Starting phenix.real_space_refine on Mon Mar 11 00:13:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmu_34154/03_2024/8gmu_34154_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmu_34154/03_2024/8gmu_34154.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmu_34154/03_2024/8gmu_34154.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmu_34154/03_2024/8gmu_34154.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmu_34154/03_2024/8gmu_34154_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmu_34154/03_2024/8gmu_34154_updated.pdb" } resolution = 2.78 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= 0.009 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 33 5.16 5 C 3880 2.51 5 N 1055 2.21 5 O 1232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 125": "OD1" <-> "OD2" Residue "A PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 187": "OD1" <-> "OD2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "F GLU 31": "OE1" <-> "OE2" Residue "F ASP 100": "OD1" <-> "OD2" Residue "F ASP 120": "OD1" <-> "OD2" Residue "F GLU 123": "OE1" <-> "OE2" Residue "F GLU 127": "OE1" <-> "OE2" Residue "F GLU 158": "OE1" <-> "OE2" Residue "F GLU 233": "OE1" <-> "OE2" Residue "F GLU 259": "OE1" <-> "OE2" Residue "F TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 276": "OD1" <-> "OD2" Residue "G GLU 31": "OE1" <-> "OE2" Residue "G GLU 38": "OE1" <-> "OE2" Residue "G GLU 68": "OE1" <-> "OE2" Residue "G GLU 96": "OE1" <-> "OE2" Residue "G ASP 112": "OD1" <-> "OD2" Residue "G ASP 139": "OD1" <-> "OD2" Residue "G GLU 154": "OE1" <-> "OE2" Residue "G ASP 224": "OD1" <-> "OD2" Residue "G GLU 233": "OE1" <-> "OE2" Residue "G GLU 266": "OE1" <-> "OE2" Residue "G ASP 276": "OD1" <-> "OD2" Residue "G GLU 281": "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: 6214 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1014 Classifications: {'peptide': 131} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 118} 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.14, per 1000 atoms: 0.67 Number of scatterers: 6214 At special positions: 0 Unit cell: (99.96, 86.87, 104.72, 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 33 16.00 P 12 15.00 Mg 2 11.99 O 1232 8.00 N 1055 7.00 C 3880 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: 2.81 Conformation dependent library (CDL) restraints added in 1.4 seconds 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1438 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 10 sheets defined 35.1% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 197 through 199 No H-bonds generated for 'chain 'A' and resid 197 through 199' 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 50 Processing helix chain 'F' and resid 72 through 86 removed outlier: 3.583A pdb=" N GLU F 86 " --> pdb=" O ALA F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 107 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: 4.691A pdb=" N GLY F 180 " --> pdb=" O ARG F 176 " (cutoff:3.500A) removed outlier: 4.390A 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 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: 3.508A 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: 4.878A pdb=" N GLY G 180 " --> pdb=" O ARG G 176 " (cutoff:3.500A) removed outlier: 4.345A 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 301 through 311 Processing helix chain 'G' and resid 313 through 327 Processing sheet with id= A, first strand: chain 'A' and resid 102 through 104 Processing sheet with id= B, first strand: chain 'A' and resid 108 through 110 removed outlier: 7.513A pdb=" N VAL A 109 " --> pdb=" O TRP A 142 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLU A 144 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA A 227 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASP A 169 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL A 225 " --> pdb=" O ASP A 169 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE A 181 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LYS A 224 " --> pdb=" O PHE A 179 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N PHE A 179 " --> pdb=" O LYS A 224 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP A 178 " --> pdb=" O LEU A 194 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'F' and resid 257 through 263 removed outlier: 6.415A pdb=" N ARG F 222 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL F 221 " --> pdb=" O ILE F 61 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU F 189 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ILE F 64 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE F 191 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N GLY F 66 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN F 193 " --> pdb=" O GLY F 66 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU F 115 " --> pdb=" O PHE F 92 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ASP F 94 " --> pdb=" O LEU F 115 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N SER F 117 " --> pdb=" O ASP F 94 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'F' and resid 195 through 197 Processing sheet with id= E, first strand: chain 'F' and resid 284 through 287 removed outlier: 6.118A pdb=" N TYR F 293 " --> pdb=" O LYS F 297 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LYS F 297 " --> pdb=" O TYR F 293 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 229 through 233 removed outlier: 6.457A pdb=" N GLU F 233 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL F 237 " --> pdb=" O GLU F 233 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 257 through 263 removed outlier: 6.348A pdb=" N ARG G 222 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL G 221 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU G 189 " --> pdb=" O VAL G 62 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ILE G 64 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N PHE G 191 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N GLY G 66 " --> pdb=" O PHE G 191 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASN G 193 " --> pdb=" O GLY G 66 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU G 115 " --> pdb=" O PHE G 92 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ASP G 94 " --> pdb=" O LEU G 115 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N SER G 117 " --> pdb=" O ASP G 94 " (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 removed outlier: 6.404A pdb=" N TYR G 293 " --> pdb=" O LYS G 297 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LYS G 297 " --> pdb=" O TYR G 293 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 229 through 233 removed outlier: 6.505A pdb=" N GLU G 233 " --> pdb=" O VAL G 237 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL G 237 " --> pdb=" O GLU G 233 " (cutoff:3.500A) 257 hydrogen bonds defined for protein. 744 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: 1.84 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 2062 1.36 - 1.51: 1584 1.51 - 1.65: 2614 1.65 - 1.80: 30 1.80 - 1.95: 25 Bond restraints: 6315 Sorted by residual: bond pdb=" CA VAL F 246 " pdb=" CB VAL F 246 " ideal model delta sigma weight residual 1.527 1.538 -0.011 1.31e-02 5.83e+03 7.48e-01 bond pdb=" C GLU A 146 " pdb=" N GLY A 147 " ideal model delta sigma weight residual 1.331 1.318 0.012 1.46e-02 4.69e+03 7.24e-01 bond pdb=" C4' DT S 9 " pdb=" O4' DT S 9 " ideal model delta sigma weight residual 1.450 1.433 0.017 2.00e-02 2.50e+03 7.17e-01 bond pdb=" CB LYS G 198 " pdb=" CG LYS G 198 " ideal model delta sigma weight residual 1.520 1.495 0.025 3.00e-02 1.11e+03 7.14e-01 bond pdb=" N ARG A 119 " pdb=" CA ARG A 119 " ideal model delta sigma weight residual 1.457 1.468 -0.010 1.29e-02 6.01e+03 6.31e-01 ... (remaining 6310 not shown) Histogram of bond angle deviations from ideal: 99.02 - 106.01: 159 106.01 - 112.99: 3453 112.99 - 119.98: 2075 119.98 - 126.97: 2800 126.97 - 133.95: 64 Bond angle restraints: 8551 Sorted by residual: angle pdb=" C LEU A 118 " pdb=" N ARG A 119 " pdb=" CA ARG A 119 " ideal model delta sigma weight residual 121.54 128.77 -7.23 1.91e+00 2.74e-01 1.43e+01 angle pdb=" CA ILE A 195 " pdb=" CB ILE A 195 " pdb=" CG1 ILE A 195 " ideal model delta sigma weight residual 110.40 115.01 -4.61 1.70e+00 3.46e-01 7.37e+00 angle pdb=" CA MET F 197 " pdb=" CB MET F 197 " pdb=" CG MET F 197 " ideal model delta sigma weight residual 114.10 119.36 -5.26 2.00e+00 2.50e-01 6.93e+00 angle pdb=" C4' DT S 9 " pdb=" O4' DT S 9 " pdb=" C1' DT S 9 " ideal model delta sigma weight residual 109.70 106.22 3.48 1.50e+00 4.44e-01 5.38e+00 angle pdb=" N ILE A 213 " pdb=" CA ILE A 213 " pdb=" C ILE A 213 " ideal model delta sigma weight residual 107.76 109.79 -2.03 1.01e+00 9.80e-01 4.05e+00 ... (remaining 8546 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.21: 3620 34.21 - 68.43: 202 68.43 - 102.64: 13 102.64 - 136.85: 0 136.85 - 171.07: 2 Dihedral angle restraints: 3837 sinusoidal: 1588 harmonic: 2249 Sorted by residual: dihedral pdb=" O1A AGS G 402 " pdb=" O3A AGS G 402 " pdb=" PA AGS G 402 " pdb=" PB AGS G 402 " ideal model delta sinusoidal sigma weight residual -67.73 103.34 -171.07 1 3.00e+01 1.11e-03 2.12e+01 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 80.51 -148.24 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" CA VAL A 145 " pdb=" C VAL A 145 " pdb=" N GLU A 146 " pdb=" CA GLU A 146 " ideal model delta harmonic sigma weight residual 180.00 162.35 17.65 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 3834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 717 0.040 - 0.081: 171 0.081 - 0.121: 75 0.121 - 0.161: 7 0.161 - 0.202: 1 Chirality restraints: 971 Sorted by residual: chirality pdb=" CB THR G 208 " pdb=" CA THR G 208 " pdb=" OG1 THR G 208 " pdb=" CG2 THR G 208 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CG LEU F 309 " pdb=" CB LEU F 309 " pdb=" CD1 LEU F 309 " pdb=" CD2 LEU F 309 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CG LEU G 309 " pdb=" CB LEU G 309 " pdb=" CD1 LEU G 309 " pdb=" CD2 LEU G 309 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 968 not shown) Planarity restraints: 1083 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 207 " 0.041 5.00e-02 4.00e+02 6.34e-02 6.42e+00 pdb=" N PRO A 208 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 208 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 208 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 195 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00 pdb=" C ILE A 195 " -0.025 2.00e-02 2.50e+03 pdb=" O ILE A 195 " 0.010 2.00e-02 2.50e+03 pdb=" N ARG A 196 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY F 66 " -0.017 5.00e-02 4.00e+02 2.50e-02 1.00e+00 pdb=" N PRO F 67 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO F 67 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO F 67 " -0.014 5.00e-02 4.00e+02 ... (remaining 1080 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 39 2.53 - 3.12: 4447 3.12 - 3.72: 9829 3.72 - 4.31: 14241 4.31 - 4.90: 23519 Nonbonded interactions: 52075 Sorted by model distance: nonbonded pdb="MG MG G 401 " pdb=" O2G AGS G 402 " model vdw 1.941 2.170 nonbonded pdb=" OG1 THR G 73 " pdb="MG MG G 401 " model vdw 1.954 2.170 nonbonded pdb="MG MG F 401 " pdb=" O2G AGS F 402 " model vdw 1.957 2.170 nonbonded pdb="MG MG G 401 " pdb=" O1B AGS G 402 " model vdw 1.969 2.170 nonbonded pdb=" OG1 THR F 73 " pdb="MG MG F 401 " model vdw 1.970 2.170 ... (remaining 52070 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' selection = chain 'G' } 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: 0.610 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: 2.750 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 22.450 Find NCS groups from input model: 0.320 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: 0.020 Load rotamer database and sin/cos tables:12.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6315 Z= 0.196 Angle : 0.546 7.234 8551 Z= 0.311 Chirality : 0.042 0.202 971 Planarity : 0.004 0.063 1083 Dihedral : 19.468 171.067 2399 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.25 % Allowed : 1.77 % Favored : 97.98 % Rotamer: Outliers : 1.73 % Allowed : 23.58 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.29), residues: 791 helix: 1.71 (0.29), residues: 292 sheet: 1.71 (0.43), residues: 132 loop : -0.59 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 308 HIS 0.003 0.001 HIS F 163 PHE 0.008 0.001 PHE A 114 TYR 0.005 0.001 TYR F 271 ARG 0.003 0.000 ARG G 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.963 Fit side-chains REVERT: A 113 MET cc_start: 0.6090 (ttp) cc_final: 0.5857 (ttt) REVERT: F 184 GLN cc_start: 0.7516 (tm-30) cc_final: 0.7303 (tm-30) outliers start: 11 outliers final: 8 residues processed: 95 average time/residue: 1.4073 time to fit residues: 139.5911 Evaluate side-chains 92 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 196 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 185 SER Chi-restraints excluded: chain G residue 195 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN G 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.0791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 6315 Z= 0.372 Angle : 0.615 6.282 8551 Z= 0.322 Chirality : 0.048 0.205 971 Planarity : 0.005 0.055 1083 Dihedral : 14.479 172.559 954 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.28 % Favored : 97.60 % Rotamer: Outliers : 4.09 % Allowed : 20.91 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.56 (0.29), residues: 791 helix: 1.33 (0.29), residues: 292 sheet: 1.10 (0.42), residues: 132 loop : -0.67 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 308 HIS 0.003 0.001 HIS F 163 PHE 0.016 0.002 PHE G 203 TYR 0.006 0.002 TYR F 218 ARG 0.006 0.001 ARG F 226 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 93 time to evaluate : 0.678 Fit side-chains REVERT: A 101 TYR cc_start: 0.7445 (OUTLIER) cc_final: 0.6545 (m-80) REVERT: A 102 GLU cc_start: 0.7838 (pt0) cc_final: 0.7427 (pt0) REVERT: A 131 SER cc_start: 0.7888 (p) cc_final: 0.7418 (m) REVERT: A 212 MET cc_start: 0.7550 (mtm) cc_final: 0.7160 (mmm) REVERT: F 184 GLN cc_start: 0.7602 (tm-30) cc_final: 0.7356 (tm-30) REVERT: F 271 TYR cc_start: 0.7833 (m-10) cc_final: 0.7428 (m-80) REVERT: G 120 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7827 (m-30) outliers start: 26 outliers final: 10 residues processed: 107 average time/residue: 1.3343 time to fit residues: 149.2422 Evaluate side-chains 97 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 172 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN G 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6315 Z= 0.207 Angle : 0.488 5.092 8551 Z= 0.263 Chirality : 0.043 0.185 971 Planarity : 0.004 0.046 1083 Dihedral : 14.244 171.665 946 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.64 % Favored : 98.23 % Rotamer: Outliers : 4.09 % Allowed : 20.60 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.73 (0.29), residues: 791 helix: 1.58 (0.29), residues: 292 sheet: 0.83 (0.40), residues: 143 loop : -0.56 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 308 HIS 0.001 0.000 HIS G 97 PHE 0.010 0.001 PHE G 203 TYR 0.006 0.001 TYR G 65 ARG 0.002 0.000 ARG F 176 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 82 time to evaluate : 0.723 Fit side-chains REVERT: A 101 TYR cc_start: 0.7425 (OUTLIER) cc_final: 0.6665 (m-80) REVERT: A 102 GLU cc_start: 0.7789 (pt0) cc_final: 0.7466 (pt0) REVERT: A 131 SER cc_start: 0.7879 (OUTLIER) cc_final: 0.7501 (m) REVERT: A 212 MET cc_start: 0.7631 (mtm) cc_final: 0.7138 (mmm) REVERT: F 184 GLN cc_start: 0.7603 (tm-30) cc_final: 0.7330 (tm-30) REVERT: F 271 TYR cc_start: 0.7905 (m-10) cc_final: 0.7473 (m-80) REVERT: F 276 ASP cc_start: 0.7184 (OUTLIER) cc_final: 0.6822 (t0) REVERT: G 120 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7901 (m-30) outliers start: 26 outliers final: 11 residues processed: 96 average time/residue: 1.5835 time to fit residues: 159.3247 Evaluate side-chains 95 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 236 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6315 Z= 0.298 Angle : 0.544 5.208 8551 Z= 0.288 Chirality : 0.045 0.213 971 Planarity : 0.004 0.043 1083 Dihedral : 14.303 173.525 945 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.53 % Favored : 97.35 % Rotamer: Outliers : 4.25 % Allowed : 21.54 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.60 (0.29), residues: 791 helix: 1.44 (0.29), residues: 292 sheet: 0.75 (0.40), residues: 143 loop : -0.59 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 308 HIS 0.001 0.001 HIS A 108 PHE 0.012 0.002 PHE G 203 TYR 0.006 0.001 TYR G 65 ARG 0.003 0.001 ARG F 226 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 85 time to evaluate : 0.717 Fit side-chains REVERT: A 101 TYR cc_start: 0.7484 (OUTLIER) cc_final: 0.6626 (m-80) REVERT: A 131 SER cc_start: 0.8014 (OUTLIER) cc_final: 0.7571 (m) REVERT: A 204 GLN cc_start: 0.8464 (pt0) cc_final: 0.8240 (pt0) REVERT: A 212 MET cc_start: 0.7828 (mtm) cc_final: 0.7327 (mmm) REVERT: F 184 GLN cc_start: 0.7648 (tm-30) cc_final: 0.7358 (tm-30) REVERT: F 226 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.8394 (mtt-85) REVERT: F 271 TYR cc_start: 0.7771 (m-10) cc_final: 0.7398 (m-80) REVERT: G 120 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7855 (m-30) REVERT: G 332 ASN cc_start: 0.0146 (OUTLIER) cc_final: -0.0530 (p0) outliers start: 27 outliers final: 14 residues processed: 100 average time/residue: 1.3958 time to fit residues: 145.8271 Evaluate side-chains 100 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 81 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 226 ARG Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 332 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 0.4980 chunk 68 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN G 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6315 Z= 0.160 Angle : 0.455 5.176 8551 Z= 0.247 Chirality : 0.042 0.178 971 Planarity : 0.003 0.039 1083 Dihedral : 14.091 172.379 945 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.52 % Favored : 98.36 % Rotamer: Outliers : 3.62 % Allowed : 21.54 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.82 (0.29), residues: 791 helix: 1.72 (0.29), residues: 292 sheet: 0.56 (0.39), residues: 153 loop : -0.45 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 308 HIS 0.001 0.000 HIS G 97 PHE 0.008 0.001 PHE G 260 TYR 0.006 0.001 TYR F 103 ARG 0.001 0.000 ARG G 85 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 82 time to evaluate : 0.730 Fit side-chains REVERT: A 101 TYR cc_start: 0.7561 (OUTLIER) cc_final: 0.6891 (m-80) REVERT: A 102 GLU cc_start: 0.7574 (pt0) cc_final: 0.7347 (pt0) REVERT: A 131 SER cc_start: 0.8042 (OUTLIER) cc_final: 0.7560 (m) REVERT: A 204 GLN cc_start: 0.8412 (pt0) cc_final: 0.8199 (pt0) REVERT: A 212 MET cc_start: 0.7832 (mtm) cc_final: 0.7329 (mmm) REVERT: A 217 GLU cc_start: 0.8082 (mp0) cc_final: 0.7874 (mt-10) REVERT: F 184 GLN cc_start: 0.7636 (tm-30) cc_final: 0.7349 (tm-30) REVERT: F 226 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8720 (mtp85) REVERT: F 271 TYR cc_start: 0.7925 (m-10) cc_final: 0.7579 (m-80) REVERT: F 276 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6821 (t0) REVERT: G 120 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7925 (m-30) outliers start: 23 outliers final: 9 residues processed: 92 average time/residue: 1.5349 time to fit residues: 147.0335 Evaluate side-chains 93 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 79 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 226 ARG Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 236 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 chunk 6 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN G 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 6315 Z= 0.358 Angle : 0.577 5.635 8551 Z= 0.302 Chirality : 0.047 0.252 971 Planarity : 0.004 0.046 1083 Dihedral : 14.323 173.423 945 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.78 % Favored : 97.09 % Rotamer: Outliers : 4.56 % Allowed : 20.28 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 791 helix: 1.38 (0.29), residues: 292 sheet: 0.47 (0.39), residues: 155 loop : -0.55 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 308 HIS 0.002 0.001 HIS F 97 PHE 0.013 0.002 PHE G 203 TYR 0.006 0.001 TYR F 218 ARG 0.004 0.001 ARG F 226 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 85 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: A 101 TYR cc_start: 0.7593 (OUTLIER) cc_final: 0.6738 (m-80) REVERT: A 131 SER cc_start: 0.8026 (OUTLIER) cc_final: 0.7560 (m) REVERT: A 157 LYS cc_start: 0.7071 (OUTLIER) cc_final: 0.6185 (mmtt) REVERT: A 212 MET cc_start: 0.7841 (mtm) cc_final: 0.7371 (mmm) REVERT: A 217 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.6901 (mp0) REVERT: F 226 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8416 (mtt-85) REVERT: F 271 TYR cc_start: 0.7811 (m-10) cc_final: 0.7484 (m-80) REVERT: G 120 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7884 (m-30) REVERT: G 332 ASN cc_start: 0.0405 (OUTLIER) cc_final: -0.0518 (p0) outliers start: 29 outliers final: 15 residues processed: 102 average time/residue: 1.3459 time to fit residues: 143.5483 Evaluate side-chains 107 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 85 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 96 GLU Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 226 ARG Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 332 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 6315 Z= 0.370 Angle : 0.593 5.690 8551 Z= 0.312 Chirality : 0.048 0.274 971 Planarity : 0.005 0.046 1083 Dihedral : 14.446 174.313 945 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.53 % Favored : 97.35 % Rotamer: Outliers : 5.03 % Allowed : 20.60 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.29 (0.29), residues: 791 helix: 1.15 (0.29), residues: 292 sheet: 0.31 (0.39), residues: 155 loop : -0.64 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 308 HIS 0.002 0.001 HIS A 108 PHE 0.013 0.002 PHE G 203 TYR 0.006 0.001 TYR F 218 ARG 0.003 0.001 ARG F 243 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 82 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: A 101 TYR cc_start: 0.7663 (OUTLIER) cc_final: 0.6606 (m-80) REVERT: A 131 SER cc_start: 0.8041 (OUTLIER) cc_final: 0.7600 (m) REVERT: A 157 LYS cc_start: 0.7058 (OUTLIER) cc_final: 0.6142 (mmtt) REVERT: A 217 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.6746 (mp0) REVERT: F 170 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8808 (ttp) REVERT: F 226 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8358 (mtt-85) REVERT: F 271 TYR cc_start: 0.7876 (m-10) cc_final: 0.7531 (m-80) REVERT: G 120 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7867 (m-30) REVERT: G 332 ASN cc_start: 0.0510 (OUTLIER) cc_final: -0.0403 (t0) outliers start: 32 outliers final: 13 residues processed: 100 average time/residue: 1.3805 time to fit residues: 144.0850 Evaluate side-chains 103 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 82 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 96 GLU Chi-restraints excluded: chain F residue 170 MET Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 226 ARG Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 332 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 5.9990 chunk 48 optimal weight: 0.1980 chunk 51 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 42 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN G 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6315 Z= 0.147 Angle : 0.454 4.861 8551 Z= 0.248 Chirality : 0.042 0.190 971 Planarity : 0.003 0.036 1083 Dihedral : 14.109 173.648 945 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.52 % Favored : 98.36 % Rotamer: Outliers : 3.46 % Allowed : 22.01 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.68 (0.29), residues: 791 helix: 1.62 (0.29), residues: 292 sheet: 0.42 (0.40), residues: 153 loop : -0.51 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 129 HIS 0.002 0.001 HIS F 97 PHE 0.008 0.001 PHE G 260 TYR 0.007 0.001 TYR F 65 ARG 0.002 0.000 ARG G 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 84 time to evaluate : 0.668 Fit side-chains REVERT: A 101 TYR cc_start: 0.7610 (OUTLIER) cc_final: 0.6882 (m-80) REVERT: A 217 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7827 (mt-10) REVERT: F 226 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8726 (mtp85) REVERT: F 271 TYR cc_start: 0.7828 (m-10) cc_final: 0.7560 (m-80) REVERT: F 276 ASP cc_start: 0.7359 (OUTLIER) cc_final: 0.7036 (t0) REVERT: G 120 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7946 (m-30) REVERT: G 332 ASN cc_start: 0.0011 (OUTLIER) cc_final: -0.0727 (t0) outliers start: 22 outliers final: 7 residues processed: 94 average time/residue: 1.4346 time to fit residues: 140.5634 Evaluate side-chains 94 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 226 ARG Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 332 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 21 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 chunk 75 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6315 Z= 0.173 Angle : 0.467 6.394 8551 Z= 0.251 Chirality : 0.042 0.193 971 Planarity : 0.003 0.036 1083 Dihedral : 14.064 174.543 945 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.77 % Favored : 98.10 % Rotamer: Outliers : 2.67 % Allowed : 22.64 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.83 (0.29), residues: 791 helix: 1.80 (0.29), residues: 292 sheet: 0.50 (0.40), residues: 153 loop : -0.47 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 308 HIS 0.002 0.001 HIS F 163 PHE 0.008 0.001 PHE G 260 TYR 0.006 0.001 TYR F 103 ARG 0.002 0.000 ARG G 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 0.762 Fit side-chains REVERT: A 101 TYR cc_start: 0.7603 (OUTLIER) cc_final: 0.7014 (m-80) REVERT: A 217 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7845 (mt-10) REVERT: F 226 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.8345 (mtt-85) REVERT: F 271 TYR cc_start: 0.7824 (m-10) cc_final: 0.7599 (m-80) REVERT: F 276 ASP cc_start: 0.7381 (OUTLIER) cc_final: 0.7053 (t0) REVERT: G 120 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7978 (m-30) REVERT: G 332 ASN cc_start: 0.0106 (OUTLIER) cc_final: -0.0625 (t0) outliers start: 17 outliers final: 7 residues processed: 89 average time/residue: 1.4797 time to fit residues: 137.2701 Evaluate side-chains 93 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 226 ARG Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 332 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 48 optimal weight: 0.0270 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 66 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 57 optimal weight: 0.0970 chunk 9 optimal weight: 0.3980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6315 Z= 0.129 Angle : 0.437 5.968 8551 Z= 0.237 Chirality : 0.041 0.146 971 Planarity : 0.003 0.034 1083 Dihedral : 13.779 173.733 942 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.39 % Favored : 98.48 % Rotamer: Outliers : 2.04 % Allowed : 23.43 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.29), residues: 791 helix: 1.99 (0.30), residues: 292 sheet: 0.62 (0.40), residues: 153 loop : -0.43 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 129 HIS 0.002 0.001 HIS F 97 PHE 0.007 0.001 PHE F 260 TYR 0.006 0.001 TYR F 65 ARG 0.001 0.000 ARG G 85 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.780 Fit side-chains REVERT: A 101 TYR cc_start: 0.7526 (OUTLIER) cc_final: 0.7215 (m-80) REVERT: A 117 GLU cc_start: 0.7459 (tp30) cc_final: 0.7123 (tm-30) REVERT: A 217 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7819 (mt-10) REVERT: F 226 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8726 (mtp85) REVERT: F 271 TYR cc_start: 0.7768 (m-10) cc_final: 0.7547 (m-80) REVERT: G 120 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7968 (m-30) REVERT: G 332 ASN cc_start: -0.0075 (OUTLIER) cc_final: -0.0782 (t0) outliers start: 13 outliers final: 7 residues processed: 90 average time/residue: 1.4272 time to fit residues: 134.1315 Evaluate side-chains 91 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 226 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 332 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 26 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 11 optimal weight: 0.0570 chunk 55 optimal weight: 9.9990 chunk 3 optimal weight: 0.7980 chunk 45 optimal weight: 0.0670 chunk 71 optimal weight: 0.0370 chunk 42 optimal weight: 7.9990 overall best weight: 0.3314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 113 ASN G 118 GLN G 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.164164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.118324 restraints weight = 6266.653| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.36 r_work: 0.3111 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6315 Z= 0.126 Angle : 0.434 8.538 8551 Z= 0.233 Chirality : 0.041 0.135 971 Planarity : 0.003 0.034 1083 Dihedral : 13.562 172.654 942 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.26 % Favored : 98.61 % Rotamer: Outliers : 1.89 % Allowed : 23.58 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.24 (0.30), residues: 791 helix: 2.25 (0.30), residues: 292 sheet: 0.75 (0.40), residues: 153 loop : -0.38 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 129 HIS 0.003 0.001 HIS F 97 PHE 0.007 0.001 PHE F 260 TYR 0.006 0.001 TYR F 65 ARG 0.002 0.000 ARG G 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2859.89 seconds wall clock time: 51 minutes 17.00 seconds (3077.00 seconds total)