Starting phenix.real_space_refine on Sun Mar 17 14:38:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g01_29641/03_2024/8g01_29641.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g01_29641/03_2024/8g01_29641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g01_29641/03_2024/8g01_29641.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g01_29641/03_2024/8g01_29641.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g01_29641/03_2024/8g01_29641.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g01_29641/03_2024/8g01_29641.pdb" } resolution = 3.4 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= 0.002 sd= 0.031 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: 5 Type Number sf(0) Gaussians S 44 5.16 5 C 5890 2.51 5 N 1472 2.21 5 O 1532 1.98 5 H 9214 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None 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: 18152 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 5758 Classifications: {'peptide': 360} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 345} Chain: "B" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1088 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "G" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1088 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "E" Number of atoms: 5758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 5758 Classifications: {'peptide': 360} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 345} Chain: "D" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 2230 Classifications: {'peptide': 149} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 143} Chain: "C" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 2230 Classifications: {'peptide': 149} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 143} Time building chain proxies: 8.41, per 1000 atoms: 0.46 Number of scatterers: 18152 At special positions: 0 Unit cell: (86.528, 106.496, 102.336, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 O 1532 8.00 N 1472 7.00 C 5890 6.00 H 9214 1.00 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: 13.62 Conformation dependent library (CDL) restraints added in 1.4 seconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2092 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 6 sheets defined 63.3% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 removed outlier: 4.180A pdb=" N LYS A 11 " --> pdb=" O GLU A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 20 removed outlier: 6.926A pdb=" N GLY A 15 " --> pdb=" O TYR A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 54 Proline residue: A 42 - end of helix Processing helix chain 'A' and resid 76 through 91 Processing helix chain 'A' and resid 95 through 121 removed outlier: 3.687A pdb=" N TRP A 99 " --> pdb=" O ASN A 95 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL A 104 " --> pdb=" O CYS A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 153 Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 174 through 194 removed outlier: 3.673A pdb=" N LEU A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 201 through 220 removed outlier: 3.696A pdb=" N THR A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N PHE A 207 " --> pdb=" O MET A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 229 Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.675A pdb=" N GLY A 237 " --> pdb=" O ARG A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 255 Processing helix chain 'A' and resid 266 through 285 removed outlier: 3.824A pdb=" N SER A 270 " --> pdb=" O GLY A 266 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ALA A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 294 Processing helix chain 'A' and resid 294 through 314 Processing helix chain 'A' and resid 323 through 331 Processing helix chain 'A' and resid 334 through 360 removed outlier: 3.533A pdb=" N ARG A 360 " --> pdb=" O THR A 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 24 Proline residue: B 21 - end of helix Processing helix chain 'B' and resid 25 through 27 No H-bonds generated for 'chain 'B' and resid 25 through 27' Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 52 Processing helix chain 'G' and resid 5 through 25 removed outlier: 4.336A pdb=" N LEU G 10 " --> pdb=" O LEU G 6 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA G 11 " --> pdb=" O SER G 7 " (cutoff:3.500A) Proline residue: G 21 - end of helix Processing helix chain 'G' and resid 26 through 28 No H-bonds generated for 'chain 'G' and resid 26 through 28' Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 35 through 50 Processing helix chain 'E' and resid 2 through 10 Processing helix chain 'E' and resid 11 through 12 No H-bonds generated for 'chain 'E' and resid 11 through 12' Processing helix chain 'E' and resid 13 through 20 Processing helix chain 'E' and resid 21 through 54 Proline residue: E 42 - end of helix Processing helix chain 'E' and resid 75 through 91 removed outlier: 4.126A pdb=" N ILE E 79 " --> pdb=" O GLY E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 121 Processing helix chain 'E' and resid 129 through 152 Processing helix chain 'E' and resid 155 through 159 Processing helix chain 'E' and resid 174 through 194 removed outlier: 3.660A pdb=" N LEU E 178 " --> pdb=" O LEU E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 201 through 221 removed outlier: 3.623A pdb=" N ASN E 221 " --> pdb=" O TRP E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 229 Processing helix chain 'E' and resid 233 through 237 removed outlier: 3.766A pdb=" N GLY E 237 " --> pdb=" O ARG E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 258 removed outlier: 3.783A pdb=" N VAL E 242 " --> pdb=" O GLU E 238 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE E 256 " --> pdb=" O GLY E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 284 removed outlier: 3.937A pdb=" N SER E 270 " --> pdb=" O GLY E 266 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ALA E 272 " --> pdb=" O VAL E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 294 Processing helix chain 'E' and resid 294 through 314 Processing helix chain 'E' and resid 323 through 332 Processing helix chain 'E' and resid 334 through 360 Processing helix chain 'D' and resid 42 through 50 Processing helix chain 'D' and resid 63 through 67 Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'D' and resid 143 through 149 removed outlier: 3.866A pdb=" N LEU D 147 " --> pdb=" O THR D 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 49 Processing helix chain 'C' and resid 63 through 67 Processing helix chain 'C' and resid 72 through 74 No H-bonds generated for 'chain 'C' and resid 72 through 74' Processing helix chain 'C' and resid 82 through 84 No H-bonds generated for 'chain 'C' and resid 82 through 84' Processing helix chain 'C' and resid 143 through 149 Processing sheet with id=AA1, first strand: chain 'B' and resid 56 through 58 removed outlier: 6.460A pdb=" N VAL D 118 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N VAL D 112 " --> pdb=" O HIS D 116 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N HIS D 116 " --> pdb=" O VAL D 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 57 through 58 removed outlier: 6.951A pdb=" N VAL C 118 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N VAL C 112 " --> pdb=" O HIS C 116 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N HIS C 116 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 22 through 25 removed outlier: 6.736A pdb=" N LEU D 22 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N THR D 17 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP D 24 " --> pdb=" O VAL D 15 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU D 7 " --> pdb=" O HIS D 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 22 through 25 removed outlier: 6.736A pdb=" N LEU D 22 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N THR D 17 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP D 24 " --> pdb=" O VAL D 15 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA D 12 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N VAL D 136 " --> pdb=" O ALA D 12 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N GLN D 14 " --> pdb=" O VAL D 134 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N VAL D 134 " --> pdb=" O GLN D 14 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ARG D 16 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N PHE D 132 " --> pdb=" O ARG D 16 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 26 removed outlier: 6.587A pdb=" N LEU C 22 " --> pdb=" O THR C 17 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR C 17 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP C 24 " --> pdb=" O VAL C 15 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 22 through 26 removed outlier: 6.587A pdb=" N LEU C 22 " --> pdb=" O THR C 17 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR C 17 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP C 24 " --> pdb=" O VAL C 15 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA C 138 " --> pdb=" O SER C 10 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA C 12 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N VAL C 136 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N GLN C 14 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N VAL C 134 " --> pdb=" O GLN C 14 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ARG C 16 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N PHE C 132 " --> pdb=" O ARG C 16 " (cutoff:3.500A) 555 hydrogen bonds defined for protein. 1584 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.25 Time building geometry restraints manager: 14.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9210 1.03 - 1.23: 4 1.23 - 1.42: 3794 1.42 - 1.62: 5280 1.62 - 1.81: 84 Bond restraints: 18372 Sorted by residual: bond pdb=" CA VAL B 54 " pdb=" CB VAL B 54 " ideal model delta sigma weight residual 1.530 1.541 -0.010 1.05e-02 9.07e+03 9.62e-01 bond pdb=" N PRO A 204 " pdb=" CA PRO A 204 " ideal model delta sigma weight residual 1.468 1.481 -0.013 1.70e-02 3.46e+03 5.64e-01 bond pdb=" N GLY D 37 " pdb=" CA GLY D 37 " ideal model delta sigma weight residual 1.443 1.452 -0.009 1.38e-02 5.25e+03 4.17e-01 bond pdb=" N SER C 26 " pdb=" CA SER C 26 " ideal model delta sigma weight residual 1.463 1.457 0.007 1.08e-02 8.57e+03 3.87e-01 bond pdb=" CG PRO A 204 " pdb=" CD PRO A 204 " ideal model delta sigma weight residual 1.512 1.496 0.016 2.70e-02 1.37e+03 3.44e-01 ... (remaining 18367 not shown) Histogram of bond angle deviations from ideal: 100.49 - 107.19: 392 107.19 - 113.89: 22164 113.89 - 120.59: 6066 120.59 - 127.29: 4597 127.29 - 133.98: 125 Bond angle restraints: 33344 Sorted by residual: angle pdb=" N PRO A 204 " pdb=" CA PRO A 204 " pdb=" C PRO A 204 " ideal model delta sigma weight residual 112.10 118.97 -6.87 2.60e+00 1.48e-01 6.99e+00 angle pdb=" N TYR C 68 " pdb=" CA TYR C 68 " pdb=" CB TYR C 68 " ideal model delta sigma weight residual 113.65 110.24 3.41 1.47e+00 4.63e-01 5.39e+00 angle pdb=" N TYR D 68 " pdb=" CA TYR D 68 " pdb=" CB TYR D 68 " ideal model delta sigma weight residual 113.65 110.41 3.24 1.47e+00 4.63e-01 4.86e+00 angle pdb=" N ASP C 6 " pdb=" CA ASP C 6 " pdb=" CB ASP C 6 " ideal model delta sigma weight residual 114.27 110.94 3.33 1.64e+00 3.72e-01 4.12e+00 angle pdb=" C MET A 203 " pdb=" N PRO A 204 " pdb=" CA PRO A 204 " ideal model delta sigma weight residual 127.00 131.54 -4.54 2.40e+00 1.74e-01 3.58e+00 ... (remaining 33339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 7878 17.14 - 34.28: 446 34.28 - 51.42: 142 51.42 - 68.56: 88 68.56 - 85.69: 4 Dihedral angle restraints: 8558 sinusoidal: 4590 harmonic: 3968 Sorted by residual: dihedral pdb=" CA SER C 10 " pdb=" C SER C 10 " pdb=" N LEU C 11 " pdb=" CA LEU C 11 " ideal model delta harmonic sigma weight residual 180.00 -160.01 -19.99 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ASP C 24 " pdb=" CB ASP C 24 " pdb=" CG ASP C 24 " pdb=" OD1 ASP C 24 " ideal model delta sinusoidal sigma weight residual -30.00 -89.60 59.60 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA ASP E 267 " pdb=" CB ASP E 267 " pdb=" CG ASP E 267 " pdb=" OD1 ASP E 267 " ideal model delta sinusoidal sigma weight residual -30.00 -88.73 58.73 1 2.00e+01 2.50e-03 1.15e+01 ... (remaining 8555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 977 0.029 - 0.058: 283 0.058 - 0.086: 120 0.086 - 0.115: 65 0.115 - 0.144: 13 Chirality restraints: 1458 Sorted by residual: chirality pdb=" CA ILE B 64 " pdb=" N ILE B 64 " pdb=" C ILE B 64 " pdb=" CB ILE B 64 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA ILE G 28 " pdb=" N ILE G 28 " pdb=" C ILE G 28 " pdb=" CB ILE G 28 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA VAL E 162 " pdb=" N VAL E 162 " pdb=" C VAL E 162 " pdb=" CB VAL E 162 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 1455 not shown) Planarity restraints: 2634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 155 " -0.019 5.00e-02 4.00e+02 2.89e-02 1.33e+00 pdb=" N PRO A 156 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 156 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 156 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 105 " -0.018 5.00e-02 4.00e+02 2.68e-02 1.15e+00 pdb=" N PRO D 106 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO D 106 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 106 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 103 " -0.016 5.00e-02 4.00e+02 2.40e-02 9.25e-01 pdb=" N PRO D 104 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO D 104 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO D 104 " -0.013 5.00e-02 4.00e+02 ... (remaining 2631 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 932 2.21 - 2.81: 38664 2.81 - 3.40: 50958 3.40 - 4.00: 65217 4.00 - 4.60: 102059 Nonbonded interactions: 257830 Sorted by model distance: nonbonded pdb="HE22 GLN A 307 " pdb=" O PHE A 319 " model vdw 1.612 1.850 nonbonded pdb=" HG SER D 10 " pdb=" OD1 ASP D 33 " model vdw 1.621 1.850 nonbonded pdb=" HD1 HIS D 52 " pdb=" OD2 ASP D 56 " model vdw 1.623 1.850 nonbonded pdb=" O PHE A 253 " pdb=" H ASN A 257 " model vdw 1.627 1.850 nonbonded pdb=" O PRO G 35 " pdb=" HG SER G 38 " model vdw 1.635 1.850 ... (remaining 257825 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 'E' } ncs_group { reference = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 0.900 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: 0.250 Extract box with map and model: 4.320 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 56.430 Find NCS groups from input model: 0.510 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 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 : 0.002 0.022 9158 Z= 0.111 Angle : 0.437 6.874 12462 Z= 0.232 Chirality : 0.038 0.144 1458 Planarity : 0.003 0.029 1540 Dihedral : 11.408 85.694 3226 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.25), residues: 1136 helix: 2.17 (0.21), residues: 629 sheet: -0.15 (0.48), residues: 106 loop : 0.54 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 90 HIS 0.004 0.000 HIS D 38 PHE 0.011 0.001 PHE E 66 TYR 0.005 0.001 TYR A 328 ARG 0.004 0.000 ARG E 337 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ILE cc_start: 0.8411 (mt) cc_final: 0.8113 (mt) REVERT: A 63 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6821 (mt-10) REVERT: A 113 PHE cc_start: 0.7887 (t80) cc_final: 0.7684 (t80) REVERT: A 161 VAL cc_start: 0.8357 (t) cc_final: 0.7980 (m) REVERT: A 244 THR cc_start: 0.6857 (p) cc_final: 0.6557 (p) REVERT: A 300 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6406 (mm-30) REVERT: A 307 GLN cc_start: 0.7197 (tp40) cc_final: 0.6840 (tp40) REVERT: A 312 LYS cc_start: 0.8212 (tptt) cc_final: 0.8010 (tppt) REVERT: A 313 LEU cc_start: 0.8428 (mt) cc_final: 0.8189 (mm) REVERT: B 23 LEU cc_start: 0.8495 (tp) cc_final: 0.8232 (tp) REVERT: B 24 LEU cc_start: 0.8722 (mt) cc_final: 0.8299 (mt) REVERT: G 44 LEU cc_start: 0.8280 (tp) cc_final: 0.8062 (tp) REVERT: E 63 GLU cc_start: 0.6610 (mt-10) cc_final: 0.6388 (mt-10) REVERT: E 94 SER cc_start: 0.8315 (t) cc_final: 0.8085 (p) REVERT: E 102 LEU cc_start: 0.8297 (mt) cc_final: 0.8024 (mp) REVERT: E 113 PHE cc_start: 0.7823 (t80) cc_final: 0.7577 (t80) REVERT: E 131 ARG cc_start: 0.7464 (mtt-85) cc_final: 0.7224 (mtt-85) REVERT: E 174 LEU cc_start: 0.7912 (mt) cc_final: 0.7635 (mm) REVERT: E 176 TYR cc_start: 0.8541 (t80) cc_final: 0.8183 (t80) REVERT: E 227 TYR cc_start: 0.7947 (t80) cc_final: 0.7727 (t80) REVERT: E 283 LEU cc_start: 0.8370 (mt) cc_final: 0.8074 (mp) REVERT: E 293 MET cc_start: 0.7668 (mtt) cc_final: 0.7461 (mtp) REVERT: E 303 SER cc_start: 0.8029 (t) cc_final: 0.7797 (t) REVERT: E 348 MET cc_start: 0.8093 (mmm) cc_final: 0.7854 (mmm) REVERT: E 350 VAL cc_start: 0.7897 (t) cc_final: 0.7635 (p) REVERT: D 66 ASP cc_start: 0.6847 (t0) cc_final: 0.6559 (t0) REVERT: D 105 VAL cc_start: 0.8415 (p) cc_final: 0.8020 (m) outliers start: 0 outliers final: 0 residues processed: 391 average time/residue: 0.4708 time to fit residues: 250.2768 Evaluate side-chains 359 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 359 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 87 optimal weight: 20.0000 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 0.1980 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 HIS G 3 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9158 Z= 0.308 Angle : 0.559 6.408 12462 Z= 0.304 Chirality : 0.042 0.158 1458 Planarity : 0.004 0.044 1540 Dihedral : 4.377 20.169 1230 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.68 % Allowed : 9.96 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.25), residues: 1136 helix: 1.69 (0.20), residues: 649 sheet: -0.35 (0.54), residues: 91 loop : 0.25 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 217 HIS 0.004 0.001 HIS A 325 PHE 0.021 0.001 PHE A 264 TYR 0.012 0.001 TYR C 71 ARG 0.003 0.000 ARG E 337 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 376 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7058 (mt-10) REVERT: A 113 PHE cc_start: 0.8022 (t80) cc_final: 0.7741 (t80) REVERT: A 140 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8212 (tp) REVERT: A 161 VAL cc_start: 0.8341 (t) cc_final: 0.7923 (m) REVERT: A 244 THR cc_start: 0.7200 (p) cc_final: 0.6918 (p) REVERT: A 300 GLU cc_start: 0.6896 (mm-30) cc_final: 0.6456 (mm-30) REVERT: A 307 GLN cc_start: 0.7454 (tp40) cc_final: 0.7039 (tp40) REVERT: A 312 LYS cc_start: 0.8318 (tptt) cc_final: 0.8049 (tppt) REVERT: A 313 LEU cc_start: 0.8521 (mt) cc_final: 0.8281 (mm) REVERT: B 23 LEU cc_start: 0.8550 (tp) cc_final: 0.8307 (tp) REVERT: B 24 LEU cc_start: 0.8810 (mt) cc_final: 0.8480 (mt) REVERT: B 40 LYS cc_start: 0.7744 (mttm) cc_final: 0.7488 (mtmm) REVERT: G 44 LEU cc_start: 0.8387 (tp) cc_final: 0.8124 (tp) REVERT: E 116 ASP cc_start: 0.7060 (m-30) cc_final: 0.6835 (m-30) REVERT: E 131 ARG cc_start: 0.7543 (mtt-85) cc_final: 0.7303 (mtt-85) REVERT: E 222 MET cc_start: 0.7114 (mmm) cc_final: 0.6875 (mmt) REVERT: E 227 TYR cc_start: 0.8012 (t80) cc_final: 0.7682 (t80) REVERT: E 232 TYR cc_start: 0.8161 (t80) cc_final: 0.7928 (t80) REVERT: E 253 PHE cc_start: 0.7776 (t80) cc_final: 0.7462 (t80) REVERT: E 279 ILE cc_start: 0.8331 (tp) cc_final: 0.8107 (tp) REVERT: E 283 LEU cc_start: 0.8423 (mt) cc_final: 0.8173 (mp) REVERT: E 348 MET cc_start: 0.8165 (mmm) cc_final: 0.7799 (mmm) REVERT: E 350 VAL cc_start: 0.7816 (t) cc_final: 0.7605 (p) REVERT: D 66 ASP cc_start: 0.7062 (t0) cc_final: 0.6692 (t0) REVERT: D 95 ARG cc_start: 0.5907 (mtt180) cc_final: 0.5127 (mtt180) REVERT: D 99 GLU cc_start: 0.6428 (mp0) cc_final: 0.5907 (mp0) REVERT: D 108 GLU cc_start: 0.6549 (tt0) cc_final: 0.6123 (tt0) REVERT: C 112 VAL cc_start: 0.8583 (p) cc_final: 0.8356 (t) REVERT: C 128 GLN cc_start: 0.6255 (mt0) cc_final: 0.6002 (mt0) outliers start: 16 outliers final: 11 residues processed: 378 average time/residue: 0.4978 time to fit residues: 250.6914 Evaluate side-chains 376 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 364 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain C residue 116 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 84 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 3 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9158 Z= 0.353 Angle : 0.584 5.550 12462 Z= 0.319 Chirality : 0.042 0.145 1458 Planarity : 0.004 0.049 1540 Dihedral : 4.716 20.851 1230 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.41 % Allowed : 12.26 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.25), residues: 1136 helix: 1.22 (0.20), residues: 650 sheet: -0.42 (0.55), residues: 96 loop : -0.18 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 217 HIS 0.005 0.001 HIS E 235 PHE 0.024 0.002 PHE C 84 TYR 0.014 0.002 TYR A 149 ARG 0.004 0.000 ARG A 285 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 397 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.7331 (ttm) cc_final: 0.7079 (ttm) REVERT: A 63 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7178 (mt-10) REVERT: A 113 PHE cc_start: 0.8117 (t80) cc_final: 0.7812 (t80) REVERT: A 140 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8291 (tp) REVERT: A 161 VAL cc_start: 0.8350 (t) cc_final: 0.7911 (m) REVERT: A 300 GLU cc_start: 0.6806 (mm-30) cc_final: 0.6350 (mm-30) REVERT: A 307 GLN cc_start: 0.7361 (tp40) cc_final: 0.7044 (tp40) REVERT: A 312 LYS cc_start: 0.8336 (tptt) cc_final: 0.8076 (tppt) REVERT: A 313 LEU cc_start: 0.8532 (mt) cc_final: 0.7806 (mt) REVERT: B 23 LEU cc_start: 0.8554 (tp) cc_final: 0.8317 (tp) REVERT: B 24 LEU cc_start: 0.8841 (mt) cc_final: 0.8530 (mt) REVERT: B 31 THR cc_start: 0.8377 (t) cc_final: 0.8115 (m) REVERT: B 40 LYS cc_start: 0.8028 (mttm) cc_final: 0.7699 (mtmm) REVERT: G 44 LEU cc_start: 0.8398 (tp) cc_final: 0.8198 (tt) REVERT: G 53 SER cc_start: 0.8047 (OUTLIER) cc_final: 0.7603 (p) REVERT: E 116 ASP cc_start: 0.7058 (m-30) cc_final: 0.6801 (m-30) REVERT: E 131 ARG cc_start: 0.7548 (mtt-85) cc_final: 0.7295 (mtt-85) REVERT: E 162 VAL cc_start: 0.8519 (t) cc_final: 0.8090 (m) REVERT: E 174 LEU cc_start: 0.8071 (mp) cc_final: 0.7756 (mm) REVERT: E 227 TYR cc_start: 0.7999 (t80) cc_final: 0.7662 (t80) REVERT: E 253 PHE cc_start: 0.7924 (t80) cc_final: 0.7448 (t80) REVERT: E 283 LEU cc_start: 0.8439 (mt) cc_final: 0.8233 (mp) REVERT: E 348 MET cc_start: 0.8159 (mmm) cc_final: 0.7825 (mmm) REVERT: D 66 ASP cc_start: 0.7252 (t0) cc_final: 0.6891 (t0) REVERT: D 73 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7280 (mm-30) REVERT: D 95 ARG cc_start: 0.5910 (mtt180) cc_final: 0.5354 (mtt180) REVERT: D 99 GLU cc_start: 0.6444 (mp0) cc_final: 0.5968 (mp0) REVERT: D 108 GLU cc_start: 0.6723 (tt0) cc_final: 0.6239 (tt0) REVERT: C 112 VAL cc_start: 0.8880 (p) cc_final: 0.8617 (t) REVERT: C 128 GLN cc_start: 0.6716 (mt0) cc_final: 0.6433 (mt0) outliers start: 23 outliers final: 13 residues processed: 403 average time/residue: 0.4914 time to fit residues: 266.5984 Evaluate side-chains 405 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 389 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 50 MET Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain D residue 14 GLN Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain C residue 116 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 9158 Z= 0.512 Angle : 0.647 5.735 12462 Z= 0.364 Chirality : 0.045 0.166 1458 Planarity : 0.005 0.061 1540 Dihedral : 5.043 22.878 1230 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.14 % Allowed : 14.57 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.24), residues: 1136 helix: 0.68 (0.20), residues: 646 sheet: -0.62 (0.55), residues: 90 loop : -0.51 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 217 HIS 0.007 0.001 HIS E 235 PHE 0.023 0.002 PHE A 264 TYR 0.016 0.002 TYR E 232 ARG 0.007 0.001 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 401 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 TYR cc_start: 0.7911 (t80) cc_final: 0.7681 (t80) REVERT: A 16 PHE cc_start: 0.8202 (m-80) cc_final: 0.7734 (m-80) REVERT: A 44 MET cc_start: 0.7074 (ttp) cc_final: 0.6760 (ttp) REVERT: A 63 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7221 (mt-10) REVERT: A 113 PHE cc_start: 0.8154 (t80) cc_final: 0.7827 (t80) REVERT: A 140 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8289 (tp) REVERT: A 161 VAL cc_start: 0.8450 (t) cc_final: 0.7993 (m) REVERT: A 162 VAL cc_start: 0.8548 (t) cc_final: 0.8121 (m) REVERT: A 300 GLU cc_start: 0.6738 (mm-30) cc_final: 0.6294 (mm-30) REVERT: A 312 LYS cc_start: 0.8365 (tptt) cc_final: 0.8070 (tppt) REVERT: B 23 LEU cc_start: 0.8543 (tp) cc_final: 0.8331 (tp) REVERT: B 24 LEU cc_start: 0.8804 (mt) cc_final: 0.8514 (mt) REVERT: B 31 THR cc_start: 0.8343 (t) cc_final: 0.8115 (m) REVERT: B 40 LYS cc_start: 0.8172 (mttm) cc_final: 0.7769 (mtmm) REVERT: G 13 LEU cc_start: 0.8234 (mt) cc_final: 0.7992 (mm) REVERT: G 53 SER cc_start: 0.8118 (OUTLIER) cc_final: 0.7692 (p) REVERT: E 25 ARG cc_start: 0.8154 (mtm110) cc_final: 0.7931 (mtm110) REVERT: E 44 MET cc_start: 0.7605 (tmm) cc_final: 0.7137 (tmm) REVERT: E 116 ASP cc_start: 0.7098 (m-30) cc_final: 0.6797 (m-30) REVERT: E 131 ARG cc_start: 0.7590 (mtt-85) cc_final: 0.7359 (mtt-85) REVERT: E 139 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8189 (m) REVERT: E 162 VAL cc_start: 0.8609 (t) cc_final: 0.8375 (m) REVERT: E 174 LEU cc_start: 0.8160 (mp) cc_final: 0.7817 (mm) REVERT: E 176 TYR cc_start: 0.8635 (t80) cc_final: 0.8428 (t80) REVERT: E 227 TYR cc_start: 0.8000 (t80) cc_final: 0.7680 (t80) REVERT: E 253 PHE cc_start: 0.8047 (t80) cc_final: 0.7489 (t80) REVERT: E 283 LEU cc_start: 0.8418 (mt) cc_final: 0.8176 (mp) REVERT: E 320 ARG cc_start: 0.8404 (mmt90) cc_final: 0.8196 (mtt180) REVERT: E 329 GLU cc_start: 0.7538 (tt0) cc_final: 0.7275 (tt0) REVERT: E 348 MET cc_start: 0.8236 (mmm) cc_final: 0.7905 (mmm) REVERT: D 1 MET cc_start: 0.0999 (ptm) cc_final: -0.4215 (mmm) REVERT: D 73 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7259 (mm-30) REVERT: D 77 GLN cc_start: 0.7691 (mm-40) cc_final: 0.7118 (mm-40) REVERT: D 78 ARG cc_start: 0.7608 (mtp85) cc_final: 0.7408 (mtp85) REVERT: D 95 ARG cc_start: 0.6020 (mtt180) cc_final: 0.5720 (mtt180) REVERT: D 99 GLU cc_start: 0.6533 (mp0) cc_final: 0.6023 (mp0) REVERT: D 108 GLU cc_start: 0.6817 (tt0) cc_final: 0.6451 (tt0) REVERT: C 112 VAL cc_start: 0.8993 (p) cc_final: 0.8723 (t) REVERT: C 128 GLN cc_start: 0.7074 (mt0) cc_final: 0.6591 (mt0) REVERT: C 149 HIS cc_start: 0.6639 (m-70) cc_final: 0.6125 (m-70) outliers start: 30 outliers final: 20 residues processed: 407 average time/residue: 0.5210 time to fit residues: 285.5914 Evaluate side-chains 421 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 397 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 50 MET Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain C residue 116 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 chunk 92 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 97 optimal weight: 0.2980 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN A 326 HIS B 3 HIS E 189 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9158 Z= 0.176 Angle : 0.519 5.956 12462 Z= 0.273 Chirality : 0.039 0.141 1458 Planarity : 0.004 0.052 1540 Dihedral : 4.492 21.594 1230 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.52 % Allowed : 17.40 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.25), residues: 1136 helix: 1.32 (0.20), residues: 639 sheet: -0.44 (0.52), residues: 104 loop : -0.16 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 99 HIS 0.003 0.001 HIS D 116 PHE 0.016 0.001 PHE E 182 TYR 0.013 0.001 TYR A 149 ARG 0.007 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 385 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7055 (ttp) cc_final: 0.6736 (ttp) REVERT: A 48 LEU cc_start: 0.8506 (mt) cc_final: 0.8259 (mp) REVERT: A 63 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7110 (mt-10) REVERT: A 113 PHE cc_start: 0.8079 (t80) cc_final: 0.7768 (t80) REVERT: A 140 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8264 (tp) REVERT: A 161 VAL cc_start: 0.8387 (t) cc_final: 0.7928 (m) REVERT: A 300 GLU cc_start: 0.6735 (mm-30) cc_final: 0.6261 (mm-30) REVERT: A 312 LYS cc_start: 0.8304 (tptt) cc_final: 0.7991 (tppt) REVERT: B 24 LEU cc_start: 0.8785 (mt) cc_final: 0.8475 (mt) REVERT: B 40 LYS cc_start: 0.8046 (mttm) cc_final: 0.7653 (mtmm) REVERT: G 53 SER cc_start: 0.8000 (OUTLIER) cc_final: 0.7541 (p) REVERT: E 44 MET cc_start: 0.7588 (tmm) cc_final: 0.7075 (tmm) REVERT: E 81 THR cc_start: 0.8563 (t) cc_final: 0.8157 (p) REVERT: E 102 LEU cc_start: 0.8542 (mp) cc_final: 0.8301 (mm) REVERT: E 116 ASP cc_start: 0.7080 (m-30) cc_final: 0.6762 (m-30) REVERT: E 131 ARG cc_start: 0.7524 (mtt-85) cc_final: 0.7233 (mtt-85) REVERT: E 162 VAL cc_start: 0.8507 (t) cc_final: 0.8251 (m) REVERT: E 174 LEU cc_start: 0.7927 (mp) cc_final: 0.7634 (mm) REVERT: E 176 TYR cc_start: 0.8600 (t80) cc_final: 0.8399 (t80) REVERT: E 227 TYR cc_start: 0.7950 (t80) cc_final: 0.7643 (t80) REVERT: E 253 PHE cc_start: 0.7946 (t80) cc_final: 0.7424 (t80) REVERT: E 283 LEU cc_start: 0.8453 (mt) cc_final: 0.8187 (mp) REVERT: D 1 MET cc_start: 0.1246 (ptm) cc_final: -0.4059 (mmm) REVERT: D 73 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7202 (mm-30) REVERT: D 77 GLN cc_start: 0.7703 (mm-40) cc_final: 0.7136 (mm-40) REVERT: D 95 ARG cc_start: 0.6025 (mtt180) cc_final: 0.5814 (mtt180) REVERT: D 99 GLU cc_start: 0.6498 (mp0) cc_final: 0.5933 (mp0) REVERT: D 108 GLU cc_start: 0.6710 (tt0) cc_final: 0.6397 (tt0) REVERT: C 112 VAL cc_start: 0.8939 (p) cc_final: 0.8664 (t) REVERT: C 128 GLN cc_start: 0.6924 (mt0) cc_final: 0.6466 (mt0) REVERT: C 149 HIS cc_start: 0.6555 (m-70) cc_final: 0.5992 (m-70) outliers start: 24 outliers final: 19 residues processed: 388 average time/residue: 0.5058 time to fit residues: 261.5250 Evaluate side-chains 406 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 385 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain C residue 116 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 0.1980 chunk 26 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 104 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9158 Z= 0.184 Angle : 0.513 5.948 12462 Z= 0.270 Chirality : 0.039 0.138 1458 Planarity : 0.004 0.055 1540 Dihedral : 4.338 21.316 1230 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.62 % Allowed : 17.19 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.25), residues: 1136 helix: 1.37 (0.20), residues: 645 sheet: -0.50 (0.53), residues: 103 loop : -0.15 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 99 HIS 0.003 0.001 HIS A 325 PHE 0.015 0.001 PHE E 182 TYR 0.013 0.001 TYR E 232 ARG 0.005 0.000 ARG G 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 393 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7055 (ttp) cc_final: 0.6728 (ttp) REVERT: A 48 LEU cc_start: 0.8517 (mt) cc_final: 0.8266 (mp) REVERT: A 63 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7097 (mt-10) REVERT: A 113 PHE cc_start: 0.8073 (t80) cc_final: 0.7798 (t80) REVERT: A 140 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8252 (tp) REVERT: A 161 VAL cc_start: 0.8373 (t) cc_final: 0.7938 (m) REVERT: A 192 ASN cc_start: 0.8406 (t0) cc_final: 0.8204 (t0) REVERT: A 300 GLU cc_start: 0.6736 (mm-30) cc_final: 0.6284 (mm-30) REVERT: A 312 LYS cc_start: 0.8301 (tptt) cc_final: 0.7969 (tppt) REVERT: B 24 LEU cc_start: 0.8759 (mt) cc_final: 0.8440 (mt) REVERT: B 40 LYS cc_start: 0.8063 (mttm) cc_final: 0.7652 (mtmm) REVERT: G 53 SER cc_start: 0.7945 (OUTLIER) cc_final: 0.7527 (p) REVERT: E 81 THR cc_start: 0.8549 (t) cc_final: 0.8126 (p) REVERT: E 116 ASP cc_start: 0.7132 (m-30) cc_final: 0.6822 (m-30) REVERT: E 131 ARG cc_start: 0.7514 (mtt-85) cc_final: 0.7246 (mtt-85) REVERT: E 162 VAL cc_start: 0.8500 (t) cc_final: 0.8200 (m) REVERT: E 174 LEU cc_start: 0.7903 (mp) cc_final: 0.7617 (mm) REVERT: E 227 TYR cc_start: 0.7947 (t80) cc_final: 0.7642 (t80) REVERT: E 253 PHE cc_start: 0.7960 (t80) cc_final: 0.7424 (t80) REVERT: E 283 LEU cc_start: 0.8442 (mt) cc_final: 0.8182 (mp) REVERT: E 314 ARG cc_start: 0.6663 (mtm-85) cc_final: 0.6385 (mtm-85) REVERT: D 1 MET cc_start: 0.1327 (ptm) cc_final: -0.3988 (mmm) REVERT: D 73 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7239 (mm-30) REVERT: D 77 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7105 (mm-40) REVERT: D 95 ARG cc_start: 0.6080 (mtt180) cc_final: 0.5872 (mtt180) REVERT: D 108 GLU cc_start: 0.6738 (tt0) cc_final: 0.6442 (tt0) REVERT: C 112 VAL cc_start: 0.8929 (p) cc_final: 0.8656 (t) REVERT: C 128 GLN cc_start: 0.6934 (mt0) cc_final: 0.6469 (mt0) REVERT: C 149 HIS cc_start: 0.6539 (m-70) cc_final: 0.5980 (m-70) outliers start: 25 outliers final: 22 residues processed: 397 average time/residue: 0.5135 time to fit residues: 271.2930 Evaluate side-chains 412 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 388 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain E residue 117 TYR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain D residue 14 GLN Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 116 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9158 Z= 0.329 Angle : 0.562 5.771 12462 Z= 0.305 Chirality : 0.041 0.141 1458 Planarity : 0.004 0.055 1540 Dihedral : 4.538 21.489 1230 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.94 % Allowed : 17.19 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.25), residues: 1136 helix: 1.23 (0.20), residues: 638 sheet: -0.63 (0.50), residues: 111 loop : -0.27 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 217 HIS 0.004 0.001 HIS E 235 PHE 0.020 0.001 PHE A 264 TYR 0.015 0.001 TYR E 232 ARG 0.004 0.000 ARG G 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 401 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.8236 (m-80) cc_final: 0.7937 (m-80) REVERT: A 40 MET cc_start: 0.7510 (ttm) cc_final: 0.7308 (ttm) REVERT: A 63 GLU cc_start: 0.7409 (mt-10) cc_final: 0.7151 (mt-10) REVERT: A 113 PHE cc_start: 0.8129 (t80) cc_final: 0.7829 (t80) REVERT: A 140 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8261 (tp) REVERT: A 161 VAL cc_start: 0.8438 (t) cc_final: 0.7978 (m) REVERT: A 300 GLU cc_start: 0.6720 (mm-30) cc_final: 0.6259 (mm-30) REVERT: A 312 LYS cc_start: 0.8351 (tptt) cc_final: 0.8026 (tppt) REVERT: B 23 LEU cc_start: 0.8618 (tp) cc_final: 0.8337 (tp) REVERT: B 24 LEU cc_start: 0.8790 (mt) cc_final: 0.8455 (mt) REVERT: B 40 LYS cc_start: 0.8126 (mttm) cc_final: 0.7711 (mtmm) REVERT: G 53 SER cc_start: 0.8023 (OUTLIER) cc_final: 0.7638 (p) REVERT: E 50 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7940 (ttmm) REVERT: E 81 THR cc_start: 0.8604 (t) cc_final: 0.8242 (p) REVERT: E 116 ASP cc_start: 0.7118 (m-30) cc_final: 0.6818 (m-30) REVERT: E 131 ARG cc_start: 0.7558 (mtt-85) cc_final: 0.7281 (mtt-85) REVERT: E 162 VAL cc_start: 0.8548 (t) cc_final: 0.8255 (m) REVERT: E 174 LEU cc_start: 0.8015 (mp) cc_final: 0.7699 (mm) REVERT: E 176 TYR cc_start: 0.8603 (t80) cc_final: 0.8330 (t80) REVERT: E 227 TYR cc_start: 0.7942 (t80) cc_final: 0.7675 (t80) REVERT: E 253 PHE cc_start: 0.8049 (t80) cc_final: 0.7429 (t80) REVERT: E 283 LEU cc_start: 0.8431 (mt) cc_final: 0.8179 (mp) REVERT: E 358 LYS cc_start: 0.8072 (tptp) cc_final: 0.7818 (tppt) REVERT: D 1 MET cc_start: 0.1605 (ptm) cc_final: -0.3769 (mmm) REVERT: D 73 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7278 (mm-30) REVERT: D 108 GLU cc_start: 0.6847 (tt0) cc_final: 0.6575 (tt0) REVERT: C 78 ARG cc_start: 0.7397 (mtt180) cc_final: 0.7139 (mtt180) REVERT: C 112 VAL cc_start: 0.8965 (p) cc_final: 0.8689 (t) REVERT: C 128 GLN cc_start: 0.7125 (mt0) cc_final: 0.6629 (mt0) REVERT: C 149 HIS cc_start: 0.6561 (m-70) cc_final: 0.5986 (m-70) outliers start: 28 outliers final: 21 residues processed: 406 average time/residue: 0.5167 time to fit residues: 279.1690 Evaluate side-chains 422 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 398 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain D residue 14 GLN Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 116 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 103 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.4768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9158 Z= 0.231 Angle : 0.529 5.838 12462 Z= 0.282 Chirality : 0.040 0.145 1458 Planarity : 0.004 0.053 1540 Dihedral : 4.398 21.645 1230 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.41 % Allowed : 18.45 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.25), residues: 1136 helix: 1.32 (0.20), residues: 639 sheet: -0.65 (0.50), residues: 111 loop : -0.20 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 136 HIS 0.003 0.001 HIS E 235 PHE 0.019 0.001 PHE E 182 TYR 0.017 0.001 TYR E 232 ARG 0.003 0.000 ARG G 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 397 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.8229 (m-80) cc_final: 0.7950 (m-80) REVERT: A 40 MET cc_start: 0.7499 (ttm) cc_final: 0.7270 (ttm) REVERT: A 48 LEU cc_start: 0.8541 (mt) cc_final: 0.8274 (mp) REVERT: A 63 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7120 (mt-10) REVERT: A 113 PHE cc_start: 0.8099 (t80) cc_final: 0.7793 (t80) REVERT: A 140 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8228 (tp) REVERT: A 161 VAL cc_start: 0.8413 (t) cc_final: 0.7956 (m) REVERT: A 300 GLU cc_start: 0.6690 (mm-30) cc_final: 0.6259 (mm-30) REVERT: A 312 LYS cc_start: 0.8335 (tptt) cc_final: 0.8008 (tppt) REVERT: B 24 LEU cc_start: 0.8761 (mt) cc_final: 0.8433 (mt) REVERT: B 40 LYS cc_start: 0.8101 (mttm) cc_final: 0.7682 (mtmm) REVERT: E 81 THR cc_start: 0.8574 (t) cc_final: 0.8146 (p) REVERT: E 116 ASP cc_start: 0.7137 (m-30) cc_final: 0.6841 (m-30) REVERT: E 131 ARG cc_start: 0.7542 (mtt-85) cc_final: 0.7259 (mtt-85) REVERT: E 162 VAL cc_start: 0.8521 (t) cc_final: 0.8220 (m) REVERT: E 174 LEU cc_start: 0.7957 (mp) cc_final: 0.7678 (mm) REVERT: E 176 TYR cc_start: 0.8583 (t80) cc_final: 0.8295 (t80) REVERT: E 227 TYR cc_start: 0.7932 (t80) cc_final: 0.7664 (t80) REVERT: E 253 PHE cc_start: 0.8035 (t80) cc_final: 0.7470 (t80) REVERT: E 283 LEU cc_start: 0.8444 (mt) cc_final: 0.8170 (mp) REVERT: E 314 ARG cc_start: 0.6739 (mtm-85) cc_final: 0.6410 (mtm-85) REVERT: E 358 LYS cc_start: 0.7992 (tptp) cc_final: 0.7740 (tppt) REVERT: D 1 MET cc_start: 0.1668 (ptm) cc_final: -0.3748 (mmm) REVERT: D 73 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7277 (mm-30) REVERT: D 99 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.6436 (tp30) REVERT: D 108 GLU cc_start: 0.7002 (tt0) cc_final: 0.6573 (tt0) REVERT: C 94 MET cc_start: 0.6832 (ttm) cc_final: 0.6571 (mtp) REVERT: C 112 VAL cc_start: 0.8959 (p) cc_final: 0.8691 (t) REVERT: C 128 GLN cc_start: 0.7127 (mt0) cc_final: 0.6628 (mt0) REVERT: C 149 HIS cc_start: 0.6553 (m-70) cc_final: 0.5988 (m-70) outliers start: 23 outliers final: 19 residues processed: 400 average time/residue: 0.4992 time to fit residues: 266.0544 Evaluate side-chains 416 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 395 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 117 TYR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain C residue 116 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 chunk 103 optimal weight: 20.0000 chunk 60 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 0.0470 chunk 95 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 0.0870 overall best weight: 1.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9158 Z= 0.286 Angle : 0.546 5.819 12462 Z= 0.294 Chirality : 0.040 0.138 1458 Planarity : 0.004 0.053 1540 Dihedral : 4.440 21.557 1230 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.83 % Allowed : 18.66 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.25), residues: 1136 helix: 1.26 (0.20), residues: 639 sheet: -0.67 (0.50), residues: 111 loop : -0.26 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 39 HIS 0.003 0.001 HIS C 123 PHE 0.019 0.001 PHE E 182 TYR 0.018 0.001 TYR E 232 ARG 0.003 0.000 ARG G 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 398 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.8220 (m-80) cc_final: 0.7998 (m-80) REVERT: A 44 MET cc_start: 0.7134 (ttp) cc_final: 0.6780 (ttp) REVERT: A 63 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7136 (mt-10) REVERT: A 140 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8289 (tp) REVERT: A 161 VAL cc_start: 0.8433 (t) cc_final: 0.7980 (m) REVERT: A 300 GLU cc_start: 0.6697 (mm-30) cc_final: 0.6269 (mm-30) REVERT: A 312 LYS cc_start: 0.8327 (tptt) cc_final: 0.8020 (tppt) REVERT: B 24 LEU cc_start: 0.8781 (mt) cc_final: 0.8447 (mt) REVERT: G 44 LEU cc_start: 0.8349 (tp) cc_final: 0.8137 (tt) REVERT: E 50 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7920 (ttmm) REVERT: E 69 ARG cc_start: 0.7237 (ttt-90) cc_final: 0.7020 (ttt-90) REVERT: E 116 ASP cc_start: 0.7113 (m-30) cc_final: 0.6830 (m-30) REVERT: E 131 ARG cc_start: 0.7558 (mtt-85) cc_final: 0.7267 (mtt-85) REVERT: E 162 VAL cc_start: 0.8539 (t) cc_final: 0.8193 (m) REVERT: E 174 LEU cc_start: 0.7982 (mp) cc_final: 0.7680 (mm) REVERT: E 176 TYR cc_start: 0.8602 (t80) cc_final: 0.8289 (t80) REVERT: E 227 TYR cc_start: 0.7936 (t80) cc_final: 0.7669 (t80) REVERT: E 283 LEU cc_start: 0.8442 (mt) cc_final: 0.8181 (mp) REVERT: E 314 ARG cc_start: 0.6747 (mtm-85) cc_final: 0.6425 (mtm-85) REVERT: E 358 LYS cc_start: 0.8015 (tptp) cc_final: 0.7788 (tppt) REVERT: D 1 MET cc_start: 0.1760 (ptm) cc_final: -0.3704 (mmm) REVERT: D 73 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7248 (mm-30) REVERT: D 99 GLU cc_start: 0.6872 (tp30) cc_final: 0.6537 (tp30) REVERT: D 108 GLU cc_start: 0.7028 (tt0) cc_final: 0.6594 (tt0) REVERT: C 78 ARG cc_start: 0.7405 (mtt180) cc_final: 0.7113 (mtt180) REVERT: C 94 MET cc_start: 0.6837 (ttm) cc_final: 0.6581 (mtp) REVERT: C 112 VAL cc_start: 0.8979 (p) cc_final: 0.8707 (t) REVERT: C 128 GLN cc_start: 0.7157 (mt0) cc_final: 0.6665 (mt0) REVERT: C 149 HIS cc_start: 0.6557 (m-70) cc_final: 0.5991 (m-70) outliers start: 27 outliers final: 21 residues processed: 404 average time/residue: 0.5098 time to fit residues: 273.6245 Evaluate side-chains 418 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 395 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 189 ASN Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain D residue 14 GLN Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 116 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.0370 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 88 optimal weight: 20.0000 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9158 Z= 0.235 Angle : 0.533 5.833 12462 Z= 0.283 Chirality : 0.040 0.167 1458 Planarity : 0.004 0.052 1540 Dihedral : 4.371 21.520 1230 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.20 % Allowed : 19.18 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.25), residues: 1136 helix: 1.33 (0.20), residues: 639 sheet: -0.48 (0.53), residues: 103 loop : -0.22 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 136 HIS 0.003 0.001 HIS E 235 PHE 0.020 0.001 PHE E 182 TYR 0.018 0.001 TYR E 232 ARG 0.003 0.000 ARG A 317 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 395 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.7512 (ttm) cc_final: 0.7295 (ttm) REVERT: A 44 MET cc_start: 0.7130 (ttp) cc_final: 0.6765 (ttp) REVERT: A 63 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7141 (mt-10) REVERT: A 99 TRP cc_start: 0.7113 (m-10) cc_final: 0.6842 (m100) REVERT: A 140 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8251 (tp) REVERT: A 161 VAL cc_start: 0.8417 (t) cc_final: 0.7945 (m) REVERT: A 300 GLU cc_start: 0.6694 (mm-30) cc_final: 0.6266 (mm-30) REVERT: A 312 LYS cc_start: 0.8301 (tptt) cc_final: 0.7993 (tppt) REVERT: B 24 LEU cc_start: 0.8739 (mt) cc_final: 0.8407 (mt) REVERT: G 44 LEU cc_start: 0.8371 (tp) cc_final: 0.8163 (tt) REVERT: G 53 SER cc_start: 0.7910 (OUTLIER) cc_final: 0.7551 (p) REVERT: E 7 GLU cc_start: 0.7284 (mt-10) cc_final: 0.7008 (mt-10) REVERT: E 50 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7892 (ttmm) REVERT: E 69 ARG cc_start: 0.7188 (ttt-90) cc_final: 0.6970 (ttt-90) REVERT: E 81 THR cc_start: 0.8574 (t) cc_final: 0.8144 (p) REVERT: E 116 ASP cc_start: 0.7112 (m-30) cc_final: 0.6828 (m-30) REVERT: E 131 ARG cc_start: 0.7544 (mtt-85) cc_final: 0.7261 (mtt-85) REVERT: E 162 VAL cc_start: 0.8519 (t) cc_final: 0.8168 (m) REVERT: E 174 LEU cc_start: 0.7953 (mp) cc_final: 0.7673 (mm) REVERT: E 176 TYR cc_start: 0.8596 (t80) cc_final: 0.8275 (t80) REVERT: E 227 TYR cc_start: 0.7929 (t80) cc_final: 0.7658 (t80) REVERT: E 283 LEU cc_start: 0.8451 (mt) cc_final: 0.8183 (mp) REVERT: E 314 ARG cc_start: 0.6735 (mtm-85) cc_final: 0.6407 (mtm-85) REVERT: E 358 LYS cc_start: 0.7984 (tptp) cc_final: 0.7759 (tppt) REVERT: D 1 MET cc_start: 0.1737 (ptm) cc_final: -0.3673 (mmm) REVERT: D 73 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7210 (mm-30) REVERT: D 99 GLU cc_start: 0.6819 (tp30) cc_final: 0.6506 (tp30) REVERT: D 108 GLU cc_start: 0.7038 (tt0) cc_final: 0.6608 (tt0) REVERT: C 16 ARG cc_start: 0.7051 (mtt180) cc_final: 0.6805 (mtt180) REVERT: C 78 ARG cc_start: 0.7427 (mtt180) cc_final: 0.7127 (mtt180) REVERT: C 112 VAL cc_start: 0.8981 (p) cc_final: 0.8710 (t) REVERT: C 128 GLN cc_start: 0.7147 (mt0) cc_final: 0.6684 (mt0) REVERT: C 149 HIS cc_start: 0.6575 (m-70) cc_final: 0.5986 (m-70) outliers start: 21 outliers final: 18 residues processed: 399 average time/residue: 0.5151 time to fit residues: 273.7831 Evaluate side-chains 417 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 396 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 117 TYR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 189 ASN Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain D residue 14 GLN Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain C residue 116 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 37 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 0.0570 overall best weight: 1.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.140438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.112994 restraints weight = 40245.868| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.29 r_work: 0.3293 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9158 Z= 0.275 Angle : 0.545 5.851 12462 Z= 0.292 Chirality : 0.040 0.137 1458 Planarity : 0.004 0.053 1540 Dihedral : 4.415 21.464 1230 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.83 % Allowed : 18.66 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.25), residues: 1136 helix: 1.29 (0.20), residues: 639 sheet: -0.56 (0.54), residues: 102 loop : -0.21 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 136 HIS 0.003 0.001 HIS E 327 PHE 0.020 0.001 PHE E 182 TYR 0.018 0.001 TYR E 232 ARG 0.003 0.000 ARG G 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5807.80 seconds wall clock time: 102 minutes 0.21 seconds (6120.21 seconds total)