Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 21:41:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ywa_34151/08_2023/7ywa_34151_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ywa_34151/08_2023/7ywa_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_34151/08_2023/7ywa_34151.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ywa_34151/08_2023/7ywa_34151.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ywa_34151/08_2023/7ywa_34151_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ywa_34151/08_2023/7ywa_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-1.21rc1-5044/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: 3.59, per 1000 atoms: 0.62 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: 2.31 Conformation dependent library (CDL) restraints added in 822.7 milliseconds 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: 1.11 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: 1.56 Time building geometry restraints manager: 2.52 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: 3300 28.74 - 57.48: 236 57.48 - 86.22: 28 86.22 - 114.96: 1 114.96 - 143.70: 2 Dihedral angle restraints: 3567 sinusoidal: 1466 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 3564 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.150 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 19.700 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.320 ------------------------------------------------------------------------------- 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 : 18.787 143.701 2223 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 % 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 *********************** 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 : 0.650 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 122 average time/residue: 0.2235 time to fit residues: 33.9642 Evaluate side-chains 82 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 0.560 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0552 time to fit residues: 1.1903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0170 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 overall best weight: 1.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 16 GLN ** F 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 304 ASN ** G 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 5890 Z= 0.245 Angle : 0.571 7.495 7970 Z= 0.296 Chirality : 0.044 0.149 914 Planarity : 0.003 0.023 1006 Dihedral : 12.380 142.908 865 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 3.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.30), residues: 738 helix: 1.42 (0.28), residues: 341 sheet: 1.05 (0.44), residues: 123 loop : -1.22 (0.34), residues: 274 *********************** 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 97 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 77 time to evaluate : 0.600 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 91 average time/residue: 0.2056 time to fit residues: 23.8168 Evaluate side-chains 82 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.620 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0589 time to fit residues: 1.8914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 36 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 22 optimal weight: 0.0870 chunk 53 optimal weight: 0.5980 overall best weight: 1.5162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 269 ASN F 304 ASN G 118 GLN G 184 GLN G 257 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 5890 Z= 0.207 Angle : 0.516 6.377 7970 Z= 0.273 Chirality : 0.043 0.144 914 Planarity : 0.003 0.022 1006 Dihedral : 12.308 141.250 865 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 2.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.30), residues: 738 helix: 1.53 (0.28), residues: 341 sheet: 1.17 (0.45), residues: 123 loop : -1.20 (0.34), residues: 274 *********************** 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 91 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 77 time to evaluate : 0.627 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 88 average time/residue: 0.2046 time to fit residues: 23.1179 Evaluate side-chains 76 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 0.638 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0564 time to fit residues: 1.7275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 70 optimal weight: 20.0000 chunk 63 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 7 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 5890 Z= 0.334 Angle : 0.585 7.520 7970 Z= 0.305 Chirality : 0.046 0.150 914 Planarity : 0.004 0.028 1006 Dihedral : 12.583 142.629 865 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 3.24 % 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: 0.49 (0.30), residues: 738 helix: 1.35 (0.28), residues: 341 sheet: 0.91 (0.45), residues: 127 loop : -1.32 (0.34), residues: 270 *********************** 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 89 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 70 time to evaluate : 0.640 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 85 average time/residue: 0.1908 time to fit residues: 21.2185 Evaluate side-chains 80 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 0.621 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0575 time to fit residues: 2.1219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 60 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 304 ASN G 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 5890 Z= 0.311 Angle : 0.573 6.903 7970 Z= 0.300 Chirality : 0.045 0.146 914 Planarity : 0.003 0.028 1006 Dihedral : 12.630 140.224 865 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 2.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.30), residues: 738 helix: 1.20 (0.28), residues: 341 sheet: 0.93 (0.46), residues: 127 loop : -1.31 (0.34), residues: 270 *********************** 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 84 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 0.680 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 81 average time/residue: 0.2001 time to fit residues: 21.2552 Evaluate side-chains 75 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.687 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0636 time to fit residues: 1.4186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 63 optimal weight: 0.0670 chunk 13 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 overall best weight: 2.5524 ------------------------------------------------------------------------------- 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: 0.6828 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 5890 Z= 0.293 Angle : 0.570 6.750 7970 Z= 0.297 Chirality : 0.045 0.146 914 Planarity : 0.003 0.028 1006 Dihedral : 12.607 138.397 865 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 2.21 % 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: 0.34 (0.30), residues: 738 helix: 1.16 (0.28), residues: 341 sheet: 0.91 (0.46), residues: 127 loop : -1.34 (0.34), residues: 270 *********************** 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 82 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 0.674 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 77 average time/residue: 0.2053 time to fit residues: 20.5525 Evaluate side-chains 75 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 0.656 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0564 time to fit residues: 1.6423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 51 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 32 optimal weight: 0.0370 chunk 43 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 304 ASN G 257 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 5890 Z= 0.165 Angle : 0.499 7.154 7970 Z= 0.267 Chirality : 0.042 0.140 914 Planarity : 0.003 0.025 1006 Dihedral : 12.277 132.766 865 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 1.36 % 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: 0.67 (0.31), residues: 738 helix: 1.43 (0.28), residues: 341 sheet: 1.19 (0.47), residues: 123 loop : -1.18 (0.35), residues: 274 *********************** 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 79 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 0.660 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 77 average time/residue: 0.2167 time to fit residues: 21.3894 Evaluate side-chains 71 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 0.584 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1131 time to fit residues: 1.6354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 0.2980 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 5890 Z= 0.266 Angle : 0.553 6.991 7970 Z= 0.288 Chirality : 0.044 0.141 914 Planarity : 0.003 0.031 1006 Dihedral : 12.417 137.530 865 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 1.87 % 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: 0.50 (0.31), residues: 738 helix: 1.32 (0.28), residues: 340 sheet: 1.06 (0.47), residues: 127 loop : -1.32 (0.34), residues: 271 *********************** 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 76 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.717 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 72 average time/residue: 0.1922 time to fit residues: 18.4324 Evaluate side-chains 68 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.642 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0599 time to fit residues: 1.6327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 69 optimal weight: 0.0570 chunk 42 optimal weight: 9.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- 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: 0.6768 moved from start: 0.2961 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= 0.159 Angle : 0.498 7.073 7970 Z= 0.265 Chirality : 0.042 0.140 914 Planarity : 0.003 0.026 1006 Dihedral : 12.134 132.243 865 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.31), residues: 738 helix: 1.39 (0.29), residues: 342 sheet: 1.29 (0.47), residues: 123 loop : -1.13 (0.35), residues: 273 *********************** 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 72 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.659 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 71 average time/residue: 0.2084 time to fit residues: 19.2833 Evaluate side-chains 70 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.648 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0703 time to fit residues: 1.5527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 0.2980 chunk 48 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 5890 Z= 0.158 Angle : 0.489 6.858 7970 Z= 0.258 Chirality : 0.042 0.162 914 Planarity : 0.003 0.027 1006 Dihedral : 11.987 131.333 865 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer Outliers : 0.00 % 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: 0.77 (0.31), residues: 738 helix: 1.43 (0.29), residues: 342 sheet: 1.34 (0.47), residues: 123 loop : -1.08 (0.35), residues: 273 ********************** 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 68 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.561 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.2028 time to fit residues: 18.1177 Evaluate side-chains 64 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.644 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 304 ASN G 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.192446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.166515 restraints weight = 6526.011| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 1.15 r_work: 0.3575 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 5890 Z= 0.330 Angle : 0.589 7.692 7970 Z= 0.306 Chirality : 0.046 0.154 914 Planarity : 0.004 0.031 1006 Dihedral : 12.418 139.445 865 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 0.34 % 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: 0.37 (0.30), residues: 738 helix: 1.18 (0.28), residues: 340 sheet: 1.04 (0.47), residues: 127 loop : -1.36 (0.33), residues: 271 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1422.71 seconds wall clock time: 26 minutes 29.34 seconds (1589.34 seconds total)