 PHE cc_start: 0.9085 (m-80) cc_final: 0.7915 (p90) REVERT: B 358 ASP cc_start: 0.8818 (t0) cc_final: 0.8588 (t0) REVERT: C 310 TYR cc_start: 0.7749 (t80) cc_final: 0.7421 (t80) REVERT: C 346 PHE cc_start: 0.8864 (m-80) cc_final: 0.8033 (p90) REVERT: D 311 LYS cc_start: 0.3648 (OUTLIER) cc_final: 0.3315 (pptt) REVERT: D 372 GLU cc_start: 0.8718 (tt0) cc_final: 0.8402 (mp0) REVERT: E 372 GLU cc_start: 0.8777 (tt0) cc_final: 0.8427 (mp0) REVERT: F 306 VAL cc_start: 0.9413 (t) cc_final: 0.9112 (p) outliers start: 18 outliers final: 16 residues processed: 107 average time/residue: 0.1100 time to fit residues: 15.2281 Evaluate side-chains 104 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 345 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 HIS E 307 GLN F 336 GLN F 362 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.6435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3498 Z= 0.191 Angle : 0.781 14.374 4680 Z= 0.349 Chirality : 0.050 0.137 528 Planarity : 0.004 0.038 594 Dihedral : 6.536 57.680 468 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.54 % Allowed : 25.51 % Favored : 70.96 % 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: -2.82 (0.29), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.22), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 330 PHE 0.021 0.002 PHE D 378 TYR 0.009 0.002 TYR A 310 ARG 0.003 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: B 336 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8340 (tp40) REVERT: B 345 ASP cc_start: 0.8894 (t0) cc_final: 0.8592 (t0) REVERT: B 346 PHE cc_start: 0.9090 (m-80) cc_final: 0.7883 (p90) REVERT: B 358 ASP cc_start: 0.8767 (t0) cc_final: 0.8516 (t0) REVERT: C 310 TYR cc_start: 0.7475 (t80) cc_final: 0.7123 (t80) REVERT: C 346 PHE cc_start: 0.8838 (m-80) cc_final: 0.8036 (p90) REVERT: D 311 LYS cc_start: 0.3769 (OUTLIER) cc_final: 0.3502 (pptt) REVERT: D 372 GLU cc_start: 0.8696 (tt0) cc_final: 0.8308 (mp0) REVERT: E 372 GLU cc_start: 0.8704 (tt0) cc_final: 0.8434 (mp0) REVERT: F 310 TYR cc_start: 0.7649 (OUTLIER) cc_final: 0.7347 (m-80) REVERT: F 336 GLN cc_start: 0.8834 (tm130) cc_final: 0.8187 (pm20) outliers start: 14 outliers final: 10 residues processed: 104 average time/residue: 0.1188 time to fit residues: 16.0497 Evaluate side-chains 101 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain F residue 310 TYR Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 345 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 HIS ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.6728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3498 Z= 0.292 Angle : 0.835 15.241 4680 Z= 0.380 Chirality : 0.050 0.139 528 Planarity : 0.005 0.036 594 Dihedral : 6.235 55.216 466 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 4.29 % Allowed : 24.75 % Favored : 70.96 % 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: -2.80 (0.30), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS A 330 PHE 0.022 0.002 PHE E 378 TYR 0.015 0.003 TYR A 310 ARG 0.004 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: B 336 GLN cc_start: 0.8746 (tm-30) cc_final: 0.8323 (tp40) REVERT: C 310 TYR cc_start: 0.7766 (t80) cc_final: 0.7461 (t80) REVERT: C 346 PHE cc_start: 0.8826 (m-80) cc_final: 0.8048 (p90) REVERT: D 311 LYS cc_start: 0.3589 (OUTLIER) cc_final: 0.3284 (pptt) REVERT: D 372 GLU cc_start: 0.8746 (tt0) cc_final: 0.8391 (mp0) REVERT: E 372 GLU cc_start: 0.8754 (tt0) cc_final: 0.8475 (mp0) REVERT: F 310 TYR cc_start: 0.7772 (OUTLIER) cc_final: 0.7346 (m-80) REVERT: F 311 LYS cc_start: 0.4081 (OUTLIER) cc_final: 0.3634 (pptt) outliers start: 17 outliers final: 13 residues processed: 102 average time/residue: 0.1132 time to fit residues: 14.8939 Evaluate side-chains 103 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 87 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain F residue 310 TYR Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 379 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.6864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3498 Z= 0.249 Angle : 0.832 14.507 4680 Z= 0.373 Chirality : 0.050 0.140 528 Planarity : 0.005 0.037 594 Dihedral : 6.155 56.897 466 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 4.29 % Allowed : 24.49 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.30), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 330 PHE 0.017 0.001 PHE D 378 TYR 0.011 0.002 TYR A 310 ARG 0.003 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 0.450 Fit side-chains REVERT: B 336 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8316 (tp40) REVERT: C 310 TYR cc_start: 0.7560 (t80) cc_final: 0.7289 (t80) REVERT: C 346 PHE cc_start: 0.8831 (m-80) cc_final: 0.8018 (p90) REVERT: D 311 LYS cc_start: 0.3762 (OUTLIER) cc_final: 0.3491 (pptt) REVERT: D 372 GLU cc_start: 0.8757 (tt0) cc_final: 0.8381 (mp0) REVERT: E 372 GLU cc_start: 0.8680 (tt0) cc_final: 0.8438 (mp0) REVERT: F 310 TYR cc_start: 0.7757 (OUTLIER) cc_final: 0.7338 (m-80) REVERT: F 311 LYS cc_start: 0.4195 (OUTLIER) cc_final: 0.3629 (pptt) outliers start: 17 outliers final: 13 residues processed: 104 average time/residue: 0.1127 time to fit residues: 15.1545 Evaluate side-chains 103 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 87 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain F residue 310 TYR Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 379 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS F 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.7179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 3498 Z= 0.317 Angle : 0.870 15.036 4680 Z= 0.399 Chirality : 0.051 0.144 528 Planarity : 0.005 0.037 594 Dihedral : 6.410 56.829 466 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 4.04 % Allowed : 25.00 % Favored : 70.96 % 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: -2.73 (0.31), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS A 330 PHE 0.023 0.002 PHE E 378 TYR 0.017 0.003 TYR A 310 ARG 0.005 0.001 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 0.453 Fit side-chains REVERT: A 372 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8503 (mp0) REVERT: B 336 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8284 (tp40) REVERT: C 310 TYR cc_start: 0.7811 (t80) cc_final: 0.7567 (t80) REVERT: C 346 PHE cc_start: 0.8834 (m-80) cc_final: 0.8009 (p90) REVERT: C 372 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8276 (mp0) REVERT: D 311 LYS cc_start: 0.3596 (OUTLIER) cc_final: 0.3362 (pptt) REVERT: D 372 GLU cc_start: 0.8808 (tt0) cc_final: 0.8448 (mp0) REVERT: E 372 GLU cc_start: 0.8763 (tt0) cc_final: 0.8440 (mp0) REVERT: F 310 TYR cc_start: 0.7852 (OUTLIER) cc_final: 0.7445 (m-80) REVERT: F 311 LYS cc_start: 0.3942 (OUTLIER) cc_final: 0.3428 (pptt) REVERT: F 336 GLN cc_start: 0.8819 (tm130) cc_final: 0.8214 (pm20) outliers start: 16 outliers final: 13 residues processed: 96 average time/residue: 0.1063 time to fit residues: 13.5121 Evaluate side-chains 96 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 80 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain F residue 310 TYR Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 379 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.7244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3498 Z= 0.241 Angle : 0.880 16.080 4680 Z= 0.391 Chirality : 0.051 0.144 528 Planarity : 0.005 0.039 594 Dihedral : 6.208 59.492 466 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 4.04 % Allowed : 26.26 % 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: -2.71 (0.31), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 330 PHE 0.017 0.001 PHE D 378 TYR 0.013 0.002 TYR A 310 ARG 0.005 0.001 ARG B 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 0.388 Fit side-chains REVERT: A 372 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8523 (mp0) REVERT: A 378 PHE cc_start: 0.8510 (t80) cc_final: 0.8214 (t80) REVERT: B 336 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8287 (tp40) REVERT: C 310 TYR cc_start: 0.7704 (t80) cc_final: 0.7441 (t80) REVERT: C 346 PHE cc_start: 0.8819 (m-80) cc_final: 0.7978 (p90) REVERT: C 372 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8301 (mp0) REVERT: D 311 LYS cc_start: 0.3752 (OUTLIER) cc_final: 0.3505 (pptt) REVERT: D 372 GLU cc_start: 0.8804 (tt0) cc_final: 0.8539 (mp0) REVERT: E 372 GLU cc_start: 0.8719 (tt0) cc_final: 0.8512 (mp0) REVERT: F 310 TYR cc_start: 0.7898 (OUTLIER) cc_final: 0.7505 (m-80) REVERT: F 311 LYS cc_start: 0.4112 (OUTLIER) cc_final: 0.3590 (pptt) outliers start: 16 outliers final: 12 residues processed: 95 average time/residue: 0.1000 time to fit residues: 12.5891 Evaluate side-chains 99 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain F residue 310 TYR Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 345 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.118652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.100599 restraints weight = 8334.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.102699 restraints weight = 4280.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.104151 restraints weight = 2808.922| |-----------------------------------------------------------------------------| r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.7361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3498 Z= 0.241 Angle : 0.863 16.348 4680 Z= 0.382 Chirality : 0.050 0.140 528 Planarity : 0.005 0.038 594 Dihedral : 6.066 57.421 466 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 3.79 % Allowed : 26.26 % Favored : 69.95 % 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: -2.70 (0.31), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 330 PHE 0.024 0.002 PHE E 378 TYR 0.013 0.002 TYR A 310 ARG 0.005 0.001 ARG B 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1112.23 seconds wall clock time: 21 minutes 13.35 seconds (1273.35 seconds total)