Starting phenix.real_space_refine on Sun Mar 10 23:00:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ywa_34151/03_2024/7ywa_34151_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ywa_34151/03_2024/7ywa_34151.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ywa_34151/03_2024/7ywa_34151.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ywa_34151/03_2024/7ywa_34151.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ywa_34151/03_2024/7ywa_34151_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ywa_34151/03_2024/7ywa_34151_updated.pdb" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 2 5.21 5 S 27 5.16 5 C 3611 2.51 5 N 998 2.21 5 O 1158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 19": "OD1" <-> "OD2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "F GLU 18": "OE1" <-> "OE2" Residue "F ASP 94": "OD1" <-> "OD2" Residue "F GLU 96": "OE1" <-> "OE2" Residue "F GLU 123": "OE1" <-> "OE2" Residue "F PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 207": "OE1" <-> "OE2" Residue "F TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 266": "OE1" <-> "OE2" Residue "F PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 276": "OD1" <-> "OD2" Residue "F GLU 281": "OE1" <-> "OE2" Residue "F TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 4": "OE1" <-> "OE2" Residue "G PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 94": "OD1" <-> "OD2" Residue "G ASP 139": "OD1" <-> "OD2" Residue "G ASP 144": "OD1" <-> "OD2" Residue "G GLU 156": "OE1" <-> "OE2" Residue "G GLU 158": "OE1" <-> "OE2" Residue "G GLU 207": "OE1" <-> "OE2" Residue "G PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 224": "OD1" <-> "OD2" Residue "G TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 314": "OE1" <-> "OE2" Residue "G GLU 325": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5808 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 608 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "F" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2508 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 9, 'TRANS': 323} Chain: "G" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2508 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 9, 'TRANS': 323} Chain: "S" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.94, per 1000 atoms: 0.68 Number of scatterers: 5808 At special positions: 0 Unit cell: (98.58, 79.05, 104.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 27 16.00 P 12 15.00 Mg 2 11.99 O 1158 8.00 N 998 7.00 C 3611 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 1.2 seconds 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1344 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 10 sheets defined 42.3% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 9 through 11 No H-bonds generated for 'chain 'A' and resid 9 through 11' Processing helix chain 'A' and resid 17 through 32 Processing helix chain 'A' and resid 57 through 72 Processing helix chain 'A' and resid 74 through 77 No H-bonds generated for 'chain 'A' and resid 74 through 77' Processing helix chain 'F' and resid 2 through 21 Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 33 through 35 No H-bonds generated for 'chain 'F' and resid 33 through 35' Processing helix chain 'F' and resid 45 through 51 Processing helix chain 'F' and resid 72 through 86 Processing helix chain 'F' and resid 101 through 106 Processing helix chain 'F' and resid 111 through 113 No H-bonds generated for 'chain 'F' and resid 111 through 113' Processing helix chain 'F' and resid 122 through 135 Processing helix chain 'F' and resid 146 through 148 No H-bonds generated for 'chain 'F' and resid 146 through 148' Processing helix chain 'F' and resid 152 through 156 Processing helix chain 'F' and resid 166 through 185 removed outlier: 4.877A pdb=" N GLY F 180 " --> pdb=" O ARG F 176 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASN F 181 " --> pdb=" O LYS F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 218 Processing helix chain 'F' and resid 270 through 280 removed outlier: 3.505A pdb=" N ASP F 276 " --> pdb=" O GLY F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 311 Processing helix chain 'F' and resid 313 through 327 Processing helix chain 'G' and resid 2 through 21 Processing helix chain 'G' and resid 29 through 31 No H-bonds generated for 'chain 'G' and resid 29 through 31' Processing helix chain 'G' and resid 33 through 35 No H-bonds generated for 'chain 'G' and resid 33 through 35' Processing helix chain 'G' and resid 45 through 50 Processing helix chain 'G' and resid 72 through 86 removed outlier: 3.632A pdb=" N GLU G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 106 Processing helix chain 'G' and resid 122 through 135 Processing helix chain 'G' and resid 146 through 148 No H-bonds generated for 'chain 'G' and resid 146 through 148' Processing helix chain 'G' and resid 152 through 156 Processing helix chain 'G' and resid 166 through 185 removed outlier: 4.922A pdb=" N GLY G 180 " --> pdb=" O ARG G 176 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASN G 181 " --> pdb=" O LYS G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 218 Processing helix chain 'G' and resid 270 through 280 Processing helix chain 'G' and resid 302 through 311 Processing helix chain 'G' and resid 313 through 327 Processing sheet with id= A, first strand: chain 'A' and resid 39 through 45 Processing sheet with id= B, first strand: chain 'F' and resid 257 through 263 removed outlier: 6.412A pdb=" N ARG F 222 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL F 221 " --> pdb=" O ILE F 61 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU F 189 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ILE F 64 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N PHE F 191 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N GLY F 66 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ASN F 193 " --> pdb=" O GLY F 66 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'F' and resid 195 through 197 Processing sheet with id= D, first strand: chain 'F' and resid 285 through 287 removed outlier: 6.150A pdb=" N TYR F 293 " --> pdb=" O LYS F 297 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LYS F 297 " --> pdb=" O TYR F 293 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'F' and resid 229 through 233 removed outlier: 6.276A pdb=" N GLU F 233 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N VAL F 237 " --> pdb=" O GLU F 233 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'G' and resid 38 through 40 removed outlier: 4.743A pdb=" N GLU G 38 " --> pdb=" O MET G 58 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 115 through 117 removed outlier: 6.378A pdb=" N VAL G 140 " --> pdb=" O ALA G 91 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ILE G 93 " --> pdb=" O VAL G 140 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL G 142 " --> pdb=" O ILE G 93 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU G 188 " --> pdb=" O ILE G 141 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL G 143 " --> pdb=" O LEU G 188 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE G 190 " --> pdb=" O VAL G 143 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY G 66 " --> pdb=" O ASN G 193 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N GLU G 63 " --> pdb=" O SER G 220 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG G 222 " --> pdb=" O GLU G 63 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N TYR G 65 " --> pdb=" O ARG G 222 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP G 224 " --> pdb=" O TYR G 65 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASP G 224 " --> pdb=" O VAL G 246 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VAL G 246 " --> pdb=" O ASP G 224 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ARG G 226 " --> pdb=" O VAL G 244 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N VAL G 244 " --> pdb=" O ARG G 226 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'G' and resid 195 through 197 Processing sheet with id= I, first strand: chain 'G' and resid 285 through 287 Processing sheet with id= J, first strand: chain 'G' and resid 229 through 233 removed outlier: 6.389A pdb=" N GLU G 233 " --> pdb=" O VAL G 237 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL G 237 " --> pdb=" O GLU G 233 " (cutoff:3.500A) 266 hydrogen bonds defined for protein. 768 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.53 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.36: 1952 1.36 - 1.53: 3403 1.53 - 1.70: 489 1.70 - 1.86: 44 1.86 - 2.03: 2 Bond restraints: 5890 Sorted by residual: bond pdb=" C4 AGS F 402 " pdb=" C5 AGS F 402 " ideal model delta sigma weight residual 1.386 1.455 -0.069 1.00e-02 1.00e+04 4.83e+01 bond pdb=" C4 AGS G 401 " pdb=" C5 AGS G 401 " ideal model delta sigma weight residual 1.386 1.453 -0.067 1.00e-02 1.00e+04 4.50e+01 bond pdb=" C5 AGS F 402 " pdb=" C6 AGS F 402 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.30e+01 bond pdb=" C5 AGS G 401 " pdb=" C6 AGS G 401 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.84e+01 bond pdb=" O3G AGS F 402 " pdb=" PG AGS F 402 " ideal model delta sigma weight residual 1.558 1.450 0.108 2.00e-02 2.50e+03 2.91e+01 ... (remaining 5885 not shown) Histogram of bond angle deviations from ideal: 97.53 - 105.30: 109 105.30 - 113.07: 3261 113.07 - 120.84: 2782 120.84 - 128.61: 1797 128.61 - 136.38: 21 Bond angle restraints: 7970 Sorted by residual: angle pdb=" C5 AGS F 402 " pdb=" C4 AGS F 402 " pdb=" N3 AGS F 402 " ideal model delta sigma weight residual 126.80 117.91 8.89 7.41e-01 1.82e+00 1.44e+02 angle pdb=" C5 AGS G 401 " pdb=" C4 AGS G 401 " pdb=" N3 AGS G 401 " ideal model delta sigma weight residual 126.80 118.34 8.46 7.41e-01 1.82e+00 1.30e+02 angle pdb=" C4 AGS G 401 " pdb=" C5 AGS G 401 " pdb=" N7 AGS G 401 " ideal model delta sigma weight residual 110.73 106.25 4.48 4.52e-01 4.89e+00 9.84e+01 angle pdb=" C5 AGS G 401 " pdb=" N7 AGS G 401 " pdb=" C8 AGS G 401 " ideal model delta sigma weight residual 103.67 107.83 -4.16 4.26e-01 5.51e+00 9.54e+01 angle pdb=" C4 AGS F 402 " pdb=" C5 AGS F 402 " pdb=" N7 AGS F 402 " ideal model delta sigma weight residual 110.73 106.59 4.14 4.52e-01 4.89e+00 8.40e+01 ... (remaining 7965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.74: 3312 28.74 - 57.48: 246 57.48 - 86.22: 28 86.22 - 114.96: 1 114.96 - 143.70: 2 Dihedral angle restraints: 3589 sinusoidal: 1488 harmonic: 2101 Sorted by residual: dihedral pdb=" O1A AGS F 402 " pdb=" O3A AGS F 402 " pdb=" PA AGS F 402 " pdb=" PB AGS F 402 " ideal model delta sinusoidal sigma weight residual -67.73 75.97 -143.70 1 3.00e+01 1.11e-03 1.93e+01 dihedral pdb=" O1A AGS G 401 " pdb=" O3A AGS G 401 " pdb=" PA AGS G 401 " pdb=" PB AGS G 401 " ideal model delta sinusoidal sigma weight residual -67.73 49.39 -117.12 1 3.00e+01 1.11e-03 1.55e+01 dihedral pdb=" CA LEU G 326 " pdb=" C LEU G 326 " pdb=" N LEU G 327 " pdb=" CA LEU G 327 " ideal model delta harmonic sigma weight residual -180.00 -161.06 -18.94 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 3586 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 781 0.068 - 0.136: 116 0.136 - 0.204: 14 0.204 - 0.272: 1 0.272 - 0.340: 2 Chirality restraints: 914 Sorted by residual: chirality pdb=" CA ILE F 262 " pdb=" N ILE F 262 " pdb=" C ILE F 262 " pdb=" CB ILE F 262 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" C2' AGS G 401 " pdb=" C1' AGS G 401 " pdb=" C3' AGS G 401 " pdb=" O2' AGS G 401 " both_signs ideal model delta sigma weight residual False -2.67 -2.38 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA PRO F 101 " pdb=" N PRO F 101 " pdb=" C PRO F 101 " pdb=" CB PRO F 101 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 911 not shown) Planarity restraints: 1006 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR F 264 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.97e+00 pdb=" C TYR F 264 " 0.039 2.00e-02 2.50e+03 pdb=" O TYR F 264 " -0.014 2.00e-02 2.50e+03 pdb=" N GLY F 265 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 77 " -0.011 2.00e-02 2.50e+03 1.30e-02 4.23e+00 pdb=" CG TRP A 77 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP A 77 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 77 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 77 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 77 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 77 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 77 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 77 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 77 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE F 262 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.43e+00 pdb=" C ILE F 262 " -0.032 2.00e-02 2.50e+03 pdb=" O ILE F 262 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU F 263 " 0.011 2.00e-02 2.50e+03 ... (remaining 1003 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 14 2.35 - 2.99: 3025 2.99 - 3.63: 8979 3.63 - 4.26: 13608 4.26 - 4.90: 22472 Nonbonded interactions: 48098 Sorted by model distance: nonbonded pdb="MG MG F 401 " pdb=" O2G AGS F 402 " model vdw 1.718 2.170 nonbonded pdb="MG MG F 403 " pdb=" O2G AGS G 401 " model vdw 1.888 2.170 nonbonded pdb=" OG1 THR G 73 " pdb="MG MG F 403 " model vdw 1.978 2.170 nonbonded pdb=" O SER A 11 " pdb=" OG SER A 11 " model vdw 2.215 2.440 nonbonded pdb=" OE1 GLN F 194 " pdb=" NH1 ARG F 196 " model vdw 2.237 2.520 ... (remaining 48093 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 'F' and resid 1 through 333) selection = (chain 'G' and resid 1 through 333) } 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.820 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 20.330 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 29.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 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 : 0.006 0.108 5890 Z= 0.363 Angle : 0.870 13.569 7970 Z= 0.597 Chirality : 0.050 0.340 914 Planarity : 0.003 0.028 1006 Dihedral : 18.909 143.701 2245 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.85 % Allowed : 23.68 % Favored : 75.47 % 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: 0.53 (0.29), residues: 738 helix: 1.41 (0.28), residues: 340 sheet: 0.74 (0.43), residues: 127 loop : -1.20 (0.32), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 77 HIS 0.001 0.001 HIS F 163 PHE 0.006 0.001 PHE G 260 TYR 0.020 0.002 TYR F 103 ARG 0.004 0.000 ARG F 196 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 118 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: F 6 LYS cc_start: 0.5170 (mtpt) cc_final: 0.4962 (tppt) REVERT: F 20 GLN cc_start: 0.6916 (tt0) cc_final: 0.6448 (tt0) REVERT: F 38 GLU cc_start: 0.5771 (tt0) cc_final: 0.5326 (tp30) REVERT: F 79 VAL cc_start: 0.7221 (p) cc_final: 0.6697 (t) REVERT: F 93 ILE cc_start: 0.7529 (mm) cc_final: 0.7231 (mm) REVERT: F 169 ARG cc_start: 0.7511 (ttp-110) cc_final: 0.7232 (ttm-80) REVERT: F 198 LYS cc_start: 0.8090 (ptpp) cc_final: 0.7704 (mtpp) REVERT: F 202 MET cc_start: 0.1797 (mmm) cc_final: 0.1009 (mtp) REVERT: F 213 ASN cc_start: 0.7975 (t0) cc_final: 0.7682 (m-40) REVERT: F 266 GLU cc_start: 0.7685 (mp0) cc_final: 0.7020 (tm-30) REVERT: G 35 MET cc_start: 0.6161 (mmt) cc_final: 0.5958 (mmt) REVERT: G 106 LYS cc_start: 0.7257 (mtpt) cc_final: 0.6871 (mtpp) REVERT: G 110 ASP cc_start: 0.5649 (t0) cc_final: 0.4978 (m-30) REVERT: G 120 ASP cc_start: 0.7082 (m-30) cc_final: 0.6211 (t0) REVERT: G 134 ARG cc_start: 0.5317 (mtm110) cc_final: 0.4781 (mtt180) REVERT: G 162 SER cc_start: 0.7260 (m) cc_final: 0.7014 (t) REVERT: G 164 MET cc_start: 0.5781 (mmm) cc_final: 0.5098 (mmm) REVERT: G 176 ARG cc_start: 0.4899 (mmt180) cc_final: 0.3240 (mtm180) REVERT: G 177 LYS cc_start: 0.7137 (mtpp) cc_final: 0.6459 (mmtt) REVERT: G 283 LEU cc_start: 0.5871 (mt) cc_final: 0.5564 (tt) REVERT: G 310 LYS cc_start: 0.6745 (ttmt) cc_final: 0.6198 (mtmm) outliers start: 5 outliers final: 4 residues processed: 122 average time/residue: 0.2254 time to fit residues: 34.0732 Evaluate side-chains 92 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 88 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain G residue 150 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 4.9990 chunk 55 optimal weight: 0.0270 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 overall best weight: 1.1240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 16 GLN F 78 GLN F 304 ASN ** G 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5890 Z= 0.191 Angle : 0.539 8.032 7970 Z= 0.281 Chirality : 0.043 0.147 914 Planarity : 0.003 0.026 1006 Dihedral : 12.879 143.045 893 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.07 % Allowed : 22.15 % Favored : 74.79 % 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 (0.30), residues: 738 helix: 1.47 (0.28), residues: 341 sheet: 1.07 (0.44), residues: 123 loop : -1.12 (0.34), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 77 HIS 0.001 0.000 HIS A 39 PHE 0.014 0.001 PHE F 260 TYR 0.010 0.001 TYR F 264 ARG 0.002 0.000 ARG F 324 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 87 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: F 38 GLU cc_start: 0.5881 (tt0) cc_final: 0.5356 (tp30) REVERT: F 93 ILE cc_start: 0.7603 (mm) cc_final: 0.7267 (mm) REVERT: F 169 ARG cc_start: 0.7493 (ttp-110) cc_final: 0.7246 (ttm-80) REVERT: F 170 MET cc_start: 0.7614 (ttp) cc_final: 0.7374 (ttp) REVERT: F 198 LYS cc_start: 0.7936 (ptpp) cc_final: 0.7436 (mtpp) REVERT: F 202 MET cc_start: 0.1882 (mmm) cc_final: 0.1263 (mtm) REVERT: F 213 ASN cc_start: 0.7921 (OUTLIER) cc_final: 0.7634 (m-40) REVERT: F 236 ASN cc_start: 0.6197 (OUTLIER) cc_final: 0.5701 (p0) REVERT: F 266 GLU cc_start: 0.7568 (mp0) cc_final: 0.7165 (tp30) REVERT: G 106 LYS cc_start: 0.7287 (mtpt) cc_final: 0.6895 (mtpp) REVERT: G 110 ASP cc_start: 0.5690 (t0) cc_final: 0.5018 (m-30) REVERT: G 134 ARG cc_start: 0.5278 (mtm110) cc_final: 0.4833 (mtm180) REVERT: G 164 MET cc_start: 0.6135 (mmm) cc_final: 0.5929 (mmm) REVERT: G 176 ARG cc_start: 0.4895 (mmt180) cc_final: 0.3264 (mtm110) REVERT: G 177 LYS cc_start: 0.7111 (mtpp) cc_final: 0.6434 (mmtt) REVERT: G 250 LYS cc_start: 0.7320 (OUTLIER) cc_final: 0.7105 (mttt) REVERT: G 282 LYS cc_start: 0.7492 (mmtt) cc_final: 0.7152 (mmmt) REVERT: G 310 LYS cc_start: 0.6745 (ttmt) cc_final: 0.6231 (mtmm) outliers start: 18 outliers final: 8 residues processed: 98 average time/residue: 0.2300 time to fit residues: 28.0688 Evaluate side-chains 93 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 213 ASN Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 250 LYS Chi-restraints excluded: chain G residue 326 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 36 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 45 optimal weight: 0.0040 chunk 18 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 71 optimal weight: 0.1980 chunk 59 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 22 optimal weight: 0.0980 chunk 53 optimal weight: 0.9980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 304 ASN G 118 GLN G 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5890 Z= 0.141 Angle : 0.473 7.873 7970 Z= 0.251 Chirality : 0.042 0.142 914 Planarity : 0.002 0.022 1006 Dihedral : 12.573 141.230 889 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.24 % Allowed : 21.64 % Favored : 75.13 % 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 (0.30), residues: 738 helix: 1.65 (0.28), residues: 341 sheet: 1.27 (0.45), residues: 123 loop : -1.05 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 77 HIS 0.003 0.001 HIS F 97 PHE 0.009 0.001 PHE F 260 TYR 0.007 0.001 TYR F 291 ARG 0.003 0.000 ARG F 324 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: A 27 ARG cc_start: 0.4523 (tmt170) cc_final: 0.4321 (mtm180) REVERT: A 72 GLU cc_start: 0.6226 (mp0) cc_final: 0.5876 (mp0) REVERT: F 27 MET cc_start: 0.6571 (ptp) cc_final: 0.5632 (ttm) REVERT: F 38 GLU cc_start: 0.5872 (tt0) cc_final: 0.5386 (tp30) REVERT: F 79 VAL cc_start: 0.7197 (p) cc_final: 0.6625 (t) REVERT: F 93 ILE cc_start: 0.7484 (mm) cc_final: 0.7135 (mm) REVERT: F 166 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6673 (tp) REVERT: F 169 ARG cc_start: 0.7470 (ttp-110) cc_final: 0.7238 (ttm-80) REVERT: F 202 MET cc_start: 0.1869 (mmm) cc_final: 0.1072 (mtm) REVERT: F 213 ASN cc_start: 0.7885 (OUTLIER) cc_final: 0.7628 (m-40) REVERT: F 224 ASP cc_start: 0.7707 (t0) cc_final: 0.7371 (t70) REVERT: F 236 ASN cc_start: 0.6224 (OUTLIER) cc_final: 0.5796 (p0) REVERT: F 266 GLU cc_start: 0.7463 (mp0) cc_final: 0.7129 (tp30) REVERT: G 76 THR cc_start: 0.7508 (OUTLIER) cc_final: 0.7199 (p) REVERT: G 106 LYS cc_start: 0.7163 (mtpt) cc_final: 0.6757 (mtpp) REVERT: G 134 ARG cc_start: 0.5326 (mtm110) cc_final: 0.4876 (mtm180) REVERT: G 164 MET cc_start: 0.6019 (mmm) cc_final: 0.5784 (mmm) REVERT: G 176 ARG cc_start: 0.4917 (mmt180) cc_final: 0.3111 (mtm110) REVERT: G 177 LYS cc_start: 0.7040 (mtpp) cc_final: 0.6391 (mmtt) REVERT: G 250 LYS cc_start: 0.7262 (OUTLIER) cc_final: 0.6770 (mtmt) REVERT: G 282 LYS cc_start: 0.7447 (mmtt) cc_final: 0.7143 (mmmt) outliers start: 19 outliers final: 9 residues processed: 98 average time/residue: 0.2360 time to fit residues: 28.7785 Evaluate side-chains 97 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 213 ASN Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 250 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 7 optimal weight: 0.0370 chunk 31 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 70 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 overall best weight: 1.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 78 GLN F 269 ASN F 304 ASN G 7 GLN G 184 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5890 Z= 0.193 Angle : 0.488 6.369 7970 Z= 0.257 Chirality : 0.042 0.143 914 Planarity : 0.003 0.023 1006 Dihedral : 12.609 145.764 889 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.09 % Allowed : 21.98 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.30), residues: 738 helix: 1.72 (0.28), residues: 341 sheet: 1.24 (0.45), residues: 123 loop : -1.11 (0.34), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 77 HIS 0.002 0.001 HIS G 97 PHE 0.012 0.001 PHE F 260 TYR 0.006 0.001 TYR F 291 ARG 0.003 0.000 ARG F 324 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 78 time to evaluate : 0.647 Fit side-chains REVERT: A 72 GLU cc_start: 0.6663 (mp0) cc_final: 0.6238 (mp0) REVERT: F 18 GLU cc_start: 0.6433 (mm-30) cc_final: 0.6049 (mm-30) REVERT: F 27 MET cc_start: 0.6509 (ptp) cc_final: 0.5732 (ttm) REVERT: F 38 GLU cc_start: 0.6017 (tt0) cc_final: 0.5370 (tp30) REVERT: F 79 VAL cc_start: 0.7288 (p) cc_final: 0.6800 (t) REVERT: F 93 ILE cc_start: 0.7527 (mm) cc_final: 0.7165 (mm) REVERT: F 169 ARG cc_start: 0.7439 (ttp-110) cc_final: 0.7180 (ttm-80) REVERT: F 202 MET cc_start: 0.1730 (mmm) cc_final: 0.0974 (mtm) REVERT: F 213 ASN cc_start: 0.7917 (OUTLIER) cc_final: 0.7636 (m-40) REVERT: F 224 ASP cc_start: 0.7794 (t0) cc_final: 0.7495 (t70) REVERT: F 236 ASN cc_start: 0.6143 (OUTLIER) cc_final: 0.5817 (p0) REVERT: F 266 GLU cc_start: 0.7494 (mp0) cc_final: 0.7161 (tp30) REVERT: G 76 THR cc_start: 0.7523 (OUTLIER) cc_final: 0.7228 (p) REVERT: G 134 ARG cc_start: 0.5405 (mtm110) cc_final: 0.4878 (mtt180) REVERT: G 159 ILE cc_start: 0.6807 (OUTLIER) cc_final: 0.6413 (mt) REVERT: G 176 ARG cc_start: 0.4961 (mmt180) cc_final: 0.3157 (mtm110) REVERT: G 177 LYS cc_start: 0.7008 (mtpp) cc_final: 0.6304 (mmtt) REVERT: G 250 LYS cc_start: 0.7420 (OUTLIER) cc_final: 0.6915 (mtmt) REVERT: G 261 GLN cc_start: 0.8752 (mt0) cc_final: 0.8426 (mt0) REVERT: G 282 LYS cc_start: 0.7523 (mmtt) cc_final: 0.7202 (mmmt) REVERT: G 310 LYS cc_start: 0.6470 (tttt) cc_final: 0.5885 (mtmm) outliers start: 24 outliers final: 14 residues processed: 95 average time/residue: 0.2229 time to fit residues: 26.5038 Evaluate side-chains 95 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 213 ASN Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 250 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 48 optimal weight: 0.2980 chunk 0 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 63 optimal weight: 0.7980 chunk 17 optimal weight: 0.3980 chunk 23 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 78 GLN G 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5890 Z= 0.142 Angle : 0.456 5.695 7970 Z= 0.243 Chirality : 0.041 0.141 914 Planarity : 0.002 0.022 1006 Dihedral : 12.411 143.524 889 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.75 % Allowed : 22.49 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.30), residues: 738 helix: 1.80 (0.28), residues: 341 sheet: 1.28 (0.45), residues: 123 loop : -1.06 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 77 HIS 0.002 0.000 HIS F 97 PHE 0.009 0.001 PHE F 260 TYR 0.005 0.001 TYR F 65 ARG 0.002 0.000 ARG G 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 77 time to evaluate : 0.687 Fit side-chains REVERT: A 72 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.6223 (mp0) REVERT: F 18 GLU cc_start: 0.6391 (mm-30) cc_final: 0.6169 (mm-30) REVERT: F 27 MET cc_start: 0.6476 (ptp) cc_final: 0.5750 (ttm) REVERT: F 38 GLU cc_start: 0.5977 (tt0) cc_final: 0.5368 (tp30) REVERT: F 79 VAL cc_start: 0.7275 (p) cc_final: 0.6803 (t) REVERT: F 93 ILE cc_start: 0.7478 (mm) cc_final: 0.7123 (mm) REVERT: F 202 MET cc_start: 0.1789 (mmm) cc_final: 0.0952 (mtm) REVERT: F 213 ASN cc_start: 0.7871 (OUTLIER) cc_final: 0.7595 (m-40) REVERT: F 224 ASP cc_start: 0.7670 (t0) cc_final: 0.7378 (t70) REVERT: F 233 GLU cc_start: 0.6324 (tm-30) cc_final: 0.5852 (tm-30) REVERT: F 236 ASN cc_start: 0.6362 (OUTLIER) cc_final: 0.5934 (p0) REVERT: F 266 GLU cc_start: 0.7486 (mp0) cc_final: 0.7106 (tp30) REVERT: G 76 THR cc_start: 0.7487 (OUTLIER) cc_final: 0.7182 (p) REVERT: G 134 ARG cc_start: 0.5423 (mtm110) cc_final: 0.4911 (mtm180) REVERT: G 159 ILE cc_start: 0.6817 (OUTLIER) cc_final: 0.6437 (mt) REVERT: G 176 ARG cc_start: 0.4947 (mmt180) cc_final: 0.3124 (mtm110) REVERT: G 177 LYS cc_start: 0.7001 (mtpp) cc_final: 0.6304 (mmtt) REVERT: G 208 THR cc_start: 0.8209 (OUTLIER) cc_final: 0.7819 (p) REVERT: G 250 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.6785 (mtmt) REVERT: G 261 GLN cc_start: 0.8831 (mt0) cc_final: 0.8607 (mt0) REVERT: G 282 LYS cc_start: 0.7588 (mmtt) cc_final: 0.7257 (mmmt) REVERT: G 310 LYS cc_start: 0.6450 (tttt) cc_final: 0.5901 (mtmm) outliers start: 22 outliers final: 10 residues processed: 92 average time/residue: 0.2299 time to fit residues: 26.5869 Evaluate side-chains 94 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 213 ASN Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 250 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 63 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 78 GLN F 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5890 Z= 0.271 Angle : 0.538 7.146 7970 Z= 0.280 Chirality : 0.044 0.145 914 Planarity : 0.003 0.025 1006 Dihedral : 12.808 149.596 889 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.94 % Allowed : 21.81 % Favored : 73.25 % 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: 0.81 (0.30), residues: 738 helix: 1.58 (0.28), residues: 341 sheet: 1.11 (0.45), residues: 127 loop : -1.13 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 77 HIS 0.002 0.001 HIS G 97 PHE 0.014 0.001 PHE F 260 TYR 0.006 0.001 TYR F 264 ARG 0.004 0.001 ARG A 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 75 time to evaluate : 0.579 Fit side-chains REVERT: A 72 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6074 (mp0) REVERT: F 27 MET cc_start: 0.6492 (ptp) cc_final: 0.5853 (ttm) REVERT: F 38 GLU cc_start: 0.5919 (tt0) cc_final: 0.5228 (tp30) REVERT: F 79 VAL cc_start: 0.7359 (p) cc_final: 0.6998 (t) REVERT: F 202 MET cc_start: 0.1764 (mmm) cc_final: 0.1060 (mtm) REVERT: F 213 ASN cc_start: 0.7959 (OUTLIER) cc_final: 0.7605 (m-40) REVERT: F 236 ASN cc_start: 0.6272 (OUTLIER) cc_final: 0.5897 (p0) REVERT: F 266 GLU cc_start: 0.7605 (mp0) cc_final: 0.7166 (tp30) REVERT: F 270 PHE cc_start: 0.6228 (t80) cc_final: 0.6011 (t80) REVERT: G 76 THR cc_start: 0.7613 (OUTLIER) cc_final: 0.7341 (p) REVERT: G 134 ARG cc_start: 0.5485 (mtm110) cc_final: 0.4950 (mtt180) REVERT: G 159 ILE cc_start: 0.6719 (OUTLIER) cc_final: 0.6316 (mt) REVERT: G 176 ARG cc_start: 0.5027 (mmt180) cc_final: 0.3248 (mtm110) REVERT: G 177 LYS cc_start: 0.6953 (mtpp) cc_final: 0.6163 (mmtt) REVERT: G 250 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7012 (mtmt) REVERT: G 282 LYS cc_start: 0.7698 (mmtt) cc_final: 0.7316 (mmmt) REVERT: G 310 LYS cc_start: 0.6527 (tttt) cc_final: 0.5935 (mtmm) outliers start: 29 outliers final: 19 residues processed: 96 average time/residue: 0.2480 time to fit residues: 30.6749 Evaluate side-chains 95 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 70 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 213 ASN Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 304 ASN Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 250 LYS Chi-restraints excluded: chain G residue 326 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 7 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 70 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 32 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 chunk 28 optimal weight: 0.0670 overall best weight: 1.0520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 304 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5890 Z= 0.176 Angle : 0.480 6.238 7970 Z= 0.255 Chirality : 0.042 0.137 914 Planarity : 0.003 0.021 1006 Dihedral : 12.659 146.906 889 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.60 % Allowed : 22.49 % Favored : 72.91 % 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: 0.89 (0.30), residues: 738 helix: 1.65 (0.28), residues: 341 sheet: 1.20 (0.45), residues: 123 loop : -1.08 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 77 HIS 0.002 0.001 HIS F 97 PHE 0.021 0.001 PHE A 78 TYR 0.006 0.001 TYR F 65 ARG 0.002 0.000 ARG G 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 73 time to evaluate : 0.651 Fit side-chains REVERT: A 72 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6245 (mp0) REVERT: F 27 MET cc_start: 0.6468 (ptp) cc_final: 0.5840 (ttm) REVERT: F 38 GLU cc_start: 0.5875 (tt0) cc_final: 0.5212 (tp30) REVERT: F 68 GLU cc_start: 0.7413 (pm20) cc_final: 0.5819 (tt0) REVERT: F 79 VAL cc_start: 0.7338 (p) cc_final: 0.6970 (t) REVERT: F 93 ILE cc_start: 0.7553 (mm) cc_final: 0.7174 (mm) REVERT: F 202 MET cc_start: 0.1771 (mmm) cc_final: 0.1064 (mtm) REVERT: F 213 ASN cc_start: 0.7924 (OUTLIER) cc_final: 0.7592 (m-40) REVERT: F 233 GLU cc_start: 0.6305 (tm-30) cc_final: 0.5810 (tm-30) REVERT: F 236 ASN cc_start: 0.6300 (OUTLIER) cc_final: 0.5951 (p0) REVERT: F 266 GLU cc_start: 0.7595 (mp0) cc_final: 0.7110 (tp30) REVERT: F 270 PHE cc_start: 0.6147 (t80) cc_final: 0.5642 (t80) REVERT: G 76 THR cc_start: 0.7568 (OUTLIER) cc_final: 0.7267 (p) REVERT: G 134 ARG cc_start: 0.5432 (mtm110) cc_final: 0.4932 (mtt180) REVERT: G 159 ILE cc_start: 0.6701 (OUTLIER) cc_final: 0.6348 (mt) REVERT: G 176 ARG cc_start: 0.4967 (mmt180) cc_final: 0.3188 (mtm110) REVERT: G 177 LYS cc_start: 0.6961 (mtpp) cc_final: 0.6227 (mmtt) REVERT: G 250 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.6850 (mtmt) REVERT: G 266 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7595 (mp0) REVERT: G 282 LYS cc_start: 0.7668 (mmtt) cc_final: 0.7282 (mmmt) REVERT: G 310 LYS cc_start: 0.6533 (tttt) cc_final: 0.5917 (mtmm) outliers start: 27 outliers final: 17 residues processed: 94 average time/residue: 0.2017 time to fit residues: 24.3538 Evaluate side-chains 96 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 72 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 213 ASN Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 250 LYS Chi-restraints excluded: chain G residue 266 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 304 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5890 Z= 0.285 Angle : 0.560 7.665 7970 Z= 0.290 Chirality : 0.045 0.141 914 Planarity : 0.003 0.026 1006 Dihedral : 13.003 150.620 889 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 5.11 % Allowed : 22.15 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.30), residues: 738 helix: 1.42 (0.28), residues: 341 sheet: 1.01 (0.46), residues: 127 loop : -1.19 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 77 HIS 0.003 0.001 HIS F 97 PHE 0.024 0.002 PHE A 78 TYR 0.006 0.001 TYR F 264 ARG 0.003 0.001 ARG G 226 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 72 time to evaluate : 0.685 Fit side-chains REVERT: A 72 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.6110 (mp0) REVERT: F 27 MET cc_start: 0.6547 (ptp) cc_final: 0.5932 (ttm) REVERT: F 38 GLU cc_start: 0.5910 (tt0) cc_final: 0.5062 (tp30) REVERT: F 68 GLU cc_start: 0.7457 (pm20) cc_final: 0.5884 (tt0) REVERT: F 79 VAL cc_start: 0.7374 (p) cc_final: 0.7061 (t) REVERT: F 202 MET cc_start: 0.2098 (mmm) cc_final: 0.1146 (mtm) REVERT: F 213 ASN cc_start: 0.8246 (OUTLIER) cc_final: 0.7942 (m-40) REVERT: F 236 ASN cc_start: 0.6285 (OUTLIER) cc_final: 0.5982 (p0) REVERT: F 266 GLU cc_start: 0.7637 (mp0) cc_final: 0.7163 (tp30) REVERT: F 270 PHE cc_start: 0.6377 (t80) cc_final: 0.6156 (t80) REVERT: G 76 THR cc_start: 0.7618 (OUTLIER) cc_final: 0.7349 (p) REVERT: G 134 ARG cc_start: 0.5425 (mtm110) cc_final: 0.4942 (mtt180) REVERT: G 159 ILE cc_start: 0.6728 (OUTLIER) cc_final: 0.6361 (mt) REVERT: G 176 ARG cc_start: 0.5004 (mmt180) cc_final: 0.3231 (mtm110) REVERT: G 177 LYS cc_start: 0.6964 (mtpp) cc_final: 0.6158 (mmtt) REVERT: G 250 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.6983 (mtmt) REVERT: G 266 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: G 282 LYS cc_start: 0.7679 (mmtt) cc_final: 0.7272 (mmmt) REVERT: G 310 LYS cc_start: 0.6592 (tttt) cc_final: 0.5988 (mtmm) outliers start: 30 outliers final: 19 residues processed: 94 average time/residue: 0.2092 time to fit residues: 25.2486 Evaluate side-chains 98 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 72 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 213 ASN Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 304 ASN Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 250 LYS Chi-restraints excluded: chain G residue 266 GLU Chi-restraints excluded: chain G residue 326 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 0.2980 chunk 67 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 20 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 304 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5890 Z= 0.200 Angle : 0.506 6.412 7970 Z= 0.266 Chirality : 0.043 0.138 914 Planarity : 0.003 0.026 1006 Dihedral : 12.870 148.217 889 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.43 % Allowed : 22.83 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.30), residues: 738 helix: 1.46 (0.28), residues: 341 sheet: 1.17 (0.46), residues: 123 loop : -1.14 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 77 HIS 0.002 0.001 HIS F 97 PHE 0.023 0.001 PHE A 78 TYR 0.008 0.001 TYR F 291 ARG 0.002 0.000 ARG G 33 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 72 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: F 27 MET cc_start: 0.6544 (ptp) cc_final: 0.5935 (ttm) REVERT: F 38 GLU cc_start: 0.5916 (tt0) cc_final: 0.5055 (tp30) REVERT: F 68 GLU cc_start: 0.7389 (pm20) cc_final: 0.5813 (tt0) REVERT: F 79 VAL cc_start: 0.7355 (p) cc_final: 0.7027 (t) REVERT: F 93 ILE cc_start: 0.7621 (mm) cc_final: 0.7248 (mm) REVERT: F 198 LYS cc_start: 0.8153 (ptpt) cc_final: 0.7749 (mtpp) REVERT: F 202 MET cc_start: 0.2252 (mmm) cc_final: 0.1305 (mtm) REVERT: F 213 ASN cc_start: 0.8098 (OUTLIER) cc_final: 0.7770 (m-40) REVERT: F 236 ASN cc_start: 0.6317 (OUTLIER) cc_final: 0.5993 (p0) REVERT: F 266 GLU cc_start: 0.7613 (mp0) cc_final: 0.7103 (tp30) REVERT: F 270 PHE cc_start: 0.6306 (t80) cc_final: 0.6097 (t80) REVERT: G 76 THR cc_start: 0.7586 (OUTLIER) cc_final: 0.7284 (p) REVERT: G 134 ARG cc_start: 0.5369 (mtm110) cc_final: 0.4909 (mtt180) REVERT: G 159 ILE cc_start: 0.6710 (OUTLIER) cc_final: 0.6339 (mt) REVERT: G 176 ARG cc_start: 0.4988 (mmt180) cc_final: 0.3196 (mtm110) REVERT: G 177 LYS cc_start: 0.6947 (mtpp) cc_final: 0.6164 (mmtt) REVERT: G 250 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.7233 (mttt) REVERT: G 266 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7557 (mp0) REVERT: G 282 LYS cc_start: 0.7649 (mmtt) cc_final: 0.7253 (mmmt) REVERT: G 310 LYS cc_start: 0.6614 (tttt) cc_final: 0.5998 (mtmm) outliers start: 26 outliers final: 20 residues processed: 94 average time/residue: 0.2025 time to fit residues: 24.5311 Evaluate side-chains 97 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 71 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 213 ASN Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 250 LYS Chi-restraints excluded: chain G residue 266 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 chunk 46 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5890 Z= 0.149 Angle : 0.466 5.965 7970 Z= 0.248 Chirality : 0.042 0.138 914 Planarity : 0.003 0.025 1006 Dihedral : 12.471 146.107 889 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.92 % Allowed : 23.34 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.31), residues: 738 helix: 1.59 (0.28), residues: 341 sheet: 1.24 (0.46), residues: 123 loop : -1.07 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 77 HIS 0.002 0.000 HIS F 97 PHE 0.021 0.001 PHE A 78 TYR 0.005 0.001 TYR G 65 ARG 0.003 0.000 ARG A 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 75 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: F 27 MET cc_start: 0.6523 (ptp) cc_final: 0.5927 (ttm) REVERT: F 38 GLU cc_start: 0.5904 (tt0) cc_final: 0.5129 (tp30) REVERT: F 68 GLU cc_start: 0.7339 (pm20) cc_final: 0.5770 (tt0) REVERT: F 79 VAL cc_start: 0.7315 (p) cc_final: 0.6949 (t) REVERT: F 93 ILE cc_start: 0.7488 (mm) cc_final: 0.7085 (mm) REVERT: F 198 LYS cc_start: 0.7985 (ptpt) cc_final: 0.7687 (mtpp) REVERT: F 202 MET cc_start: 0.2203 (mmm) cc_final: 0.1179 (mtm) REVERT: F 213 ASN cc_start: 0.7893 (OUTLIER) cc_final: 0.7554 (m-40) REVERT: F 224 ASP cc_start: 0.7740 (t0) cc_final: 0.7409 (t70) REVERT: F 233 GLU cc_start: 0.6275 (tm-30) cc_final: 0.5790 (tm-30) REVERT: F 236 ASN cc_start: 0.6339 (OUTLIER) cc_final: 0.6059 (p0) REVERT: F 266 GLU cc_start: 0.7672 (mp0) cc_final: 0.7165 (tp30) REVERT: F 270 PHE cc_start: 0.6306 (t80) cc_final: 0.5772 (t80) REVERT: G 76 THR cc_start: 0.7519 (OUTLIER) cc_final: 0.7195 (p) REVERT: G 134 ARG cc_start: 0.5466 (mtm110) cc_final: 0.4977 (mtt180) REVERT: G 159 ILE cc_start: 0.6737 (OUTLIER) cc_final: 0.6373 (mt) REVERT: G 176 ARG cc_start: 0.5007 (mmt180) cc_final: 0.3132 (mtm110) REVERT: G 177 LYS cc_start: 0.6948 (mtpp) cc_final: 0.6247 (mttt) REVERT: G 208 THR cc_start: 0.8228 (OUTLIER) cc_final: 0.7931 (p) REVERT: G 250 LYS cc_start: 0.7449 (OUTLIER) cc_final: 0.6886 (mtmt) REVERT: G 266 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: G 282 LYS cc_start: 0.7639 (mmtt) cc_final: 0.7228 (mmmt) REVERT: G 310 LYS cc_start: 0.6563 (tttt) cc_final: 0.5970 (mtmm) REVERT: G 325 GLU cc_start: 0.4888 (tm-30) cc_final: 0.4482 (tt0) outliers start: 23 outliers final: 15 residues processed: 93 average time/residue: 0.2076 time to fit residues: 24.8596 Evaluate side-chains 93 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 71 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 213 ASN Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 250 LYS Chi-restraints excluded: chain G residue 266 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.199329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.181380 restraints weight = 6439.040| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 1.12 r_work: 0.3740 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5890 Z= 0.171 Angle : 0.475 6.466 7970 Z= 0.251 Chirality : 0.042 0.139 914 Planarity : 0.003 0.024 1006 Dihedral : 12.468 146.865 889 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.09 % Allowed : 22.66 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.31), residues: 738 helix: 1.57 (0.28), residues: 341 sheet: 1.26 (0.46), residues: 123 loop : -1.06 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 71 HIS 0.002 0.001 HIS F 97 PHE 0.022 0.002 PHE A 78 TYR 0.005 0.001 TYR F 65 ARG 0.003 0.000 ARG A 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1486.13 seconds wall clock time: 27 minutes 41.75 seconds (1661.75 seconds total)