Starting phenix.real_space_refine on Fri Mar 15 23:55:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjg_33226/03_2024/7xjg_33226.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjg_33226/03_2024/7xjg_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_33226/03_2024/7xjg_33226.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjg_33226/03_2024/7xjg_33226.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjg_33226/03_2024/7xjg_33226.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjg_33226/03_2024/7xjg_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-dev-5265/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: 7.47, 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: 6.53 Conformation dependent library (CDL) restraints added in 1.7 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: 5.25 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: 4.58 Time building geometry restraints manager: 6.90 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: 7552 35.95 - 71.89: 820 71.89 - 107.84: 39 107.84 - 143.78: 8 143.78 - 179.73: 15 Dihedral angle restraints: 8434 sinusoidal: 5307 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 8431 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: 1.880 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: 7.280 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 42.010 Find NCS groups from input model: 0.490 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:11.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.400 ------------------------------------------------------------------------------- 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 : 24.504 179.725 6414 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 78 HIS 0.007 0.001 HIS B 280 PHE 0.015 0.002 PHE B 96 TYR 0.024 0.002 TYR B 184 ARG 0.008 0.001 ARG B 31 *********************** 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 : 1.080 Fit side-chains REVERT: C 282 LEU cc_start: 0.7679 (mt) cc_final: 0.7461 (mt) REVERT: C 292 ARG cc_start: 0.7893 (mtp-110) cc_final: 0.7652 (mtm180) outliers start: 33 outliers final: 30 residues processed: 204 average time/residue: 1.2378 time to fit residues: 274.5896 Evaluate side-chains 209 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 179 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 145 LYS Chi-restraints excluded: chain J residue 149 LYS Chi-restraints excluded: chain J residue 153 ARG Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 188 LYS Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain J residue 195 ASP Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 220 THR Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 234 VAL Chi-restraints excluded: chain J residue 295 SER Chi-restraints excluded: chain J residue 306 HIS 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: 4.9990 chunk 71 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 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: 0.7173 moved from start: 0.0756 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= 0.192 Angle : 0.559 6.478 19665 Z= 0.301 Chirality : 0.038 0.174 2319 Planarity : 0.004 0.046 1697 Dihedral : 25.305 179.444 4292 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 5.53 % Allowed : 24.09 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.26), residues: 1054 helix: 0.80 (0.22), residues: 566 sheet: 1.69 (0.53), residues: 90 loop : -1.20 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 78 HIS 0.006 0.001 HIS B 280 PHE 0.012 0.001 PHE B 96 TYR 0.015 0.001 TYR B 179 ARG 0.004 0.000 ARG A 11 *********************** 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 235 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 182 time to evaluate : 1.169 Fit side-chains REVERT: C 292 ARG cc_start: 0.7837 (mtp-110) cc_final: 0.7611 (mtm180) REVERT: B 142 ASN cc_start: 0.7942 (p0) cc_final: 0.7485 (p0) REVERT: J 30 ILE cc_start: 0.7070 (OUTLIER) cc_final: 0.6842 (pt) REVERT: J 230 LYS cc_start: 0.6872 (mmmt) cc_final: 0.6495 (mmmt) outliers start: 53 outliers final: 23 residues processed: 215 average time/residue: 1.2655 time to fit residues: 295.5395 Evaluate side-chains 202 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 178 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 184 LYS Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain J residue 205 PHE Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 273 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 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: 0.9990 chunk 37 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 ASN B 240 GLN J 198 ASN J 298 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13862 Z= 0.319 Angle : 0.621 8.015 19665 Z= 0.332 Chirality : 0.042 0.187 2319 Planarity : 0.005 0.063 1697 Dihedral : 25.262 179.960 4251 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 5.32 % Allowed : 24.19 % 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: 0.12 (0.25), residues: 1054 helix: 0.81 (0.22), residues: 564 sheet: 1.63 (0.53), residues: 90 loop : -1.32 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 78 HIS 0.007 0.002 HIS B 280 PHE 0.018 0.002 PHE B 10 TYR 0.019 0.002 TYR A 179 ARG 0.006 0.001 ARG A 11 *********************** 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 225 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 174 time to evaluate : 1.173 Fit side-chains revert: symmetry clash REVERT: C 292 ARG cc_start: 0.7892 (mtp-110) cc_final: 0.7654 (mtm180) REVERT: B 139 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7506 (mp) REVERT: J 30 ILE cc_start: 0.7072 (OUTLIER) cc_final: 0.6804 (pt) outliers start: 51 outliers final: 34 residues processed: 205 average time/residue: 1.2603 time to fit residues: 280.9339 Evaluate side-chains 208 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 172 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 184 LYS Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain J residue 196 ILE Chi-restraints excluded: chain J residue 205 PHE Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 256 MET Chi-restraints excluded: chain J residue 258 ASP Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 277 LYS Chi-restraints excluded: chain J residue 278 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 74 optimal weight: 0.4980 chunk 111 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 98 optimal weight: 0.0470 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 261 GLN J 136 ASN J 198 ASN J 298 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.0907 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= 0.247 Angle : 0.582 7.481 19665 Z= 0.311 Chirality : 0.039 0.183 2319 Planarity : 0.004 0.046 1697 Dihedral : 25.185 179.968 4246 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 5.42 % Allowed : 23.46 % 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: 0.30 (0.26), residues: 1054 helix: 0.96 (0.22), residues: 566 sheet: 1.65 (0.53), residues: 89 loop : -1.24 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 78 HIS 0.007 0.001 HIS B 280 PHE 0.014 0.002 PHE B 96 TYR 0.016 0.001 TYR B 179 ARG 0.006 0.000 ARG A 49 *********************** 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 226 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 174 time to evaluate : 1.189 Fit side-chains revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8457 (OUTLIER) cc_final: 0.8239 (p0) REVERT: C 292 ARG cc_start: 0.7875 (mtp-110) cc_final: 0.7674 (mtm180) REVERT: B 142 ASN cc_start: 0.7950 (p0) cc_final: 0.7511 (p0) REVERT: J 30 ILE cc_start: 0.7058 (OUTLIER) cc_final: 0.6774 (pt) outliers start: 52 outliers final: 38 residues processed: 210 average time/residue: 1.2531 time to fit residues: 286.3466 Evaluate side-chains 212 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 172 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 155 SER Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 184 LYS Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain J residue 196 ILE Chi-restraints excluded: chain J residue 205 PHE Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 256 MET Chi-restraints excluded: chain J residue 258 ASP Chi-restraints excluded: chain J residue 261 GLN Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 277 LYS Chi-restraints excluded: chain J residue 295 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 ASN J 136 ASN J 198 ASN J 298 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13862 Z= 0.236 Angle : 0.570 6.794 19665 Z= 0.304 Chirality : 0.039 0.180 2319 Planarity : 0.004 0.046 1697 Dihedral : 25.078 179.148 4245 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % 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: 0.41 (0.26), residues: 1054 helix: 1.06 (0.22), residues: 569 sheet: 1.83 (0.54), residues: 89 loop : -1.28 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 78 HIS 0.006 0.001 HIS B 280 PHE 0.014 0.002 PHE B 96 TYR 0.016 0.001 TYR B 179 ARG 0.006 0.000 ARG A 49 *********************** 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 233 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 180 time to evaluate : 1.166 Fit side-chains revert: symmetry clash REVERT: C 292 ARG cc_start: 0.7863 (mtp-110) cc_final: 0.7624 (mtm180) REVERT: B 23 LEU cc_start: 0.8653 (mt) cc_final: 0.8426 (mt) REVERT: B 139 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7507 (mp) REVERT: B 142 ASN cc_start: 0.7944 (p0) cc_final: 0.7532 (p0) REVERT: J 30 ILE cc_start: 0.7112 (OUTLIER) cc_final: 0.6801 (pt) outliers start: 53 outliers final: 44 residues processed: 212 average time/residue: 1.2754 time to fit residues: 294.3508 Evaluate side-chains 221 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 175 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 155 SER Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 184 LYS Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain J residue 196 ILE Chi-restraints excluded: chain J residue 205 PHE Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 223 GLU Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 256 MET Chi-restraints excluded: chain J residue 257 THR Chi-restraints excluded: chain J residue 258 ASP Chi-restraints excluded: chain J residue 261 GLN Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 277 LYS Chi-restraints excluded: chain J residue 295 SER Chi-restraints excluded: chain J residue 302 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 97 optimal weight: 9.9990 chunk 54 optimal weight: 0.2980 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 ASN J 136 ASN J 198 ASN J 298 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13862 Z= 0.241 Angle : 0.571 6.978 19665 Z= 0.305 Chirality : 0.039 0.180 2319 Planarity : 0.004 0.046 1697 Dihedral : 25.007 179.785 4245 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 6.05 % Allowed : 23.04 % 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: 0.41 (0.26), residues: 1054 helix: 1.09 (0.22), residues: 569 sheet: 1.79 (0.54), residues: 89 loop : -1.32 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 78 HIS 0.006 0.001 HIS B 280 PHE 0.014 0.002 PHE B 96 TYR 0.016 0.001 TYR B 179 ARG 0.009 0.000 ARG A 49 *********************** 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 233 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 175 time to evaluate : 1.237 Fit side-chains revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8449 (OUTLIER) cc_final: 0.8200 (p0) REVERT: B 23 LEU cc_start: 0.8652 (mt) cc_final: 0.8423 (mt) REVERT: B 70 ARG cc_start: 0.6929 (OUTLIER) cc_final: 0.6726 (ttt90) REVERT: B 139 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7505 (mp) REVERT: B 142 ASN cc_start: 0.7945 (p0) cc_final: 0.7531 (p0) REVERT: J 30 ILE cc_start: 0.7092 (OUTLIER) cc_final: 0.6775 (pt) outliers start: 58 outliers final: 45 residues processed: 215 average time/residue: 1.2304 time to fit residues: 288.0561 Evaluate side-chains 222 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 173 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain J residue 155 SER Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 184 LYS Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain J residue 196 ILE Chi-restraints excluded: chain J residue 205 PHE Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 223 GLU Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 256 MET Chi-restraints excluded: chain J residue 257 THR Chi-restraints excluded: chain J residue 258 ASP Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 277 LYS Chi-restraints excluded: chain J residue 278 THR Chi-restraints excluded: chain J residue 295 SER Chi-restraints excluded: chain J residue 302 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 99 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 ASN J 115 ASN J 136 ASN J 198 ASN J 298 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.1180 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= 0.232 Angle : 0.568 6.856 19665 Z= 0.303 Chirality : 0.039 0.180 2319 Planarity : 0.004 0.061 1697 Dihedral : 24.998 179.717 4243 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 5.74 % Allowed : 23.46 % Favored : 70.80 % 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: 1.11 (0.22), residues: 570 sheet: 1.83 (0.54), residues: 89 loop : -1.31 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 78 HIS 0.006 0.001 HIS B 280 PHE 0.014 0.002 PHE B 96 TYR 0.016 0.001 TYR B 179 ARG 0.008 0.000 ARG A 49 *********************** 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 229 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 174 time to evaluate : 1.274 Fit side-chains revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.8041 (p0) REVERT: C 279 LEU cc_start: 0.7154 (mt) cc_final: 0.6926 (mt) REVERT: B 23 LEU cc_start: 0.8650 (mt) cc_final: 0.8418 (mt) REVERT: B 139 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7481 (mp) REVERT: B 142 ASN cc_start: 0.7943 (p0) cc_final: 0.7528 (p0) REVERT: J 30 ILE cc_start: 0.7093 (OUTLIER) cc_final: 0.6772 (pt) outliers start: 55 outliers final: 45 residues processed: 210 average time/residue: 1.2274 time to fit residues: 280.5947 Evaluate side-chains 221 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 173 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 155 SER Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 184 LYS Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain J residue 196 ILE Chi-restraints excluded: chain J residue 205 PHE Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 223 GLU Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 256 MET Chi-restraints excluded: chain J residue 257 THR Chi-restraints excluded: chain J residue 258 ASP Chi-restraints excluded: chain J residue 261 GLN Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 277 LYS Chi-restraints excluded: chain J residue 278 THR Chi-restraints excluded: chain J residue 295 SER Chi-restraints excluded: chain J residue 302 ILE 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: 0.9990 chunk 35 optimal weight: 0.0970 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 74 optimal weight: 0.4980 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 115 ASN J 136 ASN J 198 ASN J 298 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13862 Z= 0.209 Angle : 0.557 6.752 19665 Z= 0.298 Chirality : 0.038 0.178 2319 Planarity : 0.004 0.056 1697 Dihedral : 24.977 179.718 4243 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 5.74 % Allowed : 23.46 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.26), residues: 1054 helix: 1.16 (0.22), residues: 570 sheet: 1.85 (0.54), residues: 89 loop : -1.31 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 78 HIS 0.006 0.001 HIS B 280 PHE 0.013 0.001 PHE B 96 TYR 0.016 0.001 TYR B 179 ARG 0.007 0.000 ARG A 49 *********************** 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 228 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 173 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.8074 (p0) REVERT: C 279 LEU cc_start: 0.7145 (mt) cc_final: 0.6919 (mt) REVERT: B 31 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7244 (mtm-85) REVERT: B 139 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7487 (mp) REVERT: J 30 ILE cc_start: 0.7090 (OUTLIER) cc_final: 0.6767 (pt) outliers start: 55 outliers final: 46 residues processed: 210 average time/residue: 1.2738 time to fit residues: 290.6823 Evaluate side-chains 223 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 173 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 155 SER Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 184 LYS Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain J residue 196 ILE Chi-restraints excluded: chain J residue 205 PHE Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 223 GLU Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 234 VAL Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 256 MET Chi-restraints excluded: chain J residue 257 THR Chi-restraints excluded: chain J residue 258 ASP Chi-restraints excluded: chain J residue 261 GLN Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 277 LYS Chi-restraints excluded: chain J residue 278 THR Chi-restraints excluded: chain J residue 295 SER Chi-restraints excluded: chain J residue 302 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 65 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 115 optimal weight: 0.0770 overall best weight: 1.1344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 115 ASN J 136 ASN J 198 ASN J 298 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13862 Z= 0.299 Angle : 0.603 7.641 19665 Z= 0.321 Chirality : 0.041 0.183 2319 Planarity : 0.005 0.061 1697 Dihedral : 25.004 179.458 4243 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 5.84 % Allowed : 23.36 % Favored : 70.80 % 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: 0.32 (0.25), residues: 1054 helix: 1.05 (0.22), residues: 565 sheet: 1.81 (0.54), residues: 89 loop : -1.41 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 78 HIS 0.007 0.001 HIS B 280 PHE 0.017 0.002 PHE B 10 TYR 0.019 0.002 TYR A 179 ARG 0.007 0.001 ARG A 49 *********************** 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 232 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 176 time to evaluate : 1.186 Fit side-chains revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8429 (OUTLIER) cc_final: 0.8092 (p0) REVERT: B 31 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.7253 (mtm-85) REVERT: B 139 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7493 (mp) REVERT: B 142 ASN cc_start: 0.7977 (p0) cc_final: 0.7510 (p0) REVERT: J 30 ILE cc_start: 0.7026 (OUTLIER) cc_final: 0.6708 (pt) outliers start: 56 outliers final: 48 residues processed: 212 average time/residue: 1.2197 time to fit residues: 281.6377 Evaluate side-chains 227 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 175 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain J residue 155 SER Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 184 LYS Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain J residue 196 ILE Chi-restraints excluded: chain J residue 205 PHE Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 223 GLU Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 234 VAL Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 256 MET Chi-restraints excluded: chain J residue 257 THR Chi-restraints excluded: chain J residue 258 ASP Chi-restraints excluded: chain J residue 261 GLN Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 277 LYS Chi-restraints excluded: chain J residue 278 THR Chi-restraints excluded: chain J residue 295 SER Chi-restraints excluded: chain J residue 302 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.7980 chunk 54 optimal weight: 0.2980 chunk 80 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 111 optimal weight: 0.0570 chunk 96 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN B 157 ASN J 115 ASN J 136 ASN J 198 ASN J 298 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13862 Z= 0.190 Angle : 0.562 6.968 19665 Z= 0.301 Chirality : 0.038 0.177 2319 Planarity : 0.004 0.070 1697 Dihedral : 24.978 179.516 4243 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 5.53 % Allowed : 23.88 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.26), residues: 1054 helix: 1.15 (0.22), residues: 570 sheet: 1.97 (0.53), residues: 90 loop : -1.33 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 78 HIS 0.005 0.001 HIS B 280 PHE 0.012 0.001 PHE A 10 TYR 0.016 0.001 TYR B 179 ARG 0.008 0.000 ARG A 49 ********************** 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 228 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 175 time to evaluate : 1.125 Fit side-chains revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8425 (OUTLIER) cc_final: 0.8038 (p0) REVERT: B 31 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.7237 (mtm-85) REVERT: B 139 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7475 (mp) REVERT: B 142 ASN cc_start: 0.7968 (p0) cc_final: 0.7509 (p0) REVERT: J 30 ILE cc_start: 0.7083 (OUTLIER) cc_final: 0.6756 (pt) outliers start: 53 outliers final: 44 residues processed: 209 average time/residue: 1.2604 time to fit residues: 286.6975 Evaluate side-chains 221 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 173 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 155 SER Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 184 LYS Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain J residue 196 ILE Chi-restraints excluded: chain J residue 205 PHE Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 223 GLU Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 234 VAL Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 256 MET Chi-restraints excluded: chain J residue 257 THR Chi-restraints excluded: chain J residue 258 ASP Chi-restraints excluded: chain J residue 261 GLN Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 277 LYS Chi-restraints excluded: chain J residue 278 THR Chi-restraints excluded: chain J residue 295 SER Chi-restraints excluded: chain J residue 302 ILE 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: 1.9990 chunk 26 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 99 optimal weight: 9.9990 chunk 12 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 ASN J 115 ASN J 136 ASN J 198 ASN J 298 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.178582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.142965 restraints weight = 15945.085| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 1.23 r_work: 0.3537 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 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 : 0.004 0.047 13862 Z= 0.249 Angle : 0.577 7.070 19665 Z= 0.308 Chirality : 0.039 0.179 2319 Planarity : 0.005 0.081 1697 Dihedral : 24.955 179.462 4243 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % 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: 0.45 (0.26), residues: 1054 helix: 1.12 (0.22), residues: 570 sheet: 1.95 (0.53), residues: 90 loop : -1.33 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 78 HIS 0.006 0.001 HIS B 280 PHE 0.014 0.002 PHE B 96 TYR 0.017 0.001 TYR A 179 ARG 0.007 0.000 ARG A 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5174.25 seconds wall clock time: 92 minutes 30.49 seconds (5550.49 seconds total)