Starting phenix.real_space_refine on Tue Sep 24 00:05:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf6_23300/09_2024/7lf6_23300.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf6_23300/09_2024/7lf6_23300.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/7lf6_23300/09_2024/7lf6_23300.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf6_23300/09_2024/7lf6_23300.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf6_23300/09_2024/7lf6_23300.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf6_23300/09_2024/7lf6_23300.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= 0.001 sd= 0.022 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 40 5.16 5 C 4164 2.51 5 N 1016 2.21 5 O 1068 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6288 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3144 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 18, 'TRANS': 388} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Restraints were copied for chains: B Time building chain proxies: 5.41, per 1000 atoms: 0.86 Number of scatterers: 6288 At special positions: 0 Unit cell: (78.375, 85.8, 81.675, 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 40 16.00 O 1068 8.00 N 1016 7.00 C 4164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 144 " - pdb=" SG CYS A 196 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 836.5 milliseconds 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1556 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 0 sheets defined 81.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.718A pdb=" N PHE A 39 " --> pdb=" O ARG A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 57 removed outlier: 4.070A pdb=" N VAL A 55 " --> pdb=" O MET A 51 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 102 removed outlier: 3.631A pdb=" N VAL A 101 " --> pdb=" O ARG A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 133 Proline residue: A 124 - end of helix Processing helix chain 'A' and resid 136 through 164 removed outlier: 4.436A pdb=" N ILE A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 206 removed outlier: 3.622A pdb=" N HIS A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N GLY A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Proline residue: A 193 - end of helix removed outlier: 3.854A pdb=" N PHE A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 223 removed outlier: 4.486A pdb=" N VAL A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE A 218 " --> pdb=" O MET A 214 " (cutoff:3.500A) Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 257 through 284 removed outlier: 4.806A pdb=" N LEU A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ILE A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP A 283 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 removed outlier: 3.676A pdb=" N PHE A 295 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER A 296 " --> pdb=" O GLU A 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 292 through 296' Processing helix chain 'A' and resid 298 through 333 removed outlier: 4.412A pdb=" N ALA A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) Proline residue: A 308 - end of helix removed outlier: 4.286A pdb=" N HIS A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 353 Processing helix chain 'A' and resid 354 through 364 removed outlier: 3.813A pdb=" N ALA A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 396 removed outlier: 3.728A pdb=" N GLN A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N MET A 393 " --> pdb=" O PHE A 389 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP A 394 " --> pdb=" O GLN A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 415 through 437 removed outlier: 5.617A pdb=" N TYR A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Proline residue: A 427 - end of helix Processing helix chain 'A' and resid 444 through 469 Proline residue: A 456 - end of helix removed outlier: 4.787A pdb=" N LEU A 460 " --> pdb=" O PRO A 456 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU A 461 " --> pdb=" O CYS A 457 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 removed outlier: 3.719A pdb=" N PHE B 39 " --> pdb=" O ARG B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 57 removed outlier: 4.070A pdb=" N VAL B 55 " --> pdb=" O MET B 51 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 102 removed outlier: 3.631A pdb=" N VAL B 101 " --> pdb=" O ARG B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 133 Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 136 through 164 removed outlier: 4.436A pdb=" N ILE B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 206 removed outlier: 3.622A pdb=" N HIS B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N GLY B 192 " --> pdb=" O ILE B 188 " (cutoff:3.500A) Proline residue: B 193 - end of helix removed outlier: 3.854A pdb=" N PHE B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 223 removed outlier: 4.485A pdb=" N VAL B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE B 218 " --> pdb=" O MET B 214 " (cutoff:3.500A) Proline residue: B 221 - end of helix Processing helix chain 'B' and resid 257 through 284 removed outlier: 4.807A pdb=" N LEU B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ILE B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP B 283 " --> pdb=" O ASP B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 296 removed outlier: 3.677A pdb=" N PHE B 295 " --> pdb=" O LYS B 292 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER B 296 " --> pdb=" O GLU B 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 292 through 296' Processing helix chain 'B' and resid 298 through 333 removed outlier: 4.411A pdb=" N ALA B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) Proline residue: B 308 - end of helix removed outlier: 4.285A pdb=" N HIS B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 353 Processing helix chain 'B' and resid 354 through 364 removed outlier: 3.813A pdb=" N ALA B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 396 removed outlier: 3.727A pdb=" N GLN B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N MET B 393 " --> pdb=" O PHE B 389 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TRP B 394 " --> pdb=" O GLN B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 415 through 437 removed outlier: 5.617A pdb=" N TYR B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Proline residue: B 427 - end of helix Processing helix chain 'B' and resid 444 through 469 Proline residue: B 456 - end of helix removed outlier: 4.787A pdb=" N LEU B 460 " --> pdb=" O PRO B 456 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU B 461 " --> pdb=" O CYS B 457 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA B 469 " --> pdb=" O LEU B 465 " (cutoff:3.500A) 454 hydrogen bonds defined for protein. 1350 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.55 Time building geometry restraints manager: 1.75 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: 1932 1.34 - 1.47: 1612 1.47 - 1.60: 2836 1.60 - 1.73: 0 1.73 - 1.85: 62 Bond restraints: 6442 Sorted by residual: bond pdb=" CB CYS B 196 " pdb=" SG CYS B 196 " ideal model delta sigma weight residual 1.808 1.853 -0.045 3.30e-02 9.18e+02 1.86e+00 bond pdb=" CB CYS A 196 " pdb=" SG CYS A 196 " ideal model delta sigma weight residual 1.808 1.852 -0.044 3.30e-02 9.18e+02 1.81e+00 bond pdb=" CB MET A 130 " pdb=" CG MET A 130 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.15e+00 bond pdb=" CB MET B 130 " pdb=" CG MET B 130 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.11e+00 bond pdb=" CB TRP B 394 " pdb=" CG TRP B 394 " ideal model delta sigma weight residual 1.498 1.471 0.027 3.10e-02 1.04e+03 7.83e-01 ... (remaining 6437 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 8627 2.22 - 4.45: 129 4.45 - 6.67: 34 6.67 - 8.89: 0 8.89 - 11.12: 2 Bond angle restraints: 8792 Sorted by residual: angle pdb=" N ILE B 218 " pdb=" CA ILE B 218 " pdb=" C ILE B 218 " ideal model delta sigma weight residual 113.42 108.71 4.71 1.17e+00 7.31e-01 1.62e+01 angle pdb=" N ILE A 218 " pdb=" CA ILE A 218 " pdb=" C ILE A 218 " ideal model delta sigma weight residual 113.42 108.73 4.69 1.17e+00 7.31e-01 1.61e+01 angle pdb=" CB MET A 130 " pdb=" CG MET A 130 " pdb=" SD MET A 130 " ideal model delta sigma weight residual 112.70 101.58 11.12 3.00e+00 1.11e-01 1.37e+01 angle pdb=" CB MET B 130 " pdb=" CG MET B 130 " pdb=" SD MET B 130 " ideal model delta sigma weight residual 112.70 101.59 11.11 3.00e+00 1.11e-01 1.37e+01 angle pdb=" N GLN B 361 " pdb=" CA GLN B 361 " pdb=" CB GLN B 361 " ideal model delta sigma weight residual 110.16 114.90 -4.74 1.48e+00 4.57e-01 1.02e+01 ... (remaining 8787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.55: 3355 15.55 - 31.11: 301 31.11 - 46.66: 99 46.66 - 62.21: 10 62.21 - 77.77: 8 Dihedral angle restraints: 3773 sinusoidal: 1389 harmonic: 2384 Sorted by residual: dihedral pdb=" CG ARG A 375 " pdb=" CD ARG A 375 " pdb=" NE ARG A 375 " pdb=" CZ ARG A 375 " ideal model delta sinusoidal sigma weight residual 180.00 135.34 44.66 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CG ARG B 375 " pdb=" CD ARG B 375 " pdb=" NE ARG B 375 " pdb=" CZ ARG B 375 " ideal model delta sinusoidal sigma weight residual 180.00 135.40 44.60 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CA GLN B 34 " pdb=" C GLN B 34 " pdb=" N ARG B 35 " pdb=" CA ARG B 35 " ideal model delta harmonic sigma weight residual -180.00 -165.41 -14.59 0 5.00e+00 4.00e-02 8.51e+00 ... (remaining 3770 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 798 0.047 - 0.095: 237 0.095 - 0.142: 49 0.142 - 0.190: 0 0.190 - 0.237: 2 Chirality restraints: 1086 Sorted by residual: chirality pdb=" CB VAL A 409 " pdb=" CA VAL A 409 " pdb=" CG1 VAL A 409 " pdb=" CG2 VAL A 409 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB VAL B 409 " pdb=" CA VAL B 409 " pdb=" CG1 VAL B 409 " pdb=" CG2 VAL B 409 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA VAL B 455 " pdb=" N VAL B 455 " pdb=" C VAL B 455 " pdb=" CB VAL B 455 " both_signs ideal model delta sigma weight residual False 2.44 2.31 0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 1083 not shown) Planarity restraints: 1074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 377 " 0.158 9.50e-02 1.11e+02 7.08e-02 3.24e+00 pdb=" NE ARG B 377 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 377 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 377 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 377 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 377 " -0.157 9.50e-02 1.11e+02 7.05e-02 3.22e+00 pdb=" NE ARG A 377 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 377 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 377 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 377 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 192 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO B 193 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 193 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 193 " 0.025 5.00e-02 4.00e+02 ... (remaining 1071 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 49 2.61 - 3.18: 5959 3.18 - 3.75: 10593 3.75 - 4.33: 13429 4.33 - 4.90: 21559 Nonbonded interactions: 51589 Sorted by model distance: nonbonded pdb=" SG CYS B 144 " pdb=" SG CYS B 196 " model vdw 2.032 3.760 nonbonded pdb=" O HIS B 400 " pdb=" OG1 THR B 404 " model vdw 2.220 3.040 nonbonded pdb=" O HIS A 400 " pdb=" OG1 THR A 404 " model vdw 2.220 3.040 nonbonded pdb=" NH2 ARG A 335 " pdb=" O ALA A 402 " model vdw 2.258 3.120 nonbonded pdb=" NH2 ARG B 335 " pdb=" O ALA B 402 " model vdw 2.260 3.120 ... (remaining 51584 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' } 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=0.00 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: 2.360 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.230 Find NCS groups from input model: 0.160 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 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 : 0.003 0.045 6442 Z= 0.213 Angle : 0.710 11.116 8792 Z= 0.374 Chirality : 0.045 0.237 1086 Planarity : 0.005 0.071 1074 Dihedral : 13.859 77.767 2214 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.31), residues: 802 helix: 1.06 (0.21), residues: 612 sheet: None (None), residues: 0 loop : -0.41 (0.52), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 324 HIS 0.005 0.001 HIS A 416 PHE 0.018 0.001 PHE A 384 TYR 0.017 0.002 TYR A 313 ARG 0.007 0.001 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: A 71 GLN cc_start: 0.7516 (mm110) cc_final: 0.7188 (mm110) REVERT: A 262 GLU cc_start: 0.7075 (tp30) cc_final: 0.6673 (tp30) REVERT: A 361 GLN cc_start: 0.6761 (mp10) cc_final: 0.6292 (mp10) REVERT: A 377 ARG cc_start: 0.6352 (tpm170) cc_final: 0.6020 (tpm170) REVERT: A 418 LEU cc_start: 0.8138 (tp) cc_final: 0.7904 (tp) REVERT: A 451 MET cc_start: 0.7219 (ttp) cc_final: 0.6903 (ttp) REVERT: B 38 SER cc_start: 0.7534 (p) cc_final: 0.7288 (p) REVERT: B 71 GLN cc_start: 0.7508 (mm110) cc_final: 0.6852 (mm110) REVERT: B 72 ARG cc_start: 0.7764 (tmt-80) cc_final: 0.7104 (tmt-80) REVERT: B 85 PHE cc_start: 0.8029 (t80) cc_final: 0.7706 (t80) REVERT: B 130 MET cc_start: 0.6429 (mtt) cc_final: 0.6165 (mtt) REVERT: B 188 ILE cc_start: 0.8165 (tt) cc_final: 0.7847 (tt) REVERT: B 357 LEU cc_start: 0.7020 (tt) cc_final: 0.6343 (pp) REVERT: B 361 GLN cc_start: 0.6736 (mp10) cc_final: 0.6230 (mp10) REVERT: B 414 ARG cc_start: 0.7125 (mtt-85) cc_final: 0.6850 (mtt-85) REVERT: B 451 MET cc_start: 0.7030 (ttp) cc_final: 0.6698 (ttp) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2391 time to fit residues: 52.7948 Evaluate side-chains 173 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.0070 chunk 46 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 328 HIS ** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN B 191 GLN B 452 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6442 Z= 0.236 Angle : 0.670 11.258 8792 Z= 0.344 Chirality : 0.045 0.223 1086 Planarity : 0.005 0.041 1074 Dihedral : 4.239 18.989 860 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.65 % Allowed : 13.82 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.30), residues: 802 helix: 1.07 (0.21), residues: 614 sheet: None (None), residues: 0 loop : -0.45 (0.52), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 92 HIS 0.009 0.001 HIS B 449 PHE 0.015 0.001 PHE B 459 TYR 0.019 0.002 TYR B 313 ARG 0.007 0.001 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 189 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7999 (mp) REVERT: A 71 GLN cc_start: 0.7547 (mm110) cc_final: 0.7169 (mm110) REVERT: A 77 ARG cc_start: 0.8100 (mmt90) cc_final: 0.7860 (mmt90) REVERT: A 262 GLU cc_start: 0.7240 (tp30) cc_final: 0.6568 (tp30) REVERT: A 332 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7433 (mm) REVERT: A 335 ARG cc_start: 0.6881 (ptt90) cc_final: 0.6645 (ptt90) REVERT: A 357 LEU cc_start: 0.7368 (tt) cc_final: 0.7106 (tt) REVERT: A 377 ARG cc_start: 0.6282 (tpm170) cc_final: 0.5654 (tpm170) REVERT: A 416 HIS cc_start: 0.7352 (t-90) cc_final: 0.7071 (t-170) REVERT: A 451 MET cc_start: 0.7244 (ttp) cc_final: 0.6989 (ttp) REVERT: A 452 GLN cc_start: 0.7696 (tp-100) cc_final: 0.7465 (tp-100) REVERT: B 71 GLN cc_start: 0.7569 (mm110) cc_final: 0.6875 (mm110) REVERT: B 85 PHE cc_start: 0.8045 (t80) cc_final: 0.7729 (t80) REVERT: B 164 PHE cc_start: 0.7060 (m-80) cc_final: 0.6809 (m-80) REVERT: B 357 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.6929 (tt) REVERT: B 451 MET cc_start: 0.7155 (ttp) cc_final: 0.6799 (ttp) outliers start: 18 outliers final: 9 residues processed: 193 average time/residue: 0.2163 time to fit residues: 52.2837 Evaluate side-chains 185 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 173 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 388 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 0.0870 chunk 22 optimal weight: 0.0970 chunk 60 optimal weight: 0.6980 chunk 49 optimal weight: 0.2980 chunk 20 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 58 optimal weight: 0.0670 chunk 71 optimal weight: 0.9980 overall best weight: 0.2294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 HIS B 191 GLN ** B 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6442 Z= 0.167 Angle : 0.610 9.163 8792 Z= 0.308 Chirality : 0.042 0.224 1086 Planarity : 0.004 0.045 1074 Dihedral : 3.977 16.799 860 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.53 % Allowed : 20.59 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.31), residues: 802 helix: 1.25 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -0.39 (0.53), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 324 HIS 0.013 0.001 HIS A 449 PHE 0.016 0.001 PHE B 459 TYR 0.018 0.002 TYR B 313 ARG 0.003 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 179 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7854 (mp) REVERT: A 71 GLN cc_start: 0.7509 (mm110) cc_final: 0.7115 (mm110) REVERT: A 72 ARG cc_start: 0.7786 (tmt-80) cc_final: 0.7526 (tmt-80) REVERT: A 77 ARG cc_start: 0.8095 (mmt90) cc_final: 0.7829 (mmt90) REVERT: A 117 MET cc_start: 0.6985 (mmp) cc_final: 0.6657 (mmt) REVERT: A 196 CYS cc_start: 0.4771 (OUTLIER) cc_final: 0.4570 (t) REVERT: A 262 GLU cc_start: 0.7144 (tp30) cc_final: 0.6777 (tp30) REVERT: A 266 ASP cc_start: 0.7884 (m-30) cc_final: 0.7505 (t0) REVERT: A 332 LEU cc_start: 0.7846 (mm) cc_final: 0.7574 (mm) REVERT: A 357 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7216 (tp) REVERT: A 416 HIS cc_start: 0.7267 (t-90) cc_final: 0.6997 (t-170) REVERT: A 451 MET cc_start: 0.7192 (ttp) cc_final: 0.6959 (ttp) REVERT: A 452 GLN cc_start: 0.7689 (tp-100) cc_final: 0.7234 (tp-100) REVERT: B 35 ARG cc_start: 0.6388 (tpt-90) cc_final: 0.6135 (tpt-90) REVERT: B 38 SER cc_start: 0.7650 (t) cc_final: 0.7238 (p) REVERT: B 44 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7794 (mp) REVERT: B 71 GLN cc_start: 0.7547 (mm110) cc_final: 0.6838 (mm110) REVERT: B 85 PHE cc_start: 0.8079 (t80) cc_final: 0.7751 (t80) REVERT: B 332 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7692 (mm) REVERT: B 357 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.6957 (tt) REVERT: B 383 ILE cc_start: 0.7843 (mt) cc_final: 0.7582 (tt) REVERT: B 451 MET cc_start: 0.7115 (ttp) cc_final: 0.6785 (ttp) outliers start: 24 outliers final: 10 residues processed: 186 average time/residue: 0.2184 time to fit residues: 50.6550 Evaluate side-chains 195 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 179 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 420 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 0.0980 chunk 48 optimal weight: 0.0770 chunk 73 optimal weight: 1.9990 chunk 77 optimal weight: 0.0870 chunk 38 optimal weight: 0.0980 chunk 69 optimal weight: 1.9990 chunk 20 optimal weight: 0.0670 chunk 64 optimal weight: 0.0060 overall best weight: 0.0670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN B 416 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6442 Z= 0.155 Angle : 0.594 8.328 8792 Z= 0.296 Chirality : 0.041 0.250 1086 Planarity : 0.004 0.044 1074 Dihedral : 3.800 16.095 860 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.82 % Allowed : 23.53 % Favored : 72.65 % 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: 1.28 (0.31), residues: 802 helix: 1.25 (0.21), residues: 628 sheet: None (None), residues: 0 loop : -0.39 (0.56), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 324 HIS 0.011 0.001 HIS B 449 PHE 0.010 0.001 PHE B 420 TYR 0.017 0.001 TYR B 313 ARG 0.003 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 166 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7804 (mp) REVERT: A 71 GLN cc_start: 0.7477 (mm110) cc_final: 0.7092 (mm110) REVERT: A 72 ARG cc_start: 0.7763 (tmt-80) cc_final: 0.7503 (tmt-80) REVERT: A 77 ARG cc_start: 0.8116 (mmt90) cc_final: 0.7904 (mmt90) REVERT: A 117 MET cc_start: 0.6987 (mmp) cc_final: 0.6659 (mmt) REVERT: A 182 ARG cc_start: 0.8713 (mmp80) cc_final: 0.8449 (tpp-160) REVERT: A 262 GLU cc_start: 0.7167 (tp30) cc_final: 0.6732 (tp30) REVERT: A 332 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7591 (mm) REVERT: A 357 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7275 (tp) REVERT: B 35 ARG cc_start: 0.6376 (tpt-90) cc_final: 0.6112 (tpt-90) REVERT: B 38 SER cc_start: 0.7586 (t) cc_final: 0.7306 (p) REVERT: B 44 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7731 (mp) REVERT: B 52 ILE cc_start: 0.7834 (tp) cc_final: 0.7621 (tt) REVERT: B 71 GLN cc_start: 0.7497 (mm110) cc_final: 0.6809 (mm110) REVERT: B 332 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7623 (mm) REVERT: B 357 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.6671 (tt) REVERT: B 361 GLN cc_start: 0.6970 (mp10) cc_final: 0.6601 (mp10) REVERT: B 451 MET cc_start: 0.7135 (ttp) cc_final: 0.6759 (ttp) outliers start: 26 outliers final: 15 residues processed: 173 average time/residue: 0.2389 time to fit residues: 50.8738 Evaluate side-chains 179 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 158 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain B residue 423 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 53 optimal weight: 0.0970 chunk 0 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 26 optimal weight: 0.2980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6442 Z= 0.217 Angle : 0.644 9.245 8792 Z= 0.323 Chirality : 0.043 0.277 1086 Planarity : 0.004 0.043 1074 Dihedral : 3.881 17.282 860 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.85 % Allowed : 24.41 % Favored : 70.74 % 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: 1.20 (0.31), residues: 802 helix: 1.14 (0.21), residues: 630 sheet: None (None), residues: 0 loop : -0.24 (0.56), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 92 HIS 0.012 0.002 HIS B 449 PHE 0.016 0.001 PHE A 411 TYR 0.018 0.002 TYR B 313 ARG 0.005 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 185 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 SER cc_start: 0.8142 (OUTLIER) cc_final: 0.7936 (p) REVERT: A 44 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7928 (mp) REVERT: A 71 GLN cc_start: 0.7530 (mm110) cc_final: 0.7126 (mm110) REVERT: A 72 ARG cc_start: 0.7777 (tmt-80) cc_final: 0.7494 (tmt-80) REVERT: A 77 ARG cc_start: 0.8145 (mmt90) cc_final: 0.7888 (mmt90) REVERT: A 262 GLU cc_start: 0.7346 (tp30) cc_final: 0.7047 (tp30) REVERT: A 329 SER cc_start: 0.8494 (p) cc_final: 0.8252 (p) REVERT: A 332 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7726 (mm) REVERT: A 357 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7345 (tp) REVERT: A 387 SER cc_start: 0.7983 (t) cc_final: 0.7668 (t) REVERT: A 401 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.7088 (tt0) REVERT: B 44 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7842 (mp) REVERT: B 71 GLN cc_start: 0.7566 (mm110) cc_final: 0.6860 (mm110) REVERT: B 85 PHE cc_start: 0.8144 (t80) cc_final: 0.7691 (t80) REVERT: B 332 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7729 (mm) REVERT: B 361 GLN cc_start: 0.7020 (OUTLIER) cc_final: 0.6740 (mp10) REVERT: B 383 ILE cc_start: 0.7863 (mt) cc_final: 0.7571 (tt) REVERT: B 451 MET cc_start: 0.7168 (ttp) cc_final: 0.6876 (ttp) outliers start: 33 outliers final: 14 residues processed: 197 average time/residue: 0.2160 time to fit residues: 53.2697 Evaluate side-chains 201 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 179 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 401 GLN Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 420 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 64 optimal weight: 0.0970 chunk 35 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6442 Z= 0.232 Angle : 0.666 10.175 8792 Z= 0.331 Chirality : 0.045 0.309 1086 Planarity : 0.004 0.054 1074 Dihedral : 3.946 17.631 860 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 5.29 % Allowed : 24.26 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.30), residues: 802 helix: 1.03 (0.20), residues: 630 sheet: None (None), residues: 0 loop : -0.32 (0.56), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 92 HIS 0.013 0.002 HIS A 449 PHE 0.016 0.001 PHE A 420 TYR 0.020 0.002 TYR B 313 ARG 0.006 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 184 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7955 (mp) REVERT: A 55 VAL cc_start: 0.8751 (OUTLIER) cc_final: 0.8488 (p) REVERT: A 71 GLN cc_start: 0.7563 (mm110) cc_final: 0.7163 (mm110) REVERT: A 72 ARG cc_start: 0.7783 (tmt-80) cc_final: 0.7499 (tmt-80) REVERT: A 77 ARG cc_start: 0.8102 (mmt90) cc_final: 0.7874 (mmt90) REVERT: A 196 CYS cc_start: 0.4728 (OUTLIER) cc_final: 0.4133 (t) REVERT: A 262 GLU cc_start: 0.7368 (tp30) cc_final: 0.7113 (tp30) REVERT: A 266 ASP cc_start: 0.7922 (m-30) cc_final: 0.7622 (t0) REVERT: A 332 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7757 (mm) REVERT: A 361 GLN cc_start: 0.7048 (OUTLIER) cc_final: 0.6454 (mt0) REVERT: A 387 SER cc_start: 0.7974 (t) cc_final: 0.7661 (t) REVERT: B 71 GLN cc_start: 0.7570 (mm110) cc_final: 0.6856 (mm110) REVERT: B 85 PHE cc_start: 0.8145 (t80) cc_final: 0.7682 (t80) REVERT: B 196 CYS cc_start: 0.7069 (OUTLIER) cc_final: 0.6544 (t) REVERT: B 332 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7750 (mm) REVERT: B 357 LEU cc_start: 0.7510 (tt) cc_final: 0.6977 (tt) REVERT: B 361 GLN cc_start: 0.7061 (OUTLIER) cc_final: 0.6712 (mp10) REVERT: B 383 ILE cc_start: 0.7866 (mt) cc_final: 0.7567 (tt) REVERT: B 451 MET cc_start: 0.7198 (ttp) cc_final: 0.6932 (ttp) REVERT: B 462 LEU cc_start: 0.7859 (tt) cc_final: 0.7646 (tp) outliers start: 36 outliers final: 18 residues processed: 195 average time/residue: 0.2140 time to fit residues: 52.2782 Evaluate side-chains 209 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 183 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 420 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6442 Z= 0.260 Angle : 0.702 10.402 8792 Z= 0.348 Chirality : 0.046 0.374 1086 Planarity : 0.004 0.041 1074 Dihedral : 4.078 18.922 860 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 5.74 % Allowed : 24.85 % Favored : 69.41 % 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: 0.88 (0.30), residues: 802 helix: 0.84 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -0.08 (0.59), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 92 HIS 0.013 0.002 HIS B 449 PHE 0.019 0.001 PHE B 420 TYR 0.021 0.002 TYR B 313 ARG 0.006 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 185 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7953 (mp) REVERT: A 55 VAL cc_start: 0.8732 (OUTLIER) cc_final: 0.8473 (p) REVERT: A 71 GLN cc_start: 0.7573 (mm110) cc_final: 0.7187 (mm110) REVERT: A 72 ARG cc_start: 0.7786 (tmt-80) cc_final: 0.6892 (tmt-80) REVERT: A 196 CYS cc_start: 0.4802 (OUTLIER) cc_final: 0.4328 (t) REVERT: A 262 GLU cc_start: 0.7417 (tp30) cc_final: 0.7178 (tp30) REVERT: A 266 ASP cc_start: 0.7905 (m-30) cc_final: 0.7570 (t0) REVERT: A 332 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7764 (mm) REVERT: A 335 ARG cc_start: 0.7066 (ptt90) cc_final: 0.6808 (ptt90) REVERT: A 387 SER cc_start: 0.7968 (t) cc_final: 0.7635 (t) REVERT: B 71 GLN cc_start: 0.7584 (mm110) cc_final: 0.6866 (mm110) REVERT: B 196 CYS cc_start: 0.7110 (OUTLIER) cc_final: 0.6586 (t) REVERT: B 262 GLU cc_start: 0.7309 (tp30) cc_final: 0.6882 (tp30) REVERT: B 332 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7776 (mm) REVERT: B 357 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.6915 (tt) REVERT: B 361 GLN cc_start: 0.7066 (OUTLIER) cc_final: 0.6681 (mp10) REVERT: B 383 ILE cc_start: 0.7869 (mt) cc_final: 0.7561 (tt) REVERT: B 451 MET cc_start: 0.7228 (ttp) cc_final: 0.6963 (ttp) outliers start: 39 outliers final: 22 residues processed: 198 average time/residue: 0.2172 time to fit residues: 53.9000 Evaluate side-chains 214 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 184 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 420 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 8.9990 chunk 15 optimal weight: 0.3980 chunk 14 optimal weight: 0.0570 chunk 49 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 70 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6442 Z= 0.218 Angle : 0.688 11.060 8792 Z= 0.336 Chirality : 0.045 0.390 1086 Planarity : 0.004 0.043 1074 Dihedral : 4.004 16.380 860 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 5.15 % Allowed : 27.21 % Favored : 67.65 % 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: 0.96 (0.30), residues: 802 helix: 0.92 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -0.16 (0.59), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 92 HIS 0.014 0.002 HIS B 449 PHE 0.017 0.001 PHE B 420 TYR 0.020 0.002 TYR B 313 ARG 0.006 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 184 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7939 (mp) REVERT: A 55 VAL cc_start: 0.8756 (OUTLIER) cc_final: 0.8471 (p) REVERT: A 71 GLN cc_start: 0.7556 (mm110) cc_final: 0.7157 (mm110) REVERT: A 72 ARG cc_start: 0.7779 (tmt-80) cc_final: 0.6723 (tmt-80) REVERT: A 262 GLU cc_start: 0.7303 (tp30) cc_final: 0.7048 (tp30) REVERT: A 266 ASP cc_start: 0.7850 (m-30) cc_final: 0.7574 (t0) REVERT: A 332 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7740 (mm) REVERT: A 387 SER cc_start: 0.7939 (t) cc_final: 0.7618 (t) REVERT: B 71 GLN cc_start: 0.7558 (mm110) cc_final: 0.6846 (mm110) REVERT: B 85 PHE cc_start: 0.8203 (t80) cc_final: 0.7746 (t80) REVERT: B 196 CYS cc_start: 0.7043 (OUTLIER) cc_final: 0.6481 (t) REVERT: B 332 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7654 (mm) REVERT: B 357 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.6946 (tt) REVERT: B 361 GLN cc_start: 0.7010 (OUTLIER) cc_final: 0.6634 (mp10) REVERT: B 383 ILE cc_start: 0.7839 (mt) cc_final: 0.7539 (tt) REVERT: B 451 MET cc_start: 0.7198 (ttp) cc_final: 0.6941 (ttp) outliers start: 35 outliers final: 19 residues processed: 196 average time/residue: 0.1840 time to fit residues: 45.2156 Evaluate side-chains 206 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 180 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 420 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 0.6980 chunk 73 optimal weight: 0.0970 chunk 43 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 67 optimal weight: 0.1980 chunk 47 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN B 191 GLN ** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 6442 Z= 0.254 Angle : 0.709 11.801 8792 Z= 0.350 Chirality : 0.045 0.373 1086 Planarity : 0.005 0.042 1074 Dihedral : 4.076 17.506 860 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 5.29 % Allowed : 26.62 % Favored : 68.09 % 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: 0.79 (0.31), residues: 802 helix: 0.91 (0.21), residues: 630 sheet: None (None), residues: 0 loop : -0.63 (0.55), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 92 HIS 0.018 0.002 HIS B 449 PHE 0.019 0.001 PHE B 420 TYR 0.021 0.002 TYR B 313 ARG 0.008 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 182 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7943 (mp) REVERT: A 71 GLN cc_start: 0.7560 (mm110) cc_final: 0.7166 (mm110) REVERT: A 72 ARG cc_start: 0.7788 (tmt-80) cc_final: 0.6756 (tmt-80) REVERT: A 262 GLU cc_start: 0.7278 (tp30) cc_final: 0.7031 (tp30) REVERT: A 266 ASP cc_start: 0.7792 (m-30) cc_final: 0.7525 (t0) REVERT: A 332 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7796 (mm) REVERT: A 361 GLN cc_start: 0.7310 (OUTLIER) cc_final: 0.6630 (mp-120) REVERT: A 387 SER cc_start: 0.7904 (t) cc_final: 0.7587 (t) REVERT: B 71 GLN cc_start: 0.7578 (mm110) cc_final: 0.6860 (mm110) REVERT: B 85 PHE cc_start: 0.8227 (t80) cc_final: 0.7771 (t80) REVERT: B 196 CYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6585 (t) REVERT: B 332 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7688 (mm) REVERT: B 357 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.6980 (tt) REVERT: B 361 GLN cc_start: 0.7012 (OUTLIER) cc_final: 0.6640 (mp10) REVERT: B 383 ILE cc_start: 0.7846 (mt) cc_final: 0.7540 (tt) REVERT: B 451 MET cc_start: 0.7227 (ttp) cc_final: 0.6983 (ttp) outliers start: 36 outliers final: 25 residues processed: 194 average time/residue: 0.2098 time to fit residues: 50.9521 Evaluate side-chains 211 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 179 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 191 GLN Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 420 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 6442 Z= 0.298 Angle : 0.735 12.219 8792 Z= 0.366 Chirality : 0.046 0.386 1086 Planarity : 0.005 0.043 1074 Dihedral : 4.151 19.324 860 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.71 % Allowed : 27.35 % Favored : 67.94 % 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: 0.70 (0.30), residues: 802 helix: 0.84 (0.20), residues: 630 sheet: None (None), residues: 0 loop : -0.63 (0.56), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 92 HIS 0.017 0.002 HIS B 449 PHE 0.019 0.001 PHE B 420 TYR 0.023 0.002 TYR B 313 ARG 0.004 0.000 ARG B 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 190 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7938 (mp) REVERT: A 47 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7900 (mm) REVERT: A 71 GLN cc_start: 0.7588 (mm110) cc_final: 0.7183 (mm110) REVERT: A 72 ARG cc_start: 0.7814 (tmt-80) cc_final: 0.6784 (tmt-80) REVERT: A 262 GLU cc_start: 0.7330 (tp30) cc_final: 0.6946 (tp30) REVERT: A 266 ASP cc_start: 0.7811 (m-30) cc_final: 0.7545 (t0) REVERT: A 332 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7859 (mm) REVERT: A 387 SER cc_start: 0.7898 (t) cc_final: 0.7571 (t) REVERT: B 71 GLN cc_start: 0.7587 (mm110) cc_final: 0.6873 (mm110) REVERT: B 85 PHE cc_start: 0.8241 (t80) cc_final: 0.7767 (t80) REVERT: B 196 CYS cc_start: 0.7229 (OUTLIER) cc_final: 0.6650 (t) REVERT: B 262 GLU cc_start: 0.7263 (tp30) cc_final: 0.6839 (tp30) REVERT: B 332 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7733 (mm) REVERT: B 357 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7003 (tt) REVERT: B 361 GLN cc_start: 0.7022 (OUTLIER) cc_final: 0.6649 (mp10) REVERT: B 383 ILE cc_start: 0.7865 (mt) cc_final: 0.7550 (tt) REVERT: B 451 MET cc_start: 0.7262 (ttp) cc_final: 0.7004 (ttp) outliers start: 32 outliers final: 24 residues processed: 201 average time/residue: 0.2126 time to fit residues: 53.8534 Evaluate side-chains 219 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 188 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 191 GLN Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 420 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.0870 chunk 9 optimal weight: 0.6980 chunk 17 optimal weight: 0.2980 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 0.0980 chunk 65 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 361 GLN ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.156868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.135376 restraints weight = 9760.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.140094 restraints weight = 4908.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.143251 restraints weight = 3012.486| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6442 Z= 0.235 Angle : 0.707 12.054 8792 Z= 0.349 Chirality : 0.045 0.392 1086 Planarity : 0.005 0.055 1074 Dihedral : 4.118 17.503 860 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.59 % Allowed : 26.91 % Favored : 67.50 % 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: 0.86 (0.31), residues: 802 helix: 0.85 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -0.17 (0.59), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 92 HIS 0.017 0.002 HIS B 449 PHE 0.018 0.001 PHE B 420 TYR 0.022 0.002 TYR B 313 ARG 0.006 0.000 ARG B 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1745.21 seconds wall clock time: 41 minutes 31.22 seconds (2491.22 seconds total)