Starting phenix.real_space_refine on Sun Mar 17 23:05:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ng9_12310/03_2024/7ng9_12310.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ng9_12310/03_2024/7ng9_12310.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ng9_12310/03_2024/7ng9_12310.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ng9_12310/03_2024/7ng9_12310.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ng9_12310/03_2024/7ng9_12310.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ng9_12310/03_2024/7ng9_12310.pdb" } resolution = 3.3 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= 0.017 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 9 5.16 5 C 6021 2.51 5 N 1728 2.21 5 O 1995 1.98 5 H 9615 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 47": "OD1" <-> "OD2" Residue "A ARG 55": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 56": "OD1" <-> "OD2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A ASP 121": "OD1" <-> "OD2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 199": "OD1" <-> "OD2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "A ASP 405": "OD1" <-> "OD2" Residue "B PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 47": "OD1" <-> "OD2" Residue "B ARG 55": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 56": "OD1" <-> "OD2" Residue "B ASP 77": "OD1" <-> "OD2" Residue "B ASP 121": "OD1" <-> "OD2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 199": "OD1" <-> "OD2" Residue "B ASP 350": "OD1" <-> "OD2" Residue "B ASP 368": "OD1" <-> "OD2" Residue "B ASP 405": "OD1" <-> "OD2" Residue "C PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 47": "OD1" <-> "OD2" Residue "C ARG 55": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 56": "OD1" <-> "OD2" Residue "C ASP 77": "OD1" <-> "OD2" Residue "C ASP 121": "OD1" <-> "OD2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 199": "OD1" <-> "OD2" Residue "C ASP 350": "OD1" <-> "OD2" Residue "C ASP 368": "OD1" <-> "OD2" Residue "C ASP 405": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19368 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 6456 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 8, 'TRANS': 412} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 6456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 6456 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 8, 'TRANS': 412} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 6456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 6456 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 8, 'TRANS': 412} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 8.83, per 1000 atoms: 0.46 Number of scatterers: 19368 At special positions: 0 Unit cell: (79.734, 82.2, 152.892, 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 9 16.00 O 1995 8.00 N 1728 7.00 C 6021 6.00 H 9615 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: 15.68 Conformation dependent library (CDL) restraints added in 1.9 seconds 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2406 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 10 sheets defined 72.0% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 Processing helix chain 'A' and resid 14 through 36 removed outlier: 4.298A pdb=" N ASN A 32 " --> pdb=" O PHE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 77 through 147 removed outlier: 3.564A pdb=" N TRP A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 187 removed outlier: 3.665A pdb=" N VAL A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 220 Processing helix chain 'A' and resid 220 through 242 removed outlier: 3.571A pdb=" N LEU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 291 through 359 removed outlier: 4.056A pdb=" N LYS A 297 " --> pdb=" O ASN A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 398 Processing helix chain 'A' and resid 402 through 412 removed outlier: 3.534A pdb=" N LEU A 406 " --> pdb=" O ASN A 402 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 14 through 36 removed outlier: 4.298A pdb=" N ASN B 32 " --> pdb=" O PHE B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 77 through 147 removed outlier: 3.564A pdb=" N TRP B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 187 removed outlier: 3.664A pdb=" N VAL B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 220 Processing helix chain 'B' and resid 220 through 242 removed outlier: 3.570A pdb=" N LEU B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'B' and resid 291 through 359 removed outlier: 4.055A pdb=" N LYS B 297 " --> pdb=" O ASN B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 398 Processing helix chain 'B' and resid 402 through 412 removed outlier: 3.535A pdb=" N LEU B 406 " --> pdb=" O ASN B 402 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 14 through 36 removed outlier: 4.298A pdb=" N ASN C 32 " --> pdb=" O PHE C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 77 through 147 removed outlier: 3.564A pdb=" N TRP C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 187 removed outlier: 3.665A pdb=" N VAL C 154 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 220 Processing helix chain 'C' and resid 220 through 242 removed outlier: 3.570A pdb=" N LEU C 224 " --> pdb=" O ASN C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 245 No H-bonds generated for 'chain 'C' and resid 243 through 245' Processing helix chain 'C' and resid 291 through 359 removed outlier: 4.055A pdb=" N LYS C 297 " --> pdb=" O ASN C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 398 Processing helix chain 'C' and resid 402 through 412 removed outlier: 3.535A pdb=" N LEU C 406 " --> pdb=" O ASN C 402 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA2, first strand: chain 'A' and resid 192 through 196 removed outlier: 4.825A pdb=" N LYS A 415 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 251 through 253 removed outlier: 3.588A pdb=" N LYS A 277 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR C 48 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 256 through 258 Processing sheet with id=AA5, first strand: chain 'B' and resid 66 through 68 removed outlier: 4.021A pdb=" N TYR B 48 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS C 277 " --> pdb=" O SER C 253 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 196 removed outlier: 4.825A pdb=" N LYS B 415 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 251 through 253 removed outlier: 3.588A pdb=" N LYS B 277 " --> pdb=" O SER B 253 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 256 through 258 Processing sheet with id=AA9, first strand: chain 'C' and resid 192 through 196 removed outlier: 4.825A pdb=" N LYS C 415 " --> pdb=" O SER C 195 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 256 through 258 800 hydrogen bonds defined for protein. 2373 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: 7.65 Time building geometry restraints manager: 16.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 9615 1.03 - 1.22: 0 1.22 - 1.42: 4099 1.42 - 1.61: 5753 1.61 - 1.80: 18 Bond restraints: 19485 Sorted by residual: bond pdb=" N GLU C 1 " pdb=" H GLU C 1 " ideal model delta sigma weight residual 0.860 0.889 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" N GLU A 1 " pdb=" H GLU A 1 " ideal model delta sigma weight residual 0.860 0.889 -0.029 2.00e-02 2.50e+03 2.07e+00 bond pdb=" N GLU B 1 " pdb=" H GLU B 1 " ideal model delta sigma weight residual 0.860 0.888 -0.028 2.00e-02 2.50e+03 1.98e+00 bond pdb=" N GLU B 1 " pdb=" CA GLU B 1 " ideal model delta sigma weight residual 1.458 1.481 -0.023 1.90e-02 2.77e+03 1.44e+00 bond pdb=" N GLU A 1 " pdb=" CA GLU A 1 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.90e-02 2.77e+03 1.37e+00 ... (remaining 19480 not shown) Histogram of bond angle deviations from ideal: 99.50 - 106.39: 120 106.39 - 113.28: 22798 113.28 - 120.18: 6129 120.18 - 127.07: 5951 127.07 - 133.96: 39 Bond angle restraints: 35037 Sorted by residual: angle pdb=" C ARG B 55 " pdb=" N ASP B 56 " pdb=" CA ASP B 56 " ideal model delta sigma weight residual 121.54 127.41 -5.87 1.91e+00 2.74e-01 9.43e+00 angle pdb=" C ARG A 55 " pdb=" N ASP A 56 " pdb=" CA ASP A 56 " ideal model delta sigma weight residual 121.54 127.38 -5.84 1.91e+00 2.74e-01 9.35e+00 angle pdb=" C ARG C 55 " pdb=" N ASP C 56 " pdb=" CA ASP C 56 " ideal model delta sigma weight residual 121.54 127.31 -5.77 1.91e+00 2.74e-01 9.12e+00 angle pdb=" N SER C 36 " pdb=" CA SER C 36 " pdb=" C SER C 36 " ideal model delta sigma weight residual 109.81 113.55 -3.74 2.21e+00 2.05e-01 2.86e+00 angle pdb=" N SER B 36 " pdb=" CA SER B 36 " pdb=" C SER B 36 " ideal model delta sigma weight residual 109.81 113.54 -3.73 2.21e+00 2.05e-01 2.85e+00 ... (remaining 35032 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 8382 17.77 - 35.54: 585 35.54 - 53.31: 171 53.31 - 71.08: 33 71.08 - 88.86: 18 Dihedral angle restraints: 9189 sinusoidal: 5067 harmonic: 4122 Sorted by residual: dihedral pdb=" CA ASP B 77 " pdb=" CB ASP B 77 " pdb=" CG ASP B 77 " pdb=" OD1 ASP B 77 " ideal model delta sinusoidal sigma weight residual -30.00 -88.17 58.17 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP C 77 " pdb=" CB ASP C 77 " pdb=" CG ASP C 77 " pdb=" OD1 ASP C 77 " ideal model delta sinusoidal sigma weight residual -30.00 -88.12 58.12 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP A 77 " pdb=" CB ASP A 77 " pdb=" CG ASP A 77 " pdb=" OD1 ASP A 77 " ideal model delta sinusoidal sigma weight residual -30.00 -88.11 58.11 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 9186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 891 0.025 - 0.050: 420 0.050 - 0.075: 174 0.075 - 0.099: 66 0.099 - 0.124: 15 Chirality restraints: 1566 Sorted by residual: chirality pdb=" CA PRO B 37 " pdb=" N PRO B 37 " pdb=" C PRO B 37 " pdb=" CB PRO B 37 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA PRO A 15 " pdb=" N PRO A 15 " pdb=" C PRO A 15 " pdb=" CB PRO A 15 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.72e-01 chirality pdb=" CA PRO C 15 " pdb=" N PRO C 15 " pdb=" C PRO C 15 " pdb=" CB PRO C 15 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.68e-01 ... (remaining 1563 not shown) Planarity restraints: 3021 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 14 " -0.019 5.00e-02 4.00e+02 2.81e-02 1.27e+00 pdb=" N PRO C 15 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO C 15 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 15 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 14 " -0.019 5.00e-02 4.00e+02 2.80e-02 1.25e+00 pdb=" N PRO A 15 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 15 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 15 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 14 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO B 15 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 15 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 15 " 0.015 5.00e-02 4.00e+02 ... (remaining 3018 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1250 2.20 - 2.80: 41932 2.80 - 3.40: 52821 3.40 - 4.00: 68081 4.00 - 4.60: 110656 Nonbonded interactions: 274740 Sorted by model distance: nonbonded pdb="HE22 GLN A 298 " pdb=" OE1 GLU C 33 " model vdw 1.604 1.850 nonbonded pdb=" OE1 GLU B 33 " pdb="HE22 GLN C 298 " model vdw 1.617 1.850 nonbonded pdb=" OD1 ASN A 2 " pdb=" H LEU A 3 " model vdw 1.639 1.850 nonbonded pdb=" OD1 ASN C 2 " pdb=" H LEU C 3 " model vdw 1.639 1.850 nonbonded pdb=" OD1 ASN B 2 " pdb=" H LEU B 3 " model vdw 1.640 1.850 ... (remaining 274735 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 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: 0.290 Extract box with map and model: 3.020 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 64.090 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 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 : 0.007 0.041 9870 Z= 0.420 Angle : 0.480 5.867 13401 Z= 0.276 Chirality : 0.036 0.124 1566 Planarity : 0.003 0.028 1785 Dihedral : 14.724 88.855 3636 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.85 % Allowed : 9.89 % Favored : 89.27 % 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: -0.87 (0.22), residues: 1257 helix: 1.19 (0.16), residues: 780 sheet: -4.18 (0.27), residues: 204 loop : -2.63 (0.29), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 81 HIS 0.003 0.001 HIS A 244 PHE 0.008 0.001 PHE A 325 TYR 0.009 0.001 TYR B 374 ARG 0.002 0.000 ARG C 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 ASP cc_start: 0.6068 (OUTLIER) cc_final: 0.5734 (t70) REVERT: C 261 TYR cc_start: 0.8661 (m-80) cc_final: 0.8260 (m-80) outliers start: 9 outliers final: 8 residues processed: 65 average time/residue: 0.3455 time to fit residues: 35.5844 Evaluate side-chains 53 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 317 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9870 Z= 0.204 Angle : 0.430 4.098 13401 Z= 0.237 Chirality : 0.033 0.115 1566 Planarity : 0.003 0.021 1785 Dihedral : 4.242 45.976 1389 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.32 % Allowed : 10.64 % Favored : 88.04 % 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: 1.30 (0.25), residues: 1257 helix: 2.99 (0.16), residues: 816 sheet: -4.12 (0.25), residues: 222 loop : -1.89 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 81 HIS 0.008 0.002 HIS B 244 PHE 0.009 0.001 PHE C 28 TYR 0.010 0.001 TYR A 374 ARG 0.002 0.000 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 55 time to evaluate : 1.172 Fit side-chains REVERT: B 12 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7617 (mt) REVERT: B 174 ASP cc_start: 0.7178 (m-30) cc_final: 0.6881 (m-30) REVERT: C 261 TYR cc_start: 0.8716 (m-80) cc_final: 0.8256 (m-80) REVERT: C 352 MET cc_start: 0.7752 (mtt) cc_final: 0.7318 (mtt) outliers start: 14 outliers final: 5 residues processed: 68 average time/residue: 0.4343 time to fit residues: 42.8010 Evaluate side-chains 53 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain C residue 249 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN A 230 GLN A 390 ASN B 230 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 GLN C 390 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 9870 Z= 0.265 Angle : 0.466 4.433 13401 Z= 0.260 Chirality : 0.034 0.127 1566 Planarity : 0.003 0.022 1785 Dihedral : 4.338 50.612 1383 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.75 % Allowed : 12.90 % Favored : 86.35 % 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: 1.70 (0.25), residues: 1257 helix: 3.19 (0.17), residues: 816 sheet: -3.84 (0.27), residues: 216 loop : -1.54 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 81 HIS 0.008 0.002 HIS B 244 PHE 0.016 0.002 PHE C 282 TYR 0.014 0.001 TYR A 374 ARG 0.004 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 119 time to evaluate : 1.511 Fit side-chains revert: symmetry clash REVERT: A 202 LYS cc_start: 0.7634 (ptmm) cc_final: 0.7422 (ptpt) REVERT: B 174 ASP cc_start: 0.7191 (m-30) cc_final: 0.6825 (m-30) REVERT: B 202 LYS cc_start: 0.7745 (ptmm) cc_final: 0.7451 (ptpt) REVERT: C 202 LYS cc_start: 0.7665 (ptmm) cc_final: 0.7399 (ptpt) REVERT: C 261 TYR cc_start: 0.8864 (m-80) cc_final: 0.8337 (m-80) REVERT: C 350 ASP cc_start: 0.7688 (t70) cc_final: 0.7465 (t0) REVERT: C 352 MET cc_start: 0.8069 (mtt) cc_final: 0.7786 (mtt) outliers start: 8 outliers final: 5 residues processed: 126 average time/residue: 0.4359 time to fit residues: 78.8620 Evaluate side-chains 101 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain C residue 249 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 109 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN B 14 ASN B 259 ASN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9870 Z= 0.289 Angle : 0.464 4.186 13401 Z= 0.262 Chirality : 0.035 0.125 1566 Planarity : 0.003 0.026 1785 Dihedral : 4.465 53.382 1383 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.41 % Allowed : 12.99 % Favored : 85.59 % 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: 1.66 (0.25), residues: 1257 helix: 3.15 (0.16), residues: 816 sheet: -3.73 (0.29), residues: 222 loop : -1.59 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 81 HIS 0.004 0.002 HIS B 244 PHE 0.009 0.001 PHE A 325 TYR 0.013 0.002 TYR A 374 ARG 0.002 0.000 ARG B 322 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 1.613 Fit side-chains revert: symmetry clash REVERT: A 202 LYS cc_start: 0.7685 (ptmm) cc_final: 0.7447 (ptpt) REVERT: A 272 ASP cc_start: 0.6232 (p0) cc_final: 0.5735 (p0) REVERT: B 174 ASP cc_start: 0.7185 (m-30) cc_final: 0.6838 (m-30) REVERT: B 202 LYS cc_start: 0.7820 (ptmm) cc_final: 0.7496 (ptpt) REVERT: B 272 ASP cc_start: 0.6027 (p0) cc_final: 0.5516 (p0) REVERT: B 273 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7652 (pt) REVERT: C 202 LYS cc_start: 0.7668 (ptmm) cc_final: 0.7417 (ptpt) REVERT: C 223 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7987 (tp) REVERT: C 261 TYR cc_start: 0.8775 (m-80) cc_final: 0.8325 (m-80) REVERT: C 272 ASP cc_start: 0.6128 (p0) cc_final: 0.5610 (p0) REVERT: C 350 ASP cc_start: 0.7705 (t70) cc_final: 0.7501 (t0) REVERT: C 352 MET cc_start: 0.8137 (mtt) cc_final: 0.7797 (mtt) outliers start: 15 outliers final: 8 residues processed: 116 average time/residue: 0.4390 time to fit residues: 74.0646 Evaluate side-chains 107 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 249 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9870 Z= 0.285 Angle : 0.461 4.385 13401 Z= 0.260 Chirality : 0.034 0.124 1566 Planarity : 0.003 0.026 1785 Dihedral : 4.519 54.978 1383 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.51 % Allowed : 13.94 % Favored : 84.56 % 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: 1.65 (0.25), residues: 1257 helix: 3.13 (0.16), residues: 816 sheet: -3.69 (0.30), residues: 222 loop : -1.57 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 81 HIS 0.004 0.001 HIS B 244 PHE 0.010 0.001 PHE C 325 TYR 0.013 0.001 TYR A 374 ARG 0.002 0.000 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 1.455 Fit side-chains revert: symmetry clash REVERT: A 202 LYS cc_start: 0.7851 (ptmm) cc_final: 0.7525 (ptpt) REVERT: A 272 ASP cc_start: 0.6358 (p0) cc_final: 0.5918 (p0) REVERT: B 174 ASP cc_start: 0.7162 (m-30) cc_final: 0.6828 (m-30) REVERT: B 202 LYS cc_start: 0.7822 (ptmm) cc_final: 0.7504 (ptpt) REVERT: B 272 ASP cc_start: 0.6144 (p0) cc_final: 0.5666 (p0) REVERT: C 202 LYS cc_start: 0.7793 (ptmm) cc_final: 0.7459 (ptpt) REVERT: C 223 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.8002 (tp) REVERT: C 261 TYR cc_start: 0.8785 (m-80) cc_final: 0.8397 (m-80) REVERT: C 272 ASP cc_start: 0.6205 (p0) cc_final: 0.5716 (p0) REVERT: C 327 ASN cc_start: 0.7061 (p0) cc_final: 0.6648 (p0) REVERT: C 350 ASP cc_start: 0.7749 (t70) cc_final: 0.7522 (t0) REVERT: C 352 MET cc_start: 0.8165 (mtt) cc_final: 0.7920 (mtt) outliers start: 16 outliers final: 10 residues processed: 117 average time/residue: 0.4833 time to fit residues: 79.9119 Evaluate side-chains 110 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 249 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 24 optimal weight: 0.1980 chunk 71 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 GLN ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9870 Z= 0.152 Angle : 0.402 4.247 13401 Z= 0.225 Chirality : 0.032 0.117 1566 Planarity : 0.003 0.025 1785 Dihedral : 4.328 55.879 1383 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.41 % Allowed : 14.50 % Favored : 84.09 % 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: 2.11 (0.25), residues: 1257 helix: 3.51 (0.16), residues: 816 sheet: -3.54 (0.30), residues: 222 loop : -1.48 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 81 HIS 0.002 0.001 HIS A 314 PHE 0.010 0.001 PHE A 325 TYR 0.017 0.001 TYR B 287 ARG 0.001 0.000 ARG C 135 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 1.450 Fit side-chains revert: symmetry clash REVERT: A 202 LYS cc_start: 0.7788 (ptmm) cc_final: 0.7462 (ptpt) REVERT: A 272 ASP cc_start: 0.6426 (p0) cc_final: 0.6000 (p0) REVERT: B 174 ASP cc_start: 0.7078 (m-30) cc_final: 0.6614 (m-30) REVERT: B 202 LYS cc_start: 0.7800 (ptmm) cc_final: 0.7510 (ptpt) REVERT: B 272 ASP cc_start: 0.6234 (p0) cc_final: 0.5724 (p0) REVERT: B 273 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7742 (pt) REVERT: C 202 LYS cc_start: 0.7757 (ptmm) cc_final: 0.7457 (ptpt) REVERT: C 261 TYR cc_start: 0.8733 (m-80) cc_final: 0.8334 (m-80) REVERT: C 272 ASP cc_start: 0.6246 (p0) cc_final: 0.5759 (p0) REVERT: C 350 ASP cc_start: 0.7711 (t70) cc_final: 0.7462 (t0) REVERT: C 352 MET cc_start: 0.8159 (mtt) cc_final: 0.7906 (mtt) outliers start: 15 outliers final: 12 residues processed: 100 average time/residue: 0.4796 time to fit residues: 68.1996 Evaluate side-chains 97 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 406 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN B 259 ASN B 275 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9870 Z= 0.332 Angle : 0.485 4.572 13401 Z= 0.273 Chirality : 0.036 0.135 1566 Planarity : 0.003 0.026 1785 Dihedral : 4.592 56.350 1383 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.88 % Allowed : 14.31 % Favored : 83.80 % 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: 1.80 (0.25), residues: 1257 helix: 3.19 (0.16), residues: 816 sheet: -3.56 (0.30), residues: 222 loop : -1.41 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 81 HIS 0.003 0.001 HIS B 244 PHE 0.010 0.001 PHE A 325 TYR 0.013 0.002 TYR A 374 ARG 0.003 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 124 time to evaluate : 1.477 Fit side-chains revert: symmetry clash REVERT: A 202 LYS cc_start: 0.7883 (ptmm) cc_final: 0.7571 (ptpt) REVERT: A 272 ASP cc_start: 0.6510 (p0) cc_final: 0.6056 (p0) REVERT: A 327 ASN cc_start: 0.7217 (p0) cc_final: 0.6799 (p0) REVERT: B 174 ASP cc_start: 0.7157 (m-30) cc_final: 0.6821 (m-30) REVERT: B 202 LYS cc_start: 0.7858 (ptmm) cc_final: 0.7560 (ptpt) REVERT: B 272 ASP cc_start: 0.6433 (p0) cc_final: 0.5920 (p0) REVERT: B 273 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7886 (pt) REVERT: B 327 ASN cc_start: 0.7066 (p0) cc_final: 0.6670 (p0) REVERT: C 202 LYS cc_start: 0.7825 (ptmm) cc_final: 0.7518 (ptpt) REVERT: C 261 TYR cc_start: 0.8787 (m-80) cc_final: 0.8386 (m-80) REVERT: C 272 ASP cc_start: 0.6430 (p0) cc_final: 0.5939 (p0) REVERT: C 327 ASN cc_start: 0.7147 (p0) cc_final: 0.6758 (p0) REVERT: C 350 ASP cc_start: 0.7745 (t70) cc_final: 0.7531 (t0) REVERT: C 352 MET cc_start: 0.8171 (mtt) cc_final: 0.7933 (mtt) outliers start: 20 outliers final: 15 residues processed: 140 average time/residue: 0.4326 time to fit residues: 87.0690 Evaluate side-chains 131 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 420 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 82 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 GLN ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9870 Z= 0.205 Angle : 0.433 4.889 13401 Z= 0.241 Chirality : 0.033 0.117 1566 Planarity : 0.003 0.027 1785 Dihedral : 4.451 56.730 1383 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.60 % Allowed : 14.78 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.25), residues: 1257 helix: 3.37 (0.16), residues: 816 sheet: -3.45 (0.31), residues: 222 loop : -1.44 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 81 HIS 0.004 0.001 HIS A 314 PHE 0.010 0.001 PHE A 325 TYR 0.012 0.001 TYR A 374 ARG 0.001 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 1.507 Fit side-chains revert: symmetry clash REVERT: A 202 LYS cc_start: 0.7876 (ptmm) cc_final: 0.7651 (ptpt) REVERT: A 272 ASP cc_start: 0.6541 (p0) cc_final: 0.6115 (p0) REVERT: B 174 ASP cc_start: 0.7099 (m-30) cc_final: 0.6732 (m-30) REVERT: B 202 LYS cc_start: 0.7865 (ptmm) cc_final: 0.7549 (ptpt) REVERT: B 272 ASP cc_start: 0.6438 (p0) cc_final: 0.5933 (p0) REVERT: B 273 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7840 (pt) REVERT: C 202 LYS cc_start: 0.7797 (ptmm) cc_final: 0.7515 (ptpt) REVERT: C 261 TYR cc_start: 0.8745 (m-80) cc_final: 0.8348 (m-80) REVERT: C 272 ASP cc_start: 0.6431 (p0) cc_final: 0.5949 (p0) REVERT: C 350 ASP cc_start: 0.7710 (t70) cc_final: 0.7505 (t0) REVERT: C 352 MET cc_start: 0.8175 (mtt) cc_final: 0.7843 (mtt) outliers start: 17 outliers final: 13 residues processed: 112 average time/residue: 0.4401 time to fit residues: 70.6891 Evaluate side-chains 109 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 406 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 275 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9870 Z= 0.252 Angle : 0.454 4.632 13401 Z= 0.255 Chirality : 0.034 0.167 1566 Planarity : 0.003 0.027 1785 Dihedral : 4.508 57.189 1383 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.17 % Allowed : 13.94 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.25), residues: 1257 helix: 3.31 (0.16), residues: 816 sheet: -3.46 (0.31), residues: 222 loop : -1.44 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP C 81 HIS 0.006 0.001 HIS A 314 PHE 0.010 0.001 PHE B 325 TYR 0.013 0.001 TYR A 374 ARG 0.002 0.000 ARG B 322 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 1.440 Fit side-chains revert: symmetry clash REVERT: A 202 LYS cc_start: 0.7905 (ptmm) cc_final: 0.7641 (ptpt) REVERT: A 272 ASP cc_start: 0.6571 (p0) cc_final: 0.6199 (p0) REVERT: A 327 ASN cc_start: 0.7060 (p0) cc_final: 0.6639 (p0) REVERT: B 174 ASP cc_start: 0.7102 (m-30) cc_final: 0.6732 (m-30) REVERT: B 202 LYS cc_start: 0.7883 (ptmm) cc_final: 0.7564 (ptpt) REVERT: B 273 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7845 (pt) REVERT: C 202 LYS cc_start: 0.7804 (ptmm) cc_final: 0.7521 (ptpt) REVERT: C 223 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.8007 (tp) REVERT: C 261 TYR cc_start: 0.8760 (m-80) cc_final: 0.8351 (m-80) REVERT: C 272 ASP cc_start: 0.6457 (p0) cc_final: 0.5998 (p0) REVERT: C 350 ASP cc_start: 0.7727 (t70) cc_final: 0.7521 (t0) REVERT: C 352 MET cc_start: 0.8181 (mtt) cc_final: 0.7850 (mtt) outliers start: 23 outliers final: 17 residues processed: 125 average time/residue: 0.4575 time to fit residues: 81.0801 Evaluate side-chains 121 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 420 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 ASN B 275 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9870 Z= 0.266 Angle : 0.455 4.840 13401 Z= 0.255 Chirality : 0.034 0.121 1566 Planarity : 0.003 0.027 1785 Dihedral : 4.535 57.447 1383 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.69 % Allowed : 14.69 % Favored : 83.62 % 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: 1.92 (0.25), residues: 1257 helix: 3.28 (0.16), residues: 816 sheet: -3.43 (0.31), residues: 222 loop : -1.41 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 81 HIS 0.006 0.001 HIS A 314 PHE 0.010 0.001 PHE A 325 TYR 0.012 0.001 TYR A 374 ARG 0.002 0.000 ARG A 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 1.609 Fit side-chains REVERT: A 202 LYS cc_start: 0.7883 (ptmm) cc_final: 0.7628 (ptpt) REVERT: A 272 ASP cc_start: 0.6686 (p0) cc_final: 0.6308 (p0) REVERT: A 327 ASN cc_start: 0.7077 (p0) cc_final: 0.6660 (p0) REVERT: B 174 ASP cc_start: 0.7163 (m-30) cc_final: 0.6797 (m-30) REVERT: B 202 LYS cc_start: 0.7920 (ptmm) cc_final: 0.7631 (ptpt) REVERT: B 272 ASP cc_start: 0.6587 (p0) cc_final: 0.6102 (p0) REVERT: B 273 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7897 (pt) REVERT: C 202 LYS cc_start: 0.7793 (ptmm) cc_final: 0.7530 (ptpt) REVERT: C 261 TYR cc_start: 0.8761 (m-80) cc_final: 0.8348 (m-80) REVERT: C 272 ASP cc_start: 0.6533 (p0) cc_final: 0.6096 (p0) REVERT: C 352 MET cc_start: 0.8190 (mtt) cc_final: 0.7938 (mtt) outliers start: 18 outliers final: 16 residues processed: 120 average time/residue: 0.4763 time to fit residues: 80.6938 Evaluate side-chains 122 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 420 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 9.9990 chunk 100 optimal weight: 0.0040 chunk 41 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 87 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 GLN ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.134957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.112379 restraints weight = 28405.344| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 0.77 r_work: 0.3071 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 9870 Z= 0.125 Angle : 0.396 4.541 13401 Z= 0.223 Chirality : 0.031 0.115 1566 Planarity : 0.003 0.024 1785 Dihedral : 4.291 57.470 1383 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.22 % Allowed : 15.63 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.25), residues: 1257 helix: 3.72 (0.16), residues: 816 sheet: -3.28 (0.32), residues: 222 loop : -1.44 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 81 HIS 0.004 0.001 HIS A 314 PHE 0.012 0.001 PHE B 325 TYR 0.008 0.001 TYR B 374 ARG 0.001 0.000 ARG B 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3577.83 seconds wall clock time: 64 minutes 7.74 seconds (3847.74 seconds total)