Starting phenix.real_space_refine (version: dev) on Fri Feb 17 21:12:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmu_34154/02_2023/8gmu_34154_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmu_34154/02_2023/8gmu_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_34154/02_2023/8gmu_34154.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmu_34154/02_2023/8gmu_34154.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmu_34154/02_2023/8gmu_34154_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmu_34154/02_2023/8gmu_34154_updated.pdb" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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-4877/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: 4.03, per 1000 atoms: 0.65 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: 2.64 Conformation dependent library (CDL) restraints added in 1.2 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: 0.99 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: 1.99 Time building geometry restraints manager: 2.86 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: 3607 34.21 - 68.43: 193 68.43 - 102.64: 13 102.64 - 136.85: 0 136.85 - 171.07: 2 Dihedral angle restraints: 3815 sinusoidal: 1566 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 3812 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.130 Check model and map are aligned: 0.080 Process input model: 20.840 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.070 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 : 19.275 171.067 2377 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 % 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 *********************** 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 : 0.850 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 95 average time/residue: 1.3834 time to fit residues: 137.3038 Evaluate side-chains 92 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 0.640 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.0522 time to fit residues: 0.9980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 40 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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: 0.8263 moved from start: 0.0773 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= 0.387 Angle : 0.622 6.376 8551 Z= 0.326 Chirality : 0.048 0.209 971 Planarity : 0.005 0.056 1083 Dihedral : 13.495 173.511 918 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.53 % Favored : 97.35 % Rotamer Outliers : 4.72 % 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: 0.55 (0.29), residues: 791 helix: 1.31 (0.29), residues: 292 sheet: 1.09 (0.42), residues: 132 loop : -0.68 (0.31), residues: 367 *********************** 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 123 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 93 time to evaluate : 0.751 Fit side-chains outliers start: 30 outliers final: 15 residues processed: 111 average time/residue: 1.3501 time to fit residues: 156.5987 Evaluate side-chains 99 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 0.733 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 9 residues processed: 6 average time/residue: 0.6986 time to fit residues: 5.5080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 59 optimal weight: 0.1980 chunk 48 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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: 0.8205 moved from start: 0.0793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 6315 Z= 0.153 Angle : 0.457 4.954 8551 Z= 0.249 Chirality : 0.042 0.163 971 Planarity : 0.003 0.045 1083 Dihedral : 13.185 171.982 918 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.52 % Favored : 98.36 % Rotamer Outliers : 4.25 % 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: 0.88 (0.29), residues: 791 helix: 1.76 (0.29), residues: 292 sheet: 0.91 (0.39), residues: 143 loop : -0.52 (0.32), residues: 356 *********************** 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 110 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 83 time to evaluate : 0.761 Fit side-chains outliers start: 27 outliers final: 14 residues processed: 98 average time/residue: 1.3458 time to fit residues: 138.0435 Evaluate side-chains 96 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 0.756 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 10 residues processed: 4 average time/residue: 0.1226 time to fit residues: 1.7425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 0.3980 chunk 7 optimal weight: 0.4980 chunk 34 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 76 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.8213 moved from start: 0.0922 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= 0.177 Angle : 0.464 5.382 8551 Z= 0.250 Chirality : 0.042 0.167 971 Planarity : 0.003 0.040 1083 Dihedral : 13.136 172.436 918 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.77 % Favored : 98.10 % Rotamer Outliers : 4.56 % 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: 1.89 (0.29), residues: 292 sheet: 0.75 (0.39), residues: 155 loop : -0.41 (0.33), residues: 344 *********************** 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 111 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 82 time to evaluate : 0.759 Fit side-chains outliers start: 29 outliers final: 17 residues processed: 98 average time/residue: 1.3773 time to fit residues: 141.3145 Evaluate side-chains 98 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 0.751 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 13 residues processed: 5 average time/residue: 0.4484 time to fit residues: 3.5832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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: 0.8237 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 6315 Z= 0.264 Angle : 0.518 5.183 8551 Z= 0.275 Chirality : 0.045 0.217 971 Planarity : 0.004 0.053 1083 Dihedral : 13.295 172.994 918 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.65 % Favored : 97.22 % Rotamer Outliers : 4.09 % 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: 0.85 (0.29), residues: 791 helix: 1.71 (0.29), residues: 292 sheet: 0.85 (0.41), residues: 144 loop : -0.50 (0.32), residues: 355 *********************** 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 107 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 81 time to evaluate : 0.805 Fit side-chains outliers start: 26 outliers final: 18 residues processed: 98 average time/residue: 1.3925 time to fit residues: 142.8033 Evaluate side-chains 97 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 0.744 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 5 average time/residue: 0.6049 time to fit residues: 4.2925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 8 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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: 0.8226 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 6315 Z= 0.203 Angle : 0.481 5.234 8551 Z= 0.259 Chirality : 0.043 0.198 971 Planarity : 0.003 0.039 1083 Dihedral : 13.225 172.577 918 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.77 % Favored : 98.10 % Rotamer Outliers : 3.93 % 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: 0.88 (0.29), residues: 791 helix: 1.73 (0.29), residues: 292 sheet: 0.69 (0.39), residues: 155 loop : -0.44 (0.33), residues: 344 *********************** 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 104 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 79 time to evaluate : 0.755 Fit side-chains outliers start: 25 outliers final: 16 residues processed: 93 average time/residue: 1.2964 time to fit residues: 126.3239 Evaluate side-chains 95 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 0.799 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 4 average time/residue: 0.1415 time to fit residues: 1.8829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.0000 chunk 64 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 46 optimal weight: 0.0170 chunk 35 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 overall best weight: 1.3426 ------------------------------------------------------------------------------- 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: 0.8220 moved from start: 0.1188 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= 0.196 Angle : 0.475 5.394 8551 Z= 0.255 Chirality : 0.043 0.196 971 Planarity : 0.003 0.037 1083 Dihedral : 13.181 172.174 918 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.15 % Favored : 97.72 % Rotamer Outliers : 4.09 % 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: 0.91 (0.29), residues: 791 helix: 1.79 (0.29), residues: 292 sheet: 0.68 (0.39), residues: 155 loop : -0.43 (0.33), residues: 344 *********************** 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 107 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 81 time to evaluate : 0.749 Fit side-chains outliers start: 26 outliers final: 15 residues processed: 96 average time/residue: 1.3851 time to fit residues: 139.4995 Evaluate side-chains 95 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 0.764 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 3 average time/residue: 0.1211 time to fit residues: 1.5578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 9.9990 chunk 48 optimal weight: 0.0570 chunk 51 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 59 optimal weight: 0.0970 chunk 69 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 66 optimal weight: 0.0020 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 overall best weight: 1.6308 ------------------------------------------------------------------------------- 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: 0.8227 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 6315 Z= 0.222 Angle : 0.492 5.831 8551 Z= 0.264 Chirality : 0.044 0.206 971 Planarity : 0.004 0.037 1083 Dihedral : 13.200 172.160 918 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.28 % Favored : 97.60 % Rotamer Outliers : 3.62 % 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: 0.86 (0.29), residues: 791 helix: 1.71 (0.29), residues: 292 sheet: 0.68 (0.39), residues: 155 loop : -0.45 (0.33), residues: 344 *********************** 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 103 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 80 time to evaluate : 0.737 Fit side-chains outliers start: 23 outliers final: 16 residues processed: 96 average time/residue: 1.3658 time to fit residues: 137.3096 Evaluate side-chains 95 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 0.738 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 13 residues processed: 3 average time/residue: 0.0923 time to fit residues: 1.4513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 75 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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: 0.8217 moved from start: 0.1271 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= 0.189 Angle : 0.472 6.296 8551 Z= 0.254 Chirality : 0.043 0.196 971 Planarity : 0.003 0.036 1083 Dihedral : 13.158 171.918 918 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.77 % Favored : 98.10 % Rotamer Outliers : 3.14 % 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: 0.94 (0.29), residues: 791 helix: 1.82 (0.29), residues: 292 sheet: 0.70 (0.39), residues: 155 loop : -0.43 (0.33), residues: 344 *********************** 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 98 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 78 time to evaluate : 0.798 Fit side-chains outliers start: 20 outliers final: 16 residues processed: 92 average time/residue: 1.3816 time to fit residues: 133.1290 Evaluate side-chains 93 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 77 time to evaluate : 0.812 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 13 residues processed: 3 average time/residue: 0.1419 time to fit residues: 1.6519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 62 optimal weight: 0.0010 chunk 6 optimal weight: 5.9990 chunk 48 optimal weight: 0.0370 chunk 38 optimal weight: 0.0370 chunk 49 optimal weight: 0.6980 chunk 66 optimal weight: 0.0170 chunk 19 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.1580 ------------------------------------------------------------------------------- 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: 0.8157 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 6315 Z= 0.119 Angle : 0.431 7.334 8551 Z= 0.233 Chirality : 0.041 0.136 971 Planarity : 0.003 0.033 1083 Dihedral : 12.787 168.201 918 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.14 % Favored : 98.74 % Rotamer Outliers : 2.67 % 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: 1.20 (0.29), residues: 791 helix: 2.14 (0.29), residues: 292 sheet: 0.81 (0.39), residues: 153 loop : -0.36 (0.32), residues: 346 ********************** 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: 17 poor density : 79 time to evaluate : 0.764 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 93 average time/residue: 1.3329 time to fit residues: 129.8170 Evaluate side-chains 85 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 0.766 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 1.7955 time to fit residues: 2.9109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 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 118 GLN G 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.158634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.118630 restraints weight = 6274.360| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.54 r_work: 0.2887 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.069 6315 Z= 0.380 Angle : 0.608 8.723 8551 Z= 0.314 Chirality : 0.048 0.282 971 Planarity : 0.005 0.056 1083 Dihedral : 13.364 173.908 918 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.02 % Favored : 97.85 % Rotamer Outliers : 2.52 % 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: 0.76 (0.29), residues: 791 helix: 1.63 (0.29), residues: 292 sheet: 0.80 (0.40), residues: 145 loop : -0.56 (0.32), residues: 354 =============================================================================== Job complete usr+sys time: 2608.21 seconds wall clock time: 47 minutes 21.13 seconds (2841.13 seconds total)