Starting phenix.real_space_refine on Wed Nov 15 21:02:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjg_33226/11_2023/7xjg_33226.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjg_33226/11_2023/7xjg_33226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjg_33226/11_2023/7xjg_33226.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjg_33226/11_2023/7xjg_33226.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjg_33226/11_2023/7xjg_33226.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjg_33226/11_2023/7xjg_33226.pdb" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 216 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 7594 2.51 5 N 2367 2.21 5 O 2954 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 119": "OD1" <-> "OD2" Residue "B TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 13167 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2518 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 12, 'TRANS': 301} Chain: "C" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1096 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain breaks: 2 Chain: "D" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 933 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain breaks: 1 Chain: "E" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1225 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 10, 'rna3p_pur': 20, 'rna3p_pyr': 23} Link IDs: {'rna2p': 15, 'rna3p': 42} Chain breaks: 1 Chain: "F" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 176 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna3p': 7} Chain: "B" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2518 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 12, 'TRANS': 301} Chain: "G" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 808 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain breaks: 1 Chain: "H" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1225 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 10, 'rna3p_pur': 20, 'rna3p_pyr': 23} Link IDs: {'rna2p': 15, 'rna3p': 42} Chain breaks: 1 Chain: "I" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 176 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna3p': 7} Chain: "J" Number of atoms: 2490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2490 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 6, 'TRANS': 299} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.56, per 1000 atoms: 0.57 Number of scatterers: 13167 At special positions: 0 Unit cell: (96.9, 122.4, 161.5, 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 34 16.00 P 216 15.00 Mg 2 11.99 O 2954 8.00 N 2367 7.00 C 7594 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: 6.19 Conformation dependent library (CDL) restraints added in 1.6 seconds 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2020 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 10 sheets defined 60.1% alpha, 9.8% beta 68 base pairs and 120 stacking pairs defined. Time for finding SS restraints: 5.10 Creating SS restraints... Processing helix chain 'A' and resid 3 through 16 removed outlier: 3.576A pdb=" N PHE A 10 " --> pdb=" O TYR A 6 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 15 " --> pdb=" O ARG A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 31 removed outlier: 3.748A pdb=" N MET A 26 " --> pdb=" O ASN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 43 Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 69 through 83 removed outlier: 3.616A pdb=" N LEU A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 87 Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.616A pdb=" N LEU A 127 " --> pdb=" O PHE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 140 removed outlier: 3.946A pdb=" N VAL A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 139 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY A 140 " --> pdb=" O PHE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 154 removed outlier: 3.557A pdb=" N SER A 147 " --> pdb=" O ARG A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 205 through 220 removed outlier: 3.550A pdb=" N VAL A 209 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER A 218 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 224 removed outlier: 3.598A pdb=" N GLY A 224 " --> pdb=" O PRO A 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 221 through 224' Processing helix chain 'A' and resid 256 through 272 Processing helix chain 'A' and resid 277 through 292 Processing helix chain 'A' and resid 292 through 311 Processing helix chain 'C' and resid 6 through 18 removed outlier: 3.726A pdb=" N GLN C 11 " --> pdb=" O ASP C 7 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN C 12 " --> pdb=" O GLU C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 213 Proline residue: C 208 - end of helix Processing helix chain 'C' and resid 217 through 230 removed outlier: 3.509A pdb=" N LEU C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 250 Processing helix chain 'C' and resid 263 through 274 Processing helix chain 'C' and resid 275 through 292 removed outlier: 3.585A pdb=" N LEU C 279 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG C 292 " --> pdb=" O ASN C 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 15 removed outlier: 3.888A pdb=" N LEU B 15 " --> pdb=" O ARG B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 31 removed outlier: 3.510A pdb=" N MET B 26 " --> pdb=" O ASN B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 44 Processing helix chain 'B' and resid 69 through 83 removed outlier: 3.749A pdb=" N LEU B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 87 Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 123 through 127 Processing helix chain 'B' and resid 128 through 139 removed outlier: 3.848A pdb=" N VAL B 132 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 139 " --> pdb=" O VAL B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 154 Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 175 through 186 Processing helix chain 'B' and resid 205 through 220 removed outlier: 3.600A pdb=" N VAL B 209 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP B 214 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER B 218 " --> pdb=" O ASP B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 224 Processing helix chain 'B' and resid 257 through 273 Processing helix chain 'B' and resid 277 through 292 Processing helix chain 'B' and resid 292 through 310 removed outlier: 3.778A pdb=" N LYS B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS B 309 " --> pdb=" O LYS B 305 " (cutoff:3.500A) Processing helix chain 'J' and resid 6 through 14 Processing helix chain 'J' and resid 45 through 55 removed outlier: 3.759A pdb=" N LEU J 49 " --> pdb=" O TRP J 45 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS J 55 " --> pdb=" O GLN J 51 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 79 through 91 Processing helix chain 'J' and resid 100 through 111 Processing helix chain 'J' and resid 125 through 129 Processing helix chain 'J' and resid 133 through 138 Processing helix chain 'J' and resid 138 through 147 Processing helix chain 'J' and resid 155 through 162 removed outlier: 3.768A pdb=" N LEU J 159 " --> pdb=" O SER J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 172 removed outlier: 3.742A pdb=" N ARG J 171 " --> pdb=" O ILE J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 190 Processing helix chain 'J' and resid 202 through 213 Proline residue: J 208 - end of helix Processing helix chain 'J' and resid 217 through 229 Processing helix chain 'J' and resid 233 through 235 No H-bonds generated for 'chain 'J' and resid 233 through 235' Processing helix chain 'J' and resid 236 through 250 removed outlier: 3.757A pdb=" N VAL J 240 " --> pdb=" O SER J 236 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG J 241 " --> pdb=" O LYS J 237 " (cutoff:3.500A) Processing helix chain 'J' and resid 263 through 274 Processing helix chain 'J' and resid 275 through 292 removed outlier: 3.814A pdb=" N LEU J 279 " --> pdb=" O ASP J 275 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG J 292 " --> pdb=" O ASN J 288 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 53 removed outlier: 3.604A pdb=" N ARG A 63 " --> pdb=" O VAL A 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 195 Processing sheet with id=AA3, first strand: chain 'A' and resid 242 through 243 Processing sheet with id=AA4, first strand: chain 'C' and resid 253 through 256 Processing sheet with id=AA5, first strand: chain 'B' and resid 48 through 52 Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 195 removed outlier: 4.570A pdb=" N VAL B 226 " --> pdb=" O GLU B 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 191 through 195 Processing sheet with id=AA8, first strand: chain 'B' and resid 242 through 243 Processing sheet with id=AA9, first strand: chain 'J' and resid 59 through 62 removed outlier: 6.601A pdb=" N ILE J 30 " --> pdb=" O ASP J 60 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N PHE J 62 " --> pdb=" O ILE J 30 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE J 32 " --> pdb=" O PHE J 62 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE J 94 " --> pdb=" O ILE J 121 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE J 123 " --> pdb=" O ILE J 94 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU J 96 " --> pdb=" O ILE J 123 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N LEU J 152 " --> pdb=" O LEU J 120 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N CYS J 122 " --> pdb=" O LEU J 152 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 253 through 256 449 hydrogen bonds defined for protein. 1281 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 170 hydrogen bonds 308 hydrogen bond angles 0 basepair planarities 68 basepair parallelities 120 stacking parallelities Total time for adding SS restraints: 5.18 Time building geometry restraints manager: 6.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1964 1.33 - 1.45: 4683 1.45 - 1.57: 6743 1.57 - 1.69: 422 1.69 - 1.81: 50 Bond restraints: 13862 Sorted by residual: bond pdb=" CA SER B 218 " pdb=" CB SER B 218 " ideal model delta sigma weight residual 1.532 1.473 0.059 1.53e-02 4.27e+03 1.50e+01 bond pdb=" N ARG B 213 " pdb=" CA ARG B 213 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.23e-02 6.61e+03 8.28e+00 bond pdb=" N ILE A 41 " pdb=" CA ILE A 41 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.23e-02 6.61e+03 8.22e+00 bond pdb=" N VAL B 210 " pdb=" CA VAL B 210 " ideal model delta sigma weight residual 1.459 1.496 -0.036 1.30e-02 5.92e+03 7.77e+00 bond pdb=" N ARG A 47 " pdb=" CA ARG A 47 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.66e+00 ... (remaining 13857 not shown) Histogram of bond angle deviations from ideal: 98.87 - 105.90: 1271 105.90 - 112.92: 7572 112.92 - 119.95: 4927 119.95 - 126.98: 5302 126.98 - 134.00: 593 Bond angle restraints: 19665 Sorted by residual: angle pdb=" C GLU B 59 " pdb=" CA GLU B 59 " pdb=" CB GLU B 59 " ideal model delta sigma weight residual 116.54 109.75 6.79 1.15e+00 7.56e-01 3.49e+01 angle pdb=" C ILE B 219 " pdb=" N ILE B 220 " pdb=" CA ILE B 220 " ideal model delta sigma weight residual 122.13 111.81 10.32 1.85e+00 2.92e-01 3.11e+01 angle pdb=" C4' DC G 3 " pdb=" C3' DC G 3 " pdb=" O3' DC G 3 " ideal model delta sigma weight residual 110.00 116.83 -6.83 1.50e+00 4.44e-01 2.07e+01 angle pdb=" CB LYS J 184 " pdb=" CG LYS J 184 " pdb=" CD LYS J 184 " ideal model delta sigma weight residual 111.30 121.22 -9.92 2.30e+00 1.89e-01 1.86e+01 angle pdb=" C LYS B 211 " pdb=" CA LYS B 211 " pdb=" CB LYS B 211 " ideal model delta sigma weight residual 110.38 119.11 -8.73 2.04e+00 2.40e-01 1.83e+01 ... (remaining 19660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 7159 35.95 - 71.89: 589 71.89 - 107.84: 11 107.84 - 143.78: 8 143.78 - 179.73: 15 Dihedral angle restraints: 7782 sinusoidal: 4655 harmonic: 3127 Sorted by residual: dihedral pdb=" O4' U H 68 " pdb=" C1' U H 68 " pdb=" N1 U H 68 " pdb=" C2 U H 68 " ideal model delta sinusoidal sigma weight residual 200.00 20.41 179.59 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U E 68 " pdb=" C1' U E 68 " pdb=" N1 U E 68 " pdb=" C2 U E 68 " ideal model delta sinusoidal sigma weight residual 200.00 53.56 146.44 1 1.50e+01 4.44e-03 7.82e+01 dihedral pdb=" O4' C H 65 " pdb=" C1' C H 65 " pdb=" N1 C H 65 " pdb=" C2 C H 65 " ideal model delta sinusoidal sigma weight residual 200.00 63.30 136.70 1 1.50e+01 4.44e-03 7.37e+01 ... (remaining 7779 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1927 0.056 - 0.111: 305 0.111 - 0.167: 70 0.167 - 0.222: 16 0.222 - 0.278: 1 Chirality restraints: 2319 Sorted by residual: chirality pdb=" P G F 1 " pdb=" OP1 G F 1 " pdb=" OP2 G F 1 " pdb=" O5' G F 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.69 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA TYR A 195 " pdb=" N TYR A 195 " pdb=" C TYR A 195 " pdb=" CB TYR A 195 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" P G I 1 " pdb=" OP1 G I 1 " pdb=" OP2 G I 1 " pdb=" O5' G I 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.63 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 2316 not shown) Planarity restraints: 1697 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU J 223 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.05e+00 pdb=" CD GLU J 223 " -0.043 2.00e-02 2.50e+03 pdb=" OE1 GLU J 223 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU J 223 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE J 302 " 0.040 5.00e-02 4.00e+02 6.02e-02 5.80e+00 pdb=" N PRO J 303 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO J 303 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO J 303 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 124 " 0.039 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO A 125 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 125 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 125 " 0.033 5.00e-02 4.00e+02 ... (remaining 1694 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 60 2.55 - 3.14: 9033 3.14 - 3.72: 21354 3.72 - 4.31: 31367 4.31 - 4.90: 47292 Nonbonded interactions: 109106 Sorted by model distance: nonbonded pdb=" O LEU A 39 " pdb=" OG1 THR A 43 " model vdw 1.962 2.440 nonbonded pdb=" NZ LYS B 60 " pdb=" OE2 GLU B 121 " model vdw 2.010 2.520 nonbonded pdb=" N2 G E 20 " pdb=" O2 U E 41 " model vdw 2.209 2.520 nonbonded pdb=" OP1 DG D 14 " pdb=" NH2 ARG J 276 " model vdw 2.211 2.520 nonbonded pdb=" O TYR C 211 " pdb=" NH2 ARG B 31 " model vdw 2.234 2.520 ... (remaining 109101 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'D' and (resid 1 through 19 or resid 66 through 85)) selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'I' } 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: 1.620 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: 7.410 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 41.100 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 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 : 0.005 0.059 13862 Z= 0.297 Angle : 0.712 10.322 19665 Z= 0.419 Chirality : 0.046 0.278 2319 Planarity : 0.005 0.060 1697 Dihedral : 22.256 179.725 5762 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.44 % Allowed : 26.38 % Favored : 70.18 % 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: -0.23 (0.25), residues: 1054 helix: 0.43 (0.23), residues: 547 sheet: 1.77 (0.53), residues: 87 loop : -1.32 (0.28), residues: 420 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 172 time to evaluate : 1.075 Fit side-chains outliers start: 33 outliers final: 30 residues processed: 204 average time/residue: 1.2534 time to fit residues: 278.3277 Evaluate side-chains 208 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 178 time to evaluate : 1.057 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 29 residues processed: 1 average time/residue: 0.1131 time to fit residues: 1.6368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 6.9990 chunk 92 optimal weight: 0.0770 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 49 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 71 optimal weight: 0.6980 chunk 110 optimal weight: 7.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS B 157 ASN J 198 ASN J 298 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.0733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13862 Z= 0.192 Angle : 0.557 6.524 19665 Z= 0.300 Chirality : 0.038 0.171 2319 Planarity : 0.004 0.045 1697 Dihedral : 22.187 179.717 3579 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 7.09 % Allowed : 22.73 % Favored : 70.18 % 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: 0.21 (0.26), residues: 1054 helix: 0.81 (0.22), residues: 566 sheet: 1.77 (0.54), residues: 89 loop : -1.20 (0.29), residues: 399 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 181 time to evaluate : 1.036 Fit side-chains outliers start: 68 outliers final: 41 residues processed: 226 average time/residue: 1.2413 time to fit residues: 306.0386 Evaluate side-chains 217 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 176 time to evaluate : 1.215 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 29 residues processed: 12 average time/residue: 0.5897 time to fit residues: 9.8720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 chunk 98 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 ASN J 198 ASN J 298 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.0795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13862 Z= 0.315 Angle : 0.616 7.935 19665 Z= 0.329 Chirality : 0.041 0.186 2319 Planarity : 0.005 0.062 1697 Dihedral : 22.194 179.855 3579 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 6.99 % Allowed : 23.04 % Favored : 69.97 % 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: 0.17 (0.25), residues: 1054 helix: 0.83 (0.22), residues: 564 sheet: 1.76 (0.53), residues: 89 loop : -1.30 (0.29), residues: 401 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 171 time to evaluate : 1.016 Fit side-chains revert: symmetry clash outliers start: 67 outliers final: 50 residues processed: 218 average time/residue: 1.2088 time to fit residues: 287.2914 Evaluate side-chains 226 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 176 time to evaluate : 1.095 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 36 residues processed: 14 average time/residue: 0.7777 time to fit residues: 13.7820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 111 optimal weight: 0.0270 chunk 117 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 98 optimal weight: 0.0170 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 ASN J 198 ASN J 298 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13862 Z= 0.158 Angle : 0.526 7.311 19665 Z= 0.281 Chirality : 0.037 0.176 2319 Planarity : 0.004 0.045 1697 Dihedral : 22.072 179.844 3579 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.84 % Allowed : 23.67 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.26), residues: 1054 helix: 1.27 (0.22), residues: 566 sheet: 1.49 (0.53), residues: 93 loop : -1.12 (0.30), residues: 395 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 180 time to evaluate : 1.189 Fit side-chains revert: symmetry clash outliers start: 56 outliers final: 44 residues processed: 222 average time/residue: 1.2360 time to fit residues: 299.1339 Evaluate side-chains 221 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 177 time to evaluate : 1.222 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 34 residues processed: 10 average time/residue: 0.6473 time to fit residues: 9.1095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 105 optimal weight: 0.0570 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN B 142 ASN J 198 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13862 Z= 0.179 Angle : 0.534 6.719 19665 Z= 0.285 Chirality : 0.037 0.178 2319 Planarity : 0.004 0.042 1697 Dihedral : 21.969 179.867 3579 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.53 % Allowed : 23.57 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.26), residues: 1054 helix: 1.37 (0.22), residues: 568 sheet: 2.00 (0.53), residues: 89 loop : -1.15 (0.29), residues: 397 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 178 time to evaluate : 1.179 Fit side-chains revert: symmetry clash outliers start: 53 outliers final: 46 residues processed: 219 average time/residue: 1.2179 time to fit residues: 290.7490 Evaluate side-chains 227 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 181 time to evaluate : 1.129 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 35 residues processed: 11 average time/residue: 0.9243 time to fit residues: 12.9025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 54 optimal weight: 0.4980 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN C 261 GLN B 142 ASN B 157 ASN B 240 GLN J 198 ASN J 298 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13862 Z= 0.269 Angle : 0.586 7.449 19665 Z= 0.313 Chirality : 0.040 0.182 2319 Planarity : 0.004 0.048 1697 Dihedral : 21.993 179.658 3579 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 5.53 % Allowed : 23.36 % Favored : 71.12 % 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: 0.51 (0.26), residues: 1054 helix: 1.15 (0.22), residues: 573 sheet: 1.92 (0.53), residues: 89 loop : -1.27 (0.29), residues: 392 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 181 time to evaluate : 1.031 Fit side-chains revert: symmetry clash outliers start: 53 outliers final: 46 residues processed: 219 average time/residue: 1.2133 time to fit residues: 289.8202 Evaluate side-chains 219 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 173 time to evaluate : 1.094 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 36 residues processed: 10 average time/residue: 0.7869 time to fit residues: 10.4097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 99 optimal weight: 10.0000 chunk 65 optimal weight: 0.0980 chunk 117 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 0.0010 chunk 72 optimal weight: 1.9990 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 142 ASN B 157 ASN J 198 ASN J 298 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13862 Z= 0.161 Angle : 0.540 6.313 19665 Z= 0.290 Chirality : 0.037 0.176 2319 Planarity : 0.004 0.065 1697 Dihedral : 21.979 179.618 3579 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 5.84 % Allowed : 22.94 % Favored : 71.22 % 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 (0.26), residues: 1054 helix: 1.37 (0.22), residues: 566 sheet: 2.01 (0.53), residues: 89 loop : -1.18 (0.29), residues: 399 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 177 time to evaluate : 1.144 Fit side-chains revert: symmetry clash outliers start: 56 outliers final: 44 residues processed: 220 average time/residue: 1.2219 time to fit residues: 293.4896 Evaluate side-chains 218 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 174 time to evaluate : 1.103 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 35 residues processed: 9 average time/residue: 0.5699 time to fit residues: 7.5005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 6.9990 chunk 70 optimal weight: 0.0060 chunk 35 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 0.2980 chunk 10 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 76 GLN B 142 ASN B 157 ASN J 198 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13862 Z= 0.187 Angle : 0.542 6.660 19665 Z= 0.291 Chirality : 0.037 0.177 2319 Planarity : 0.004 0.082 1697 Dihedral : 21.920 179.627 3579 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.69 % Allowed : 23.67 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.26), residues: 1054 helix: 1.37 (0.22), residues: 570 sheet: 2.04 (0.53), residues: 89 loop : -1.24 (0.29), residues: 395 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 172 time to evaluate : 1.254 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 44 residues processed: 208 average time/residue: 1.3540 time to fit residues: 306.6543 Evaluate side-chains 216 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 172 time to evaluate : 1.141 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 36 residues processed: 8 average time/residue: 0.9915 time to fit residues: 10.2754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.0970 chunk 102 optimal weight: 2.9990 chunk 109 optimal weight: 20.0000 chunk 65 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 142 ASN B 157 ASN J 198 ASN J 298 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13862 Z= 0.300 Angle : 0.605 7.676 19665 Z= 0.323 Chirality : 0.041 0.185 2319 Planarity : 0.005 0.058 1697 Dihedral : 21.956 179.606 3579 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.80 % Allowed : 23.88 % Favored : 71.32 % 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: 0.44 (0.26), residues: 1054 helix: 1.10 (0.22), residues: 573 sheet: 1.96 (0.53), residues: 89 loop : -1.33 (0.29), residues: 392 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 178 time to evaluate : 1.254 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 45 residues processed: 217 average time/residue: 1.2779 time to fit residues: 301.6632 Evaluate side-chains 224 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 179 time to evaluate : 1.197 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 38 residues processed: 7 average time/residue: 1.0872 time to fit residues: 10.0029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 111 optimal weight: 0.0070 chunk 96 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 74 optimal weight: 0.0970 chunk 59 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 103 optimal weight: 0.3980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 228 ASN B 142 ASN B 157 ASN J 198 ASN J 298 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13862 Z= 0.148 Angle : 0.523 6.501 19665 Z= 0.281 Chirality : 0.036 0.172 2319 Planarity : 0.004 0.044 1697 Dihedral : 21.871 179.969 3579 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.38 % Allowed : 24.50 % Favored : 71.12 % 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: 0.73 (0.26), residues: 1054 helix: 1.38 (0.22), residues: 572 sheet: 1.80 (0.54), residues: 93 loop : -1.24 (0.29), residues: 389 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 176 time to evaluate : 1.192 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 40 residues processed: 212 average time/residue: 1.2927 time to fit residues: 298.0499 Evaluate side-chains 214 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 174 time to evaluate : 1.106 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 36 residues processed: 4 average time/residue: 0.7956 time to fit residues: 5.1118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 12 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 76 GLN B 142 ASN B 157 ASN J 198 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.178408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.142767 restraints weight = 15942.113| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.26 r_work: 0.3536 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13862 Z= 0.273 Angle : 0.589 8.104 19665 Z= 0.313 Chirality : 0.040 0.184 2319 Planarity : 0.005 0.097 1697 Dihedral : 21.892 179.810 3579 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.59 % Allowed : 24.40 % Favored : 71.01 % 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: 0.56 (0.26), residues: 1054 helix: 1.19 (0.22), residues: 571 sheet: 2.06 (0.53), residues: 89 loop : -1.27 (0.29), residues: 394 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5276.69 seconds wall clock time: 94 minutes 12.52 seconds (5652.52 seconds total)