Starting phenix.real_space_refine on Thu Feb 15 22:16:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9f_25756/02_2024/7t9f_25756.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9f_25756/02_2024/7t9f_25756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9f_25756/02_2024/7t9f_25756.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9f_25756/02_2024/7t9f_25756.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9f_25756/02_2024/7t9f_25756.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9f_25756/02_2024/7t9f_25756.pdb" } resolution = 3.23 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 4456 2.51 5 N 1046 2.21 5 O 1128 1.98 5 H 6958 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 116": "OD1" <-> "OD2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 116": "OD1" <-> "OD2" Residue "B TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13640 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 6820 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 15, 'TRANS': 429} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 6820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 6820 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 15, 'TRANS': 429} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.51, per 1000 atoms: 0.48 Number of scatterers: 13640 At special positions: 0 Unit cell: (88.81, 100.43, 76.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 O 1128 8.00 N 1046 7.00 C 4456 6.00 H 6958 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.93 Conformation dependent library (CDL) restraints added in 1.6 seconds 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1656 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 0 sheets defined 84.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 19 through 38 Processing helix chain 'A' and resid 42 through 62 Processing helix chain 'A' and resid 65 through 80 Proline residue: A 74 - end of helix Processing helix chain 'A' and resid 84 through 90 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 114 removed outlier: 3.718A pdb=" N PHE A 98 " --> pdb=" O ASN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 127 Processing helix chain 'A' and resid 130 through 147 removed outlier: 3.652A pdb=" N ALA A 134 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 135 " --> pdb=" O MET A 131 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N PHE A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 166 removed outlier: 3.795A pdb=" N MET A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N MET A 158 " --> pdb=" O THR A 154 " (cutoff:3.500A) Proline residue: A 160 - end of helix Processing helix chain 'A' and resid 175 through 193 removed outlier: 4.400A pdb=" N VAL A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 211 removed outlier: 3.770A pdb=" N ALA A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 240 Proline residue: A 223 - end of helix Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 260 through 277 Processing helix chain 'A' and resid 277 through 286 Processing helix chain 'A' and resid 290 through 306 Processing helix chain 'A' and resid 310 through 318 Processing helix chain 'A' and resid 319 through 339 removed outlier: 3.633A pdb=" N LEU A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 356 removed outlier: 5.025A pdb=" N ASP A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N MET A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 375 removed outlier: 4.334A pdb=" N PHE A 375 " --> pdb=" O PHE A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 397 Proline residue: A 387 - end of helix removed outlier: 3.765A pdb=" N THR A 391 " --> pdb=" O PRO A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 413 removed outlier: 4.066A pdb=" N LEU A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 429 Processing helix chain 'A' and resid 434 through 460 Processing helix chain 'B' and resid 19 through 38 Processing helix chain 'B' and resid 42 through 62 Processing helix chain 'B' and resid 65 through 80 Proline residue: B 74 - end of helix Processing helix chain 'B' and resid 84 through 90 Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 94 through 114 removed outlier: 3.719A pdb=" N PHE B 98 " --> pdb=" O ASN B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 127 Processing helix chain 'B' and resid 130 through 147 removed outlier: 3.652A pdb=" N ALA B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL B 135 " --> pdb=" O MET B 131 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N PHE B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 166 removed outlier: 3.795A pdb=" N MET B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N MET B 158 " --> pdb=" O THR B 154 " (cutoff:3.500A) Proline residue: B 160 - end of helix Processing helix chain 'B' and resid 175 through 193 removed outlier: 4.400A pdb=" N VAL B 185 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 211 removed outlier: 3.771A pdb=" N ALA B 204 " --> pdb=" O SER B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 240 Proline residue: B 223 - end of helix Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 260 through 277 Processing helix chain 'B' and resid 277 through 286 Processing helix chain 'B' and resid 290 through 306 Processing helix chain 'B' and resid 310 through 318 Processing helix chain 'B' and resid 319 through 339 removed outlier: 3.632A pdb=" N LEU B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY B 327 " --> pdb=" O LEU B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 356 removed outlier: 5.026A pdb=" N ASP B 351 " --> pdb=" O ASN B 347 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N MET B 352 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 375 removed outlier: 4.334A pdb=" N PHE B 375 " --> pdb=" O PHE B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 397 Proline residue: B 387 - end of helix removed outlier: 3.765A pdb=" N THR B 391 " --> pdb=" O PRO B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 413 removed outlier: 4.066A pdb=" N LEU B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 429 Processing helix chain 'B' and resid 434 through 460 512 hydrogen bonds defined for protein. 1536 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: 4.81 Time building geometry restraints manager: 12.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6952 1.03 - 1.23: 6 1.23 - 1.42: 2758 1.42 - 1.62: 3984 1.62 - 1.82: 98 Bond restraints: 13798 Sorted by residual: bond pdb=" CA ASP A 251 " pdb=" HA ASP A 251 " ideal model delta sigma weight residual 0.970 0.930 0.040 2.00e-02 2.50e+03 3.91e+00 bond pdb=" CB PHE B 428 " pdb=" CG PHE B 428 " ideal model delta sigma weight residual 1.502 1.544 -0.042 2.30e-02 1.89e+03 3.27e+00 bond pdb=" CB PHE A 428 " pdb=" CG PHE A 428 " ideal model delta sigma weight residual 1.502 1.542 -0.040 2.30e-02 1.89e+03 2.97e+00 bond pdb=" CB ASP B 251 " pdb=" CG ASP B 251 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.87e+00 bond pdb=" CB ASP A 251 " pdb=" CG ASP A 251 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.80e+00 ... (remaining 13793 not shown) Histogram of bond angle deviations from ideal: 69.22 - 83.64: 21 83.64 - 98.06: 7 98.06 - 112.49: 16547 112.49 - 126.91: 8401 126.91 - 141.33: 108 Bond angle restraints: 25084 Sorted by residual: angle pdb=" N ASP A 251 " pdb=" CA ASP A 251 " pdb=" HA ASP A 251 " ideal model delta sigma weight residual 110.00 69.22 40.78 3.00e+00 1.11e-01 1.85e+02 angle pdb=" C ASP A 251 " pdb=" CA ASP A 251 " pdb=" HA ASP A 251 " ideal model delta sigma weight residual 109.00 69.94 39.06 3.00e+00 1.11e-01 1.70e+02 angle pdb=" C SER A 213 " pdb=" CA SER A 213 " pdb=" HA SER A 213 " ideal model delta sigma weight residual 109.00 70.70 38.30 3.00e+00 1.11e-01 1.63e+02 angle pdb=" N SER A 213 " pdb=" CA SER A 213 " pdb=" HA SER A 213 " ideal model delta sigma weight residual 110.00 74.82 35.18 3.00e+00 1.11e-01 1.38e+02 angle pdb=" CB SER A 213 " pdb=" CA SER A 213 " pdb=" HA SER A 213 " ideal model delta sigma weight residual 109.00 74.29 34.71 3.00e+00 1.11e-01 1.34e+02 ... (remaining 25079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 5715 17.97 - 35.94: 515 35.94 - 53.91: 174 53.91 - 71.87: 50 71.87 - 89.84: 16 Dihedral angle restraints: 6470 sinusoidal: 3394 harmonic: 3076 Sorted by residual: dihedral pdb=" CA MET B 398 " pdb=" C MET B 398 " pdb=" N SER B 399 " pdb=" CA SER B 399 " ideal model delta harmonic sigma weight residual -180.00 -151.99 -28.01 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA MET A 398 " pdb=" C MET A 398 " pdb=" N SER A 399 " pdb=" CA SER A 399 " ideal model delta harmonic sigma weight residual -180.00 -152.04 -27.96 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA GLY B 397 " pdb=" C GLY B 397 " pdb=" N MET B 398 " pdb=" CA MET B 398 " ideal model delta harmonic sigma weight residual 180.00 156.91 23.09 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 6467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.398: 1156 0.398 - 0.795: 0 0.795 - 1.193: 0 1.193 - 1.590: 0 1.590 - 1.988: 2 Chirality restraints: 1158 Sorted by residual: chirality pdb=" CG LEU A 250 " pdb=" CB LEU A 250 " pdb=" CD1 LEU A 250 " pdb=" CD2 LEU A 250 " both_signs ideal model delta sigma weight residual False -2.59 -0.60 -1.99 2.00e-01 2.50e+01 9.88e+01 chirality pdb=" CG LEU B 250 " pdb=" CB LEU B 250 " pdb=" CD1 LEU B 250 " pdb=" CD2 LEU B 250 " both_signs ideal model delta sigma weight residual False -2.59 -0.60 -1.99 2.00e-01 2.50e+01 9.86e+01 chirality pdb=" CA ASP B 251 " pdb=" N ASP B 251 " pdb=" C ASP B 251 " pdb=" CB ASP B 251 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.41e-01 ... (remaining 1155 not shown) Planarity restraints: 1986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 28 " 0.015 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" CG ASP B 28 " -0.052 2.00e-02 2.50e+03 pdb=" OD1 ASP B 28 " 0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP B 28 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 28 " 0.015 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" CG ASP A 28 " -0.052 2.00e-02 2.50e+03 pdb=" OD1 ASP A 28 " 0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP A 28 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 428 " 0.004 2.00e-02 2.50e+03 1.02e-02 3.11e+00 pdb=" CG PHE A 428 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 428 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE A 428 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 428 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 428 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 428 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE A 428 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE A 428 " 0.007 2.00e-02 2.50e+03 pdb=" HE1 PHE A 428 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 428 " 0.005 2.00e-02 2.50e+03 pdb=" HZ PHE A 428 " -0.006 2.00e-02 2.50e+03 ... (remaining 1983 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.16: 456 2.16 - 2.77: 26456 2.77 - 3.38: 40023 3.38 - 3.99: 48857 3.99 - 4.60: 77944 Nonbonded interactions: 193736 Sorted by model distance: nonbonded pdb=" H ASP A 251 " pdb=" HA ASP A 251 " model vdw 1.556 1.816 nonbonded pdb=" H SER A 213 " pdb=" HA SER A 213 " model vdw 1.612 1.816 nonbonded pdb=" OE1 GLU B 313 " pdb=" H GLU B 313 " model vdw 1.639 1.850 nonbonded pdb=" OE1 GLU A 313 " pdb=" H GLU A 313 " model vdw 1.639 1.850 nonbonded pdb=" HB3 ARG A 252 " pdb=" HG2 ARG A 252 " model vdw 1.692 1.952 ... (remaining 193731 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 0.210 Extract box with map and model: 4.250 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 47.450 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 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 0.052 6840 Z= 0.290 Angle : 0.841 13.513 9326 Z= 0.428 Chirality : 0.092 1.988 1158 Planarity : 0.004 0.043 1128 Dihedral : 13.184 88.850 2300 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.28 % Allowed : 1.42 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.29), residues: 886 helix: 0.92 (0.19), residues: 720 sheet: None (None), residues: 0 loop : -3.50 (0.41), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 217 HIS 0.004 0.001 HIS A 19 PHE 0.026 0.002 PHE B 428 TYR 0.011 0.002 TYR B 187 ARG 0.004 0.001 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 125 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.6506 (mpp) cc_final: 0.6298 (mpp) REVERT: A 313 GLU cc_start: 0.7787 (mp0) cc_final: 0.7512 (mp0) outliers start: 2 outliers final: 2 residues processed: 125 average time/residue: 0.3433 time to fit residues: 60.3919 Evaluate side-chains 111 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 247 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 0.0000 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 51 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6840 Z= 0.193 Angle : 0.615 11.272 9326 Z= 0.313 Chirality : 0.084 1.808 1158 Planarity : 0.004 0.037 1128 Dihedral : 5.531 55.363 914 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.99 % Allowed : 6.68 % Favored : 92.33 % 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: 0.47 (0.29), residues: 886 helix: 1.15 (0.20), residues: 724 sheet: None (None), residues: 0 loop : -3.56 (0.40), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 311 HIS 0.001 0.000 HIS A 310 PHE 0.011 0.001 PHE A 371 TYR 0.009 0.001 TYR B 178 ARG 0.002 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.6701 (mpp) cc_final: 0.6473 (mpp) REVERT: B 131 MET cc_start: 0.6802 (mpp) cc_final: 0.6588 (mpp) REVERT: B 247 MET cc_start: 0.7266 (OUTLIER) cc_final: 0.6875 (mmm) outliers start: 7 outliers final: 6 residues processed: 115 average time/residue: 0.3326 time to fit residues: 55.6886 Evaluate side-chains 114 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 367 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6840 Z= 0.242 Angle : 0.604 11.120 9326 Z= 0.309 Chirality : 0.083 1.808 1158 Planarity : 0.004 0.037 1128 Dihedral : 5.137 45.607 914 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.85 % Allowed : 8.66 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.29), residues: 886 helix: 1.30 (0.20), residues: 728 sheet: None (None), residues: 0 loop : -3.55 (0.38), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 311 HIS 0.005 0.001 HIS B 310 PHE 0.012 0.001 PHE B 371 TYR 0.010 0.001 TYR A 178 ARG 0.002 0.000 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 112 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.6764 (mpp) cc_final: 0.6550 (mpp) REVERT: B 131 MET cc_start: 0.7014 (mpp) cc_final: 0.6812 (mpp) outliers start: 6 outliers final: 4 residues processed: 112 average time/residue: 0.3222 time to fit residues: 51.7696 Evaluate side-chains 110 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 106 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 367 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6840 Z= 0.290 Angle : 0.606 11.247 9326 Z= 0.312 Chirality : 0.083 1.791 1158 Planarity : 0.004 0.037 1128 Dihedral : 4.860 56.499 911 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.14 % Allowed : 9.94 % Favored : 88.92 % 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: 0.63 (0.28), residues: 886 helix: 1.27 (0.19), residues: 724 sheet: None (None), residues: 0 loop : -3.59 (0.37), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 311 HIS 0.003 0.001 HIS A 310 PHE 0.011 0.001 PHE A 98 TYR 0.013 0.001 TYR B 178 ARG 0.002 0.000 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 108 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 110 average time/residue: 0.3167 time to fit residues: 50.4099 Evaluate side-chains 106 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain B residue 144 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6840 Z= 0.270 Angle : 0.592 11.143 9326 Z= 0.304 Chirality : 0.082 1.748 1158 Planarity : 0.004 0.035 1128 Dihedral : 4.360 24.403 908 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.85 % Allowed : 10.51 % Favored : 88.64 % 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: 0.71 (0.29), residues: 886 helix: 1.35 (0.19), residues: 724 sheet: None (None), residues: 0 loop : -3.68 (0.36), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 311 HIS 0.003 0.001 HIS B 310 PHE 0.017 0.001 PHE A 100 TYR 0.006 0.001 TYR B 178 ARG 0.002 0.000 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 106 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 108 average time/residue: 0.3358 time to fit residues: 51.8446 Evaluate side-chains 106 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 103 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain B residue 144 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6840 Z= 0.301 Angle : 0.598 10.985 9326 Z= 0.309 Chirality : 0.082 1.750 1158 Planarity : 0.004 0.035 1128 Dihedral : 4.367 24.615 908 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.71 % Allowed : 11.22 % Favored : 88.07 % 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: 0.74 (0.29), residues: 886 helix: 1.36 (0.19), residues: 724 sheet: None (None), residues: 0 loop : -3.62 (0.37), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 311 HIS 0.004 0.001 HIS A 310 PHE 0.012 0.001 PHE A 98 TYR 0.014 0.001 TYR A 178 ARG 0.002 0.000 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 108 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 111 average time/residue: 0.3240 time to fit residues: 52.0190 Evaluate side-chains 110 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 106 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain B residue 421 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 52 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6840 Z= 0.312 Angle : 0.600 10.936 9326 Z= 0.312 Chirality : 0.082 1.740 1158 Planarity : 0.004 0.034 1128 Dihedral : 4.392 25.514 908 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.85 % Allowed : 13.64 % Favored : 85.51 % 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: 0.71 (0.28), residues: 886 helix: 1.34 (0.19), residues: 724 sheet: None (None), residues: 0 loop : -3.59 (0.37), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 311 HIS 0.004 0.001 HIS A 65 PHE 0.013 0.001 PHE A 100 TYR 0.005 0.001 TYR A 178 ARG 0.002 0.000 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 107 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 112 average time/residue: 0.3420 time to fit residues: 55.5069 Evaluate side-chains 110 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 105 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain B residue 421 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6840 Z= 0.303 Angle : 0.609 10.801 9326 Z= 0.314 Chirality : 0.082 1.743 1158 Planarity : 0.004 0.034 1128 Dihedral : 4.413 25.144 908 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.14 % Allowed : 14.06 % Favored : 84.80 % 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: 0.75 (0.28), residues: 886 helix: 1.34 (0.19), residues: 726 sheet: None (None), residues: 0 loop : -3.53 (0.38), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 311 HIS 0.003 0.001 HIS B 65 PHE 0.011 0.001 PHE A 98 TYR 0.006 0.001 TYR B 187 ARG 0.003 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 427 VAL cc_start: 0.6832 (OUTLIER) cc_final: 0.6577 (p) outliers start: 8 outliers final: 6 residues processed: 113 average time/residue: 0.3233 time to fit residues: 52.7408 Evaluate side-chains 113 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 106 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 427 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.3980 chunk 81 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6840 Z= 0.186 Angle : 0.570 10.970 9326 Z= 0.288 Chirality : 0.080 1.712 1158 Planarity : 0.004 0.035 1128 Dihedral : 4.350 25.489 908 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.14 % Allowed : 13.78 % Favored : 85.09 % 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: 1.01 (0.29), residues: 886 helix: 1.49 (0.19), residues: 730 sheet: None (None), residues: 0 loop : -3.42 (0.39), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 311 HIS 0.003 0.001 HIS B 65 PHE 0.007 0.001 PHE A 268 TYR 0.004 0.001 TYR A 237 ARG 0.001 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 427 VAL cc_start: 0.6806 (OUTLIER) cc_final: 0.6554 (p) outliers start: 8 outliers final: 5 residues processed: 117 average time/residue: 0.3182 time to fit residues: 53.8649 Evaluate side-chains 111 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 427 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6840 Z= 0.301 Angle : 0.629 10.922 9326 Z= 0.318 Chirality : 0.082 1.740 1158 Planarity : 0.004 0.035 1128 Dihedral : 4.367 24.917 908 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.85 % Allowed : 14.77 % Favored : 84.38 % 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: 0.92 (0.29), residues: 886 helix: 1.43 (0.19), residues: 728 sheet: None (None), residues: 0 loop : -3.37 (0.40), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 311 HIS 0.004 0.001 HIS B 65 PHE 0.012 0.001 PHE A 98 TYR 0.009 0.001 TYR B 178 ARG 0.003 0.000 ARG B 252 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 107 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 427 VAL cc_start: 0.6838 (OUTLIER) cc_final: 0.6589 (p) outliers start: 6 outliers final: 5 residues processed: 112 average time/residue: 0.3219 time to fit residues: 52.0582 Evaluate side-chains 113 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 107 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 427 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.127423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.094458 restraints weight = 40204.094| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.71 r_work: 0.3194 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6840 Z= 0.222 Angle : 0.597 10.937 9326 Z= 0.299 Chirality : 0.081 1.723 1158 Planarity : 0.004 0.035 1128 Dihedral : 4.352 25.216 908 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.71 % Allowed : 14.63 % Favored : 84.66 % 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: 0.99 (0.29), residues: 886 helix: 1.49 (0.19), residues: 730 sheet: None (None), residues: 0 loop : -3.47 (0.39), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 311 HIS 0.003 0.001 HIS B 65 PHE 0.009 0.001 PHE A 98 TYR 0.010 0.001 TYR B 178 ARG 0.001 0.000 ARG B 252 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3275.58 seconds wall clock time: 58 minutes 34.78 seconds (3514.78 seconds total)