Starting phenix.real_space_refine on Thu Sep 26 12:56:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjg_33226/09_2024/7xjg_33226.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjg_33226/09_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_33226/09_2024/7xjg_33226.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjg_33226/09_2024/7xjg_33226.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjg_33226/09_2024/7xjg_33226.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjg_33226/09_2024/7xjg_33226.cif" } 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. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 8.53, per 1000 atoms: 0.65 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 - 3.00 Amino acid : True - 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: 3.29 Conformation dependent library (CDL) restraints added in 1.2 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: 5.23 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: 4.22 Time building geometry restraints manager: 3.85 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: 0.00 - 2.06: 19163 2.06 - 4.13: 437 4.13 - 6.19: 57 6.19 - 8.26: 4 8.26 - 10.32: 4 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 3.040 nonbonded pdb=" NZ LYS B 60 " pdb=" OE2 GLU B 121 " model vdw 2.010 3.120 nonbonded pdb=" N2 G E 20 " pdb=" O2 U E 41 " model vdw 2.209 3.120 nonbonded pdb=" OP1 DG D 14 " pdb=" NH2 ARG J 276 " model vdw 2.211 3.120 nonbonded pdb=" O TYR C 211 " pdb=" NH2 ARG B 31 " model vdw 2.234 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 1.920 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: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 34.550 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 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:11.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.790 ------------------------------------------------------------------------------- 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 : 1.070 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: 1.2661 time to fit residues: 281.0305 Evaluate side-chains 209 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 179 time to evaluate : 1.126 ------------------------------------------------------------------------------- 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: 3.9990 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 95 optimal weight: 0.0070 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 0.0970 chunk 71 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 overall best weight: 1.0198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS B 104 ASN B 157 ASN ** J 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 198 ASN J 298 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.0683 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= 0.282 Angle : 0.622 7.523 19665 Z= 0.334 Chirality : 0.041 0.186 2319 Planarity : 0.005 0.048 1697 Dihedral : 25.386 178.371 4292 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 5.74 % Allowed : 22.94 % 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: -0.04 (0.25), residues: 1054 helix: 0.58 (0.22), residues: 566 sheet: 1.66 (0.53), residues: 89 loop : -1.28 (0.29), residues: 399 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 0.016 0.002 PHE B 96 TYR 0.017 0.002 TYR B 179 ARG 0.005 0.001 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 231 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 176 time to evaluate : 1.185 Fit side-chains REVERT: A 63 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.6795 (ttm-80) REVERT: C 292 ARG cc_start: 0.7867 (mtp-110) cc_final: 0.7630 (mtm180) REVERT: J 30 ILE cc_start: 0.7081 (OUTLIER) cc_final: 0.6853 (pt) REVERT: J 86 ILE cc_start: 0.7796 (tt) cc_final: 0.7376 (pt) outliers start: 55 outliers final: 27 residues processed: 210 average time/residue: 1.2754 time to fit residues: 290.7543 Evaluate side-chains 203 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 174 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 72 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 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 119 LYS Chi-restraints excluded: chain J residue 149 LYS 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 Chi-restraints excluded: chain J residue 295 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 92 optimal weight: 0.0470 chunk 75 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 119 optimal weight: 0.4980 chunk 98 optimal weight: 0.3980 chunk 37 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 0.0000 overall best weight: 0.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 ASN ** J 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 198 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13862 Z= 0.152 Angle : 0.542 6.570 19665 Z= 0.291 Chirality : 0.037 0.173 2319 Planarity : 0.004 0.043 1697 Dihedral : 25.126 179.838 4257 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.38 % Allowed : 23.67 % Favored : 71.95 % 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: 1.06 (0.22), residues: 569 sheet: 1.78 (0.53), residues: 90 loop : -1.18 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 78 HIS 0.004 0.001 HIS B 280 PHE 0.011 0.001 PHE J 205 TYR 0.013 0.001 TYR B 179 ARG 0.005 0.000 ARG J 153 *********************** 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 218 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 176 time to evaluate : 1.230 Fit side-chains REVERT: J 30 ILE cc_start: 0.7041 (OUTLIER) cc_final: 0.6782 (pt) REVERT: J 298 ASN cc_start: 0.8315 (t0) cc_final: 0.8086 (t0) outliers start: 42 outliers final: 22 residues processed: 202 average time/residue: 1.2512 time to fit residues: 274.9868 Evaluate side-chains 198 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 175 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 72 LEU 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 30 ILE Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 115 ASN 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 0.0770 chunk 52 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 111 optimal weight: 0.3980 chunk 117 optimal weight: 2.9990 chunk 58 optimal weight: 0.0000 chunk 105 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN ** J 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 ASN J 198 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13862 Z= 0.161 Angle : 0.537 7.817 19665 Z= 0.286 Chirality : 0.037 0.172 2319 Planarity : 0.004 0.039 1697 Dihedral : 24.995 178.841 4244 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.38 % Allowed : 24.09 % Favored : 71.53 % 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: 0.69 (0.26), residues: 1054 helix: 1.32 (0.22), residues: 568 sheet: 1.80 (0.53), residues: 90 loop : -1.15 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 78 HIS 0.005 0.001 HIS B 280 PHE 0.011 0.001 PHE J 205 TYR 0.013 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 214 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 172 time to evaluate : 1.234 Fit side-chains REVERT: B 139 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7468 (mp) REVERT: J 30 ILE cc_start: 0.7119 (OUTLIER) cc_final: 0.6830 (pt) REVERT: J 298 ASN cc_start: 0.8323 (t0) cc_final: 0.8079 (t0) outliers start: 42 outliers final: 25 residues processed: 196 average time/residue: 1.2481 time to fit residues: 266.0242 Evaluate side-chains 197 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 170 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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 219 ILE Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 139 LEU 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 30 ILE Chi-restraints excluded: chain J residue 49 LEU 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 0 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 261 GLN B 157 ASN B 240 GLN ** J 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 ASN J 198 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 13862 Z= 0.403 Angle : 0.675 8.676 19665 Z= 0.357 Chirality : 0.045 0.185 2319 Planarity : 0.005 0.054 1697 Dihedral : 25.163 179.417 4242 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.80 % Allowed : 23.57 % 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: 0.22 (0.25), residues: 1054 helix: 0.89 (0.22), residues: 565 sheet: 1.68 (0.53), residues: 89 loop : -1.30 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP B 78 HIS 0.008 0.002 HIS B 280 PHE 0.023 0.003 PHE B 10 TYR 0.022 0.002 TYR A 179 ARG 0.006 0.001 ARG B 213 *********************** 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 230 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 184 time to evaluate : 1.230 Fit side-chains REVERT: C 292 ARG cc_start: 0.7876 (mtp-110) cc_final: 0.7631 (mtm180) REVERT: B 139 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7503 (mp) REVERT: J 30 ILE cc_start: 0.7054 (OUTLIER) cc_final: 0.6677 (pp) REVERT: J 298 ASN cc_start: 0.8369 (t0) cc_final: 0.8153 (t0) outliers start: 46 outliers final: 35 residues processed: 214 average time/residue: 1.2120 time to fit residues: 283.2758 Evaluate side-chains 209 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 172 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 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 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 276 SER Chi-restraints excluded: chain B residue 301 THR 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 93 VAL Chi-restraints excluded: chain J residue 119 LYS 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 257 THR 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 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: 1.9990 chunk 69 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 118 optimal weight: 0.5980 chunk 97 optimal weight: 9.9990 chunk 54 optimal weight: 0.0010 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 113 optimal weight: 0.0470 overall best weight: 0.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN A 240 GLN B 157 ASN ** J 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 ASN J 198 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13862 Z= 0.157 Angle : 0.540 6.866 19665 Z= 0.289 Chirality : 0.037 0.169 2319 Planarity : 0.004 0.044 1697 Dihedral : 24.974 179.375 4242 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.96 % Allowed : 24.61 % Favored : 71.43 % 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: 0.60 (0.26), residues: 1054 helix: 1.28 (0.22), residues: 566 sheet: 1.46 (0.54), residues: 94 loop : -1.18 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 78 HIS 0.004 0.001 HIS B 280 PHE 0.011 0.001 PHE J 205 TYR 0.013 0.001 TYR B 179 ARG 0.006 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 213 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 175 time to evaluate : 1.128 Fit side-chains REVERT: B 139 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7456 (mp) REVERT: J 30 ILE cc_start: 0.7102 (OUTLIER) cc_final: 0.6774 (pt) REVERT: J 298 ASN cc_start: 0.8315 (t0) cc_final: 0.8065 (t0) outliers start: 38 outliers final: 26 residues processed: 199 average time/residue: 1.2359 time to fit residues: 267.7239 Evaluate side-chains 203 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 175 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 219 ILE Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 139 LEU 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 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 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 205 PHE Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 257 THR Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 277 LYS 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: 0.3980 chunk 86 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 99 optimal weight: 8.9990 chunk 65 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 54 optimal weight: 0.0170 chunk 72 optimal weight: 0.7980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN B 157 ASN ** J 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 ASN J 198 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.1424 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= 0.183 Angle : 0.549 6.925 19665 Z= 0.292 Chirality : 0.037 0.172 2319 Planarity : 0.004 0.042 1697 Dihedral : 24.912 179.243 4242 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.86 % Allowed : 24.92 % 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: 0.72 (0.26), residues: 1054 helix: 1.36 (0.22), residues: 566 sheet: 1.93 (0.53), residues: 89 loop : -1.17 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 78 HIS 0.006 0.001 HIS B 280 PHE 0.011 0.001 PHE B 96 TYR 0.016 0.001 TYR B 179 ARG 0.009 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 211 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 174 time to evaluate : 1.117 Fit side-chains REVERT: B 31 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7209 (mtm-85) REVERT: B 139 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7469 (mp) REVERT: J 30 ILE cc_start: 0.7072 (OUTLIER) cc_final: 0.6710 (pp) REVERT: J 298 ASN cc_start: 0.8331 (t0) cc_final: 0.8101 (t0) outliers start: 37 outliers final: 29 residues processed: 197 average time/residue: 1.2693 time to fit residues: 271.8432 Evaluate side-chains 206 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 174 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET 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 219 ILE Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 139 LEU 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 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 189 GLU 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 257 THR 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 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: 1.9990 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 92 optimal weight: 0.3980 chunk 106 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 ASN ** J 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 ASN J 198 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13862 Z= 0.232 Angle : 0.578 7.161 19665 Z= 0.307 Chirality : 0.039 0.174 2319 Planarity : 0.004 0.048 1697 Dihedral : 24.931 179.347 4242 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.65 % Allowed : 25.34 % 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: 0.62 (0.26), residues: 1054 helix: 1.27 (0.22), residues: 565 sheet: 1.85 (0.53), residues: 89 loop : -1.19 (0.29), residues: 400 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 10 TYR 0.017 0.001 TYR B 179 ARG 0.009 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 206 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 171 time to evaluate : 1.179 Fit side-chains REVERT: A 11 ARG cc_start: 0.7866 (tpt-90) cc_final: 0.7614 (mtp85) REVERT: B 31 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7223 (mtm-85) REVERT: B 139 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7501 (mp) REVERT: J 30 ILE cc_start: 0.7074 (OUTLIER) cc_final: 0.6691 (pp) REVERT: J 298 ASN cc_start: 0.8338 (t0) cc_final: 0.8098 (t0) outliers start: 35 outliers final: 28 residues processed: 196 average time/residue: 1.3460 time to fit residues: 285.5987 Evaluate side-chains 204 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 173 time to evaluate : 1.223 ------------------------------------------------------------------------------- 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 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 256 MET Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 139 LEU 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 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 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 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 257 THR Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 277 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 ASN ** J 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 13862 Z= 0.354 Angle : 0.650 8.139 19665 Z= 0.344 Chirality : 0.043 0.181 2319 Planarity : 0.005 0.048 1697 Dihedral : 25.052 179.556 4242 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.96 % Allowed : 24.82 % 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: 0.29 (0.25), residues: 1054 helix: 1.04 (0.22), residues: 559 sheet: 1.51 (0.54), residues: 93 loop : -1.37 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 78 HIS 0.007 0.002 HIS B 280 PHE 0.020 0.002 PHE B 10 TYR 0.021 0.002 TYR A 179 ARG 0.009 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 213 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 175 time to evaluate : 1.158 Fit side-chains REVERT: B 31 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7234 (mtm-85) REVERT: B 139 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7492 (mp) REVERT: J 30 ILE cc_start: 0.7037 (OUTLIER) cc_final: 0.6669 (pp) REVERT: J 298 ASN cc_start: 0.8365 (t0) cc_final: 0.8127 (t0) outliers start: 38 outliers final: 31 residues processed: 201 average time/residue: 1.2624 time to fit residues: 276.2887 Evaluate side-chains 207 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 173 time to evaluate : 1.359 ------------------------------------------------------------------------------- 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 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 256 MET Chi-restraints excluded: chain B residue 31 ARG 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 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 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 257 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.2980 chunk 54 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 10 optimal weight: 0.0370 chunk 74 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- 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 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 ASN J 198 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13862 Z= 0.199 Angle : 0.579 6.747 19665 Z= 0.309 Chirality : 0.038 0.171 2319 Planarity : 0.004 0.059 1697 Dihedral : 24.993 179.354 4242 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.55 % Allowed : 25.23 % 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: 0.45 (0.26), residues: 1054 helix: 1.17 (0.22), residues: 567 sheet: 1.59 (0.54), residues: 93 loop : -1.33 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 78 HIS 0.007 0.001 HIS B 280 PHE 0.012 0.001 PHE A 10 TYR 0.015 0.001 TYR B 179 ARG 0.009 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 207 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 173 time to evaluate : 1.366 Fit side-chains REVERT: A 11 ARG cc_start: 0.7868 (tpt-90) cc_final: 0.7585 (mtp85) REVERT: B 31 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.7236 (mtm-85) REVERT: B 139 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7484 (mp) REVERT: J 30 ILE cc_start: 0.7032 (OUTLIER) cc_final: 0.6650 (pp) REVERT: J 298 ASN cc_start: 0.8326 (t0) cc_final: 0.8067 (t0) outliers start: 34 outliers final: 28 residues processed: 196 average time/residue: 1.3285 time to fit residues: 282.8755 Evaluate side-chains 203 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 172 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 219 ILE Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 139 LEU 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 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 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 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 230 LYS Chi-restraints excluded: chain J residue 257 THR Chi-restraints excluded: chain J residue 261 GLN Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 277 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 12 optimal weight: 0.0010 chunk 17 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 5 optimal weight: 0.0270 overall best weight: 0.7248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 ASN ** J 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 ASN J 198 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.179044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.143321 restraints weight = 15967.433| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 1.25 r_work: 0.3542 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13862 Z= 0.219 Angle : 0.579 7.069 19665 Z= 0.308 Chirality : 0.039 0.171 2319 Planarity : 0.004 0.050 1697 Dihedral : 24.959 179.395 4242 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.65 % Allowed : 25.03 % 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: 0.52 (0.26), residues: 1054 helix: 1.23 (0.22), residues: 565 sheet: 1.67 (0.54), residues: 93 loop : -1.31 (0.29), residues: 396 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 0.014 0.002 PHE B 96 TYR 0.016 0.001 TYR B 179 ARG 0.008 0.000 ARG A 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5235.73 seconds wall clock time: 92 minutes 10.88 seconds (5530.88 seconds total)