Starting phenix.real_space_refine on Fri Aug 2 16:09:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zx6_60539/08_2024/8zx6_60539.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zx6_60539/08_2024/8zx6_60539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zx6_60539/08_2024/8zx6_60539.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zx6_60539/08_2024/8zx6_60539.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zx6_60539/08_2024/8zx6_60539.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zx6_60539/08_2024/8zx6_60539.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2172 2.51 5 N 642 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 342": "OE1" <-> "OE2" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 342": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 3468 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "C" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "B" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "E" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "D" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "F" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Time building chain proxies: 2.65, per 1000 atoms: 0.76 Number of scatterers: 3468 At special positions: 0 Unit cell: (155.21, 83.83, 34.86, 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 648 8.00 N 642 7.00 C 2172 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 1.3 seconds 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 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 20 sheets defined 0.0% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310 removed outlier: 6.678A pdb=" N GLN A 307 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N TYR B 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL A 309 " --> pdb=" O TYR B 310 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.879A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 318 removed outlier: 6.830A pdb=" N LYS A 317 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LYS B 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 322 removed outlier: 6.356A pdb=" N LYS A 321 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS B 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 337 through 338 Processing sheet with id=AA6, first strand: chain 'A' and resid 345 through 346 removed outlier: 6.236A pdb=" N ASP A 345 " --> pdb=" O PHE B 346 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP B 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 353 through 354 removed outlier: 6.722A pdb=" N LYS A 353 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYS B 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 362 Processing sheet with id=AA9, first strand: chain 'A' and resid 369 through 371 removed outlier: 6.812A pdb=" N LYS A 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LYS B 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 377 Processing sheet with id=AB2, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.669A pdb=" N GLN C 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N TYR E 310 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL C 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLN E 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N TYR F 310 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL E 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.871A pdb=" N VAL C 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL E 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 317 through 318 removed outlier: 6.824A pdb=" N LYS C 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LYS E 317 " --> pdb=" O VAL F 318 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 321 through 322 removed outlier: 6.352A pdb=" N LYS C 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LYS E 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 337 through 338 Processing sheet with id=AB7, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.229A pdb=" N ASP C 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ASP E 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 353 through 354 removed outlier: 6.720A pdb=" N LYS C 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LYS E 353 " --> pdb=" O ILE F 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 359 through 362 Processing sheet with id=AC1, first strand: chain 'C' and resid 369 through 371 removed outlier: 6.806A pdb=" N LYS C 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LYS E 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 374 through 377 28 hydrogen bonds defined for protein. 84 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: 0.79 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: 1.23 - 1.34: 1146 1.34 - 1.46: 573 1.46 - 1.57: 1797 1.57 - 1.69: 0 1.69 - 1.80: 6 Bond restraints: 3522 Sorted by residual: bond pdb=" N LYS B 370 " pdb=" CA LYS B 370 " ideal model delta sigma weight residual 1.464 1.452 0.011 1.25e-02 6.40e+03 8.04e-01 bond pdb=" CA LYS E 370 " pdb=" C LYS E 370 " ideal model delta sigma weight residual 1.526 1.516 0.009 1.08e-02 8.57e+03 7.70e-01 bond pdb=" N LYS A 370 " pdb=" CA LYS A 370 " ideal model delta sigma weight residual 1.464 1.453 0.011 1.25e-02 6.40e+03 7.58e-01 bond pdb=" N LYS E 370 " pdb=" CA LYS E 370 " ideal model delta sigma weight residual 1.464 1.453 0.011 1.25e-02 6.40e+03 7.52e-01 bond pdb=" CA LYS F 370 " pdb=" C LYS F 370 " ideal model delta sigma weight residual 1.526 1.516 0.009 1.08e-02 8.57e+03 7.35e-01 ... (remaining 3517 not shown) Histogram of bond angle deviations from ideal: 102.54 - 108.32: 259 108.32 - 114.10: 2002 114.10 - 119.89: 814 119.89 - 125.67: 1587 125.67 - 131.45: 48 Bond angle restraints: 4710 Sorted by residual: angle pdb=" C ASP E 348 " pdb=" N ARG E 349 " pdb=" CA ARG E 349 " ideal model delta sigma weight residual 122.61 125.95 -3.34 1.56e+00 4.11e-01 4.59e+00 angle pdb=" C ASP C 348 " pdb=" N ARG C 349 " pdb=" CA ARG C 349 " ideal model delta sigma weight residual 122.61 125.94 -3.33 1.56e+00 4.11e-01 4.55e+00 angle pdb=" C ASP F 348 " pdb=" N ARG F 349 " pdb=" CA ARG F 349 " ideal model delta sigma weight residual 122.61 125.93 -3.32 1.56e+00 4.11e-01 4.54e+00 angle pdb=" C ASP D 348 " pdb=" N ARG D 349 " pdb=" CA ARG D 349 " ideal model delta sigma weight residual 122.61 125.91 -3.30 1.56e+00 4.11e-01 4.46e+00 angle pdb=" C ASP A 348 " pdb=" N ARG A 349 " pdb=" CA ARG A 349 " ideal model delta sigma weight residual 122.61 125.89 -3.28 1.56e+00 4.11e-01 4.42e+00 ... (remaining 4705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.10: 1932 15.10 - 30.20: 174 30.20 - 45.30: 30 45.30 - 60.40: 0 60.40 - 75.50: 6 Dihedral angle restraints: 2142 sinusoidal: 894 harmonic: 1248 Sorted by residual: dihedral pdb=" CA ASP E 358 " pdb=" C ASP E 358 " pdb=" N ASN E 359 " pdb=" CA ASN E 359 " ideal model delta harmonic sigma weight residual 180.00 165.31 14.69 0 5.00e+00 4.00e-02 8.63e+00 dihedral pdb=" CA ASP D 358 " pdb=" C ASP D 358 " pdb=" N ASN D 359 " pdb=" CA ASN D 359 " ideal model delta harmonic sigma weight residual 180.00 165.32 14.68 0 5.00e+00 4.00e-02 8.62e+00 dihedral pdb=" CA ASP F 358 " pdb=" C ASP F 358 " pdb=" N ASN F 359 " pdb=" CA ASN F 359 " ideal model delta harmonic sigma weight residual 180.00 165.35 14.65 0 5.00e+00 4.00e-02 8.59e+00 ... (remaining 2139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 258 0.026 - 0.051: 136 0.051 - 0.077: 35 0.077 - 0.102: 36 0.102 - 0.128: 63 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA VAL B 339 " pdb=" N VAL B 339 " pdb=" C VAL B 339 " pdb=" CB VAL B 339 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA ILE B 371 " pdb=" N ILE B 371 " pdb=" C ILE B 371 " pdb=" CB ILE B 371 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA VAL D 339 " pdb=" N VAL D 339 " pdb=" C VAL D 339 " pdb=" CB VAL D 339 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.96e-01 ... (remaining 525 not shown) Planarity restraints: 600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " 0.008 2.00e-02 2.50e+03 5.82e-03 6.78e-01 pdb=" CG TYR E 310 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " 0.008 2.00e-02 2.50e+03 5.69e-03 6.48e-01 pdb=" CG TYR F 310 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " 0.008 2.00e-02 2.50e+03 5.68e-03 6.44e-01 pdb=" CG TYR C 310 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " 0.001 2.00e-02 2.50e+03 ... (remaining 597 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1075 2.85 - 3.36: 2650 3.36 - 3.88: 5547 3.88 - 4.39: 5314 4.39 - 4.90: 11791 Nonbonded interactions: 26377 Sorted by model distance: nonbonded pdb=" OE1 GLU C 338 " pdb=" NZ LYS B 331 " model vdw 2.338 3.120 nonbonded pdb=" OE1 GLU E 338 " pdb=" NZ LYS D 331 " model vdw 2.341 3.120 nonbonded pdb=" OE1 GLU A 338 " pdb=" NZ LYS C 331 " model vdw 2.344 3.120 nonbonded pdb=" OE1 GLU B 338 " pdb=" NZ LYS E 331 " model vdw 2.344 3.120 nonbonded pdb=" OE1 GLU D 338 " pdb=" NZ LYS F 331 " model vdw 2.345 3.120 ... (remaining 26372 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.310 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 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 : 0.004 0.026 3522 Z= 0.292 Angle : 0.769 5.310 4710 Z= 0.429 Chirality : 0.052 0.128 528 Planarity : 0.002 0.014 600 Dihedral : 12.489 75.495 1350 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % 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: -4.38 (0.26), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.20), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.005 0.001 PHE E 378 TYR 0.014 0.003 TYR E 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.425 Fit side-chains REVERT: D 342 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7409 (pm20) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.4164 time to fit residues: 14.3667 Evaluate side-chains 23 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0070 chunk 31 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 3522 Z= 0.162 Angle : 0.564 5.547 4710 Z= 0.279 Chirality : 0.050 0.115 528 Planarity : 0.002 0.026 600 Dihedral : 5.144 13.633 468 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.25 % Allowed : 5.81 % Favored : 93.94 % 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: -3.68 (0.28), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.22), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 362 PHE 0.003 0.001 PHE E 378 TYR 0.013 0.003 TYR D 310 ARG 0.003 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.428 Fit side-chains REVERT: D 325 LEU cc_start: 0.8688 (mt) cc_final: 0.8320 (mp) REVERT: D 375 LYS cc_start: 0.8016 (ttmt) cc_final: 0.7047 (tttp) REVERT: F 325 LEU cc_start: 0.8648 (mt) cc_final: 0.8261 (mp) REVERT: F 342 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7458 (pm20) REVERT: F 375 LYS cc_start: 0.7832 (ttmt) cc_final: 0.7344 (mtpp) outliers start: 1 outliers final: 0 residues processed: 33 average time/residue: 0.4431 time to fit residues: 16.2173 Evaluate side-chains 26 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 0.0020 chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 overall best weight: 2.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 3522 Z= 0.217 Angle : 0.577 4.122 4710 Z= 0.294 Chirality : 0.050 0.117 528 Planarity : 0.003 0.029 600 Dihedral : 5.043 13.241 468 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.02 % Allowed : 6.31 % Favored : 91.67 % 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: -3.41 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 362 PHE 0.005 0.001 PHE F 378 TYR 0.019 0.005 TYR C 310 ARG 0.001 0.000 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 25 time to evaluate : 0.514 Fit side-chains REVERT: D 325 LEU cc_start: 0.8691 (mt) cc_final: 0.8384 (mp) REVERT: D 342 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7450 (pm20) REVERT: D 375 LYS cc_start: 0.8051 (ttmt) cc_final: 0.7059 (tmtt) REVERT: F 325 LEU cc_start: 0.8640 (mt) cc_final: 0.8311 (mp) REVERT: F 342 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7352 (pm20) REVERT: F 375 LYS cc_start: 0.7892 (ttmt) cc_final: 0.7415 (mtpp) outliers start: 8 outliers final: 4 residues processed: 32 average time/residue: 0.4267 time to fit residues: 15.2317 Evaluate side-chains 28 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 24 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain E residue 358 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 3522 Z= 0.428 Angle : 0.722 5.026 4710 Z= 0.375 Chirality : 0.054 0.122 528 Planarity : 0.004 0.028 600 Dihedral : 5.628 15.426 468 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 1.52 % Allowed : 6.31 % Favored : 92.17 % 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: -3.56 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS E 362 PHE 0.009 0.003 PHE F 378 TYR 0.032 0.008 TYR C 310 ARG 0.001 0.000 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 31 time to evaluate : 0.426 Fit side-chains REVERT: B 378 PHE cc_start: 0.8240 (t80) cc_final: 0.7956 (t80) REVERT: D 325 LEU cc_start: 0.8702 (mt) cc_final: 0.8460 (mp) REVERT: D 342 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7530 (pm20) REVERT: D 375 LYS cc_start: 0.8059 (ttmt) cc_final: 0.7059 (tmtt) REVERT: F 325 LEU cc_start: 0.8596 (mt) cc_final: 0.8337 (mp) REVERT: F 342 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7534 (pm20) REVERT: F 375 LYS cc_start: 0.7934 (ttmt) cc_final: 0.6934 (tmtt) outliers start: 6 outliers final: 5 residues processed: 36 average time/residue: 0.3339 time to fit residues: 13.6636 Evaluate side-chains 33 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 28 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain F residue 358 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: 3.9990 chunk 34 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.044 3522 Z= 0.514 Angle : 0.791 5.501 4710 Z= 0.418 Chirality : 0.057 0.127 528 Planarity : 0.005 0.033 600 Dihedral : 5.980 16.247 468 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.94 % Favored : 88.06 % Rotamer: Outliers : 2.02 % Allowed : 9.60 % Favored : 88.38 % 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: -3.76 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS F 362 PHE 0.011 0.003 PHE F 378 TYR 0.034 0.009 TYR A 310 ARG 0.001 0.000 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 30 time to evaluate : 0.423 Fit side-chains REVERT: A 328 ILE cc_start: 0.9092 (mt) cc_final: 0.8709 (mp) REVERT: B 328 ILE cc_start: 0.8768 (mt) cc_final: 0.8452 (mp) REVERT: B 378 PHE cc_start: 0.8289 (t80) cc_final: 0.7977 (t80) REVERT: D 325 LEU cc_start: 0.8688 (mt) cc_final: 0.8467 (mp) REVERT: D 342 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7515 (pm20) REVERT: D 375 LYS cc_start: 0.8071 (ttmt) cc_final: 0.7095 (tmtt) REVERT: F 325 LEU cc_start: 0.8601 (mt) cc_final: 0.8332 (mp) REVERT: F 342 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7494 (pm20) REVERT: F 375 LYS cc_start: 0.7992 (ttmt) cc_final: 0.6944 (tttm) outliers start: 8 outliers final: 6 residues processed: 35 average time/residue: 0.3228 time to fit residues: 12.8807 Evaluate side-chains 37 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 31 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain F residue 358 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 3522 Z= 0.157 Angle : 0.593 7.941 4710 Z= 0.297 Chirality : 0.050 0.119 528 Planarity : 0.003 0.029 600 Dihedral : 4.982 14.050 468 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.52 % Allowed : 7.83 % Favored : 90.66 % 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: -3.48 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.003 0.001 PHE F 378 TYR 0.013 0.003 TYR F 310 ARG 0.001 0.000 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 29 time to evaluate : 0.416 Fit side-chains REVERT: D 325 LEU cc_start: 0.8635 (mt) cc_final: 0.8396 (mp) REVERT: D 342 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7358 (pm20) REVERT: D 375 LYS cc_start: 0.8061 (ttmt) cc_final: 0.7073 (tmtt) REVERT: F 325 LEU cc_start: 0.8595 (mt) cc_final: 0.8311 (mp) REVERT: F 342 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7418 (pm20) REVERT: F 375 LYS cc_start: 0.7928 (ttmt) cc_final: 0.6925 (tmtt) outliers start: 6 outliers final: 5 residues processed: 30 average time/residue: 0.3594 time to fit residues: 12.2303 Evaluate side-chains 32 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 27 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain D residue 358 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 20.0000 chunk 34 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 3522 Z= 0.305 Angle : 0.659 5.444 4710 Z= 0.339 Chirality : 0.052 0.123 528 Planarity : 0.004 0.030 600 Dihedral : 5.224 14.297 468 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 2.02 % Allowed : 8.59 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 362 PHE 0.007 0.002 PHE F 378 TYR 0.023 0.006 TYR A 310 ARG 0.001 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 25 time to evaluate : 0.592 Fit side-chains REVERT: A 311 LYS cc_start: 0.7776 (ttpt) cc_final: 0.7546 (ptpt) REVERT: A 328 ILE cc_start: 0.9074 (mt) cc_final: 0.8690 (mp) REVERT: D 325 LEU cc_start: 0.8662 (mt) cc_final: 0.8434 (mp) REVERT: D 342 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7409 (pm20) REVERT: D 375 LYS cc_start: 0.8011 (ttmt) cc_final: 0.7015 (tmtt) REVERT: F 325 LEU cc_start: 0.8562 (mt) cc_final: 0.8305 (mp) REVERT: F 342 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7467 (pm20) REVERT: F 375 LYS cc_start: 0.7936 (ttmt) cc_final: 0.6928 (tmtt) outliers start: 8 outliers final: 6 residues processed: 30 average time/residue: 0.3388 time to fit residues: 11.7272 Evaluate side-chains 30 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 24 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain F residue 358 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 3522 Z= 0.304 Angle : 0.669 5.079 4710 Z= 0.344 Chirality : 0.052 0.124 528 Planarity : 0.004 0.028 600 Dihedral : 5.288 14.597 468 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.52 % Allowed : 9.34 % Favored : 89.14 % 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 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 362 PHE 0.008 0.002 PHE F 378 TYR 0.023 0.006 TYR A 310 ARG 0.001 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 24 time to evaluate : 0.417 Fit side-chains REVERT: A 311 LYS cc_start: 0.7746 (ttpt) cc_final: 0.7544 (ptpt) REVERT: A 328 ILE cc_start: 0.9072 (mt) cc_final: 0.8685 (mp) REVERT: D 325 LEU cc_start: 0.8659 (mt) cc_final: 0.8434 (mp) REVERT: D 342 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7407 (pm20) REVERT: D 375 LYS cc_start: 0.7986 (ttmt) cc_final: 0.6993 (tmtt) REVERT: F 325 LEU cc_start: 0.8562 (mt) cc_final: 0.8317 (mp) REVERT: F 342 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7453 (pm20) REVERT: F 375 LYS cc_start: 0.7965 (ttmt) cc_final: 0.6925 (tmtt) outliers start: 6 outliers final: 6 residues processed: 27 average time/residue: 0.3649 time to fit residues: 11.2624 Evaluate side-chains 30 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 24 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain F residue 358 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 39 optimal weight: 0.0670 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 3522 Z= 0.126 Angle : 0.565 5.532 4710 Z= 0.284 Chirality : 0.050 0.118 528 Planarity : 0.003 0.026 600 Dihedral : 4.634 13.414 468 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.51 % Allowed : 10.10 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 362 PHE 0.003 0.001 PHE F 378 TYR 0.010 0.002 TYR F 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 25 time to evaluate : 0.411 Fit side-chains REVERT: D 325 LEU cc_start: 0.8520 (mt) cc_final: 0.8282 (mp) REVERT: D 342 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7275 (pm20) REVERT: D 375 LYS cc_start: 0.8020 (ttmt) cc_final: 0.6995 (tmtt) REVERT: F 325 LEU cc_start: 0.8563 (mt) cc_final: 0.8290 (mp) REVERT: F 342 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7353 (pm20) REVERT: F 375 LYS cc_start: 0.7907 (ttmt) cc_final: 0.6901 (tmtt) outliers start: 2 outliers final: 1 residues processed: 25 average time/residue: 0.3317 time to fit residues: 9.5556 Evaluate side-chains 26 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 25 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 358 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 35 optimal weight: 0.4980 chunk 10 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3522 Z= 0.277 Angle : 0.635 6.363 4710 Z= 0.327 Chirality : 0.052 0.122 528 Planarity : 0.003 0.029 600 Dihedral : 5.021 13.928 468 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.76 % Allowed : 9.60 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 362 PHE 0.007 0.002 PHE F 378 TYR 0.022 0.005 TYR C 310 ARG 0.001 0.000 ARG F 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.383 Fit side-chains REVERT: A 328 ILE cc_start: 0.9064 (mt) cc_final: 0.8687 (mp) REVERT: D 342 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7423 (pm20) REVERT: D 375 LYS cc_start: 0.7978 (ttmt) cc_final: 0.6976 (tmtt) REVERT: F 325 LEU cc_start: 0.8559 (mt) cc_final: 0.8311 (mp) REVERT: F 342 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7466 (pm20) REVERT: F 375 LYS cc_start: 0.7922 (ttmt) cc_final: 0.6905 (tmtt) outliers start: 3 outliers final: 3 residues processed: 24 average time/residue: 0.4268 time to fit residues: 11.5322 Evaluate side-chains 25 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain F residue 358 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.117609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.099116 restraints weight = 4848.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.101668 restraints weight = 2335.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.103278 restraints weight = 1529.926| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 3522 Z= 0.385 Angle : 0.718 6.571 4710 Z= 0.376 Chirality : 0.054 0.127 528 Planarity : 0.004 0.027 600 Dihedral : 5.455 15.001 468 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 1.26 % Allowed : 8.84 % Favored : 89.90 % 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: -3.42 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS D 362 PHE 0.009 0.002 PHE F 378 TYR 0.029 0.007 TYR C 310 ARG 0.001 0.000 ARG F 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1134.97 seconds wall clock time: 21 minutes 5.01 seconds (1265.01 seconds total)