Starting phenix.real_space_refine on Thu Mar 14 21:39:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4j_31713/03_2024/7v4j_31713.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4j_31713/03_2024/7v4j_31713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4j_31713/03_2024/7v4j_31713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4j_31713/03_2024/7v4j_31713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4j_31713/03_2024/7v4j_31713.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4j_31713/03_2024/7v4j_31713.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.014 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: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 6265 2.51 5 N 1625 2.21 5 O 1900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 170": "OD1" <-> "OD2" Residue "B ASP 109": "OD1" <-> "OD2" Residue "B TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9850 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1970 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 18, 'TRANS': 236} Chain breaks: 4 Chain: "B" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1970 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 18, 'TRANS': 236} Chain breaks: 4 Chain: "C" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1970 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 18, 'TRANS': 236} Chain breaks: 4 Chain: "D" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1970 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 18, 'TRANS': 236} Chain breaks: 4 Chain: "E" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1970 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 18, 'TRANS': 236} Chain breaks: 4 Time building chain proxies: 5.39, per 1000 atoms: 0.55 Number of scatterers: 9850 At special positions: 0 Unit cell: (120.19, 122.715, 58.075, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 1900 8.00 N 1625 7.00 C 6265 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.00 Conformation dependent library (CDL) restraints added in 1.6 seconds 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2310 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 15 sheets defined 31.8% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 46 through 50 removed outlier: 3.537A pdb=" N LEU A 50 " --> pdb=" O PRO A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 116 through 122 Processing helix chain 'A' and resid 168 through 182 removed outlier: 3.663A pdb=" N VAL A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 229 Processing helix chain 'A' and resid 339 through 352 removed outlier: 3.769A pdb=" N ILE A 347 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 348 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 50 removed outlier: 3.516A pdb=" N LEU B 50 " --> pdb=" O PRO B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 116 through 123 Processing helix chain 'B' and resid 168 through 182 removed outlier: 4.217A pdb=" N VAL B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 229 Processing helix chain 'B' and resid 339 through 352 Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 46 through 50 removed outlier: 3.547A pdb=" N LEU C 50 " --> pdb=" O PRO C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 removed outlier: 3.641A pdb=" N THR C 60 " --> pdb=" O ASP C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 116 through 123 Processing helix chain 'C' and resid 168 through 180 removed outlier: 3.835A pdb=" N VAL C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 229 removed outlier: 3.704A pdb=" N GLY C 211 " --> pdb=" O GLY C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 352 removed outlier: 3.602A pdb=" N VAL C 343 " --> pdb=" O ASP C 339 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE C 347 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA C 348 " --> pdb=" O THR C 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 61 Processing helix chain 'D' and resid 107 through 116 Processing helix chain 'D' and resid 116 through 123 Processing helix chain 'D' and resid 168 through 182 removed outlier: 3.797A pdb=" N VAL D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 229 removed outlier: 3.672A pdb=" N GLY D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 352 removed outlier: 3.546A pdb=" N VAL D 343 " --> pdb=" O ASP D 339 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE D 347 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA D 348 " --> pdb=" O THR D 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 50 Processing helix chain 'E' and resid 56 through 61 removed outlier: 3.547A pdb=" N THR E 60 " --> pdb=" O ASP E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 115 Processing helix chain 'E' and resid 116 through 121 Processing helix chain 'E' and resid 168 through 183 removed outlier: 3.768A pdb=" N VAL E 172 " --> pdb=" O GLY E 168 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY E 183 " --> pdb=" O CYS E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 229 Processing helix chain 'E' and resid 339 through 352 removed outlier: 3.577A pdb=" N VAL E 343 " --> pdb=" O ASP E 339 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 39 removed outlier: 3.578A pdb=" N ARG A 34 " --> pdb=" O TRP A 25 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 36 " --> pdb=" O TYR A 23 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE A 88 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE A 26 " --> pdb=" O CYS A 92 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR A 78 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 56 removed outlier: 3.611A pdb=" N TRP A 53 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 95 through 96 removed outlier: 3.682A pdb=" N GLU A 100 " --> pdb=" O THR A 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 188 through 189 removed outlier: 3.818A pdb=" N GLY A 188 " --> pdb=" O GLN A 201 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS A 249 " --> pdb=" O GLU A 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 33 through 38 removed outlier: 3.503A pdb=" N LYS B 36 " --> pdb=" O TYR B 23 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU B 22 " --> pdb=" O ILE B 88 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 188 through 189 removed outlier: 4.191A pdb=" N GLY B 188 " --> pdb=" O GLN B 201 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN B 201 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR B 132 " --> pdb=" O TRP B 198 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE B 200 " --> pdb=" O GLN B 130 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR B 133 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 188 through 189 removed outlier: 4.191A pdb=" N GLY B 188 " --> pdb=" O GLN B 201 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN B 201 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR B 132 " --> pdb=" O TRP B 198 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE B 200 " --> pdb=" O GLN B 130 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU B 129 " --> pdb=" O HIS B 249 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N HIS B 249 " --> pdb=" O GLU B 129 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 33 through 38 removed outlier: 3.589A pdb=" N LYS C 36 " --> pdb=" O TYR C 23 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU C 22 " --> pdb=" O ILE C 88 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 71 through 72 removed outlier: 3.548A pdb=" N TYR C 95 " --> pdb=" O ILE C 71 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 186 through 191 removed outlier: 4.844A pdb=" N GLN C 201 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE C 189 " --> pdb=" O GLU C 199 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU C 199 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLY C 191 " --> pdb=" O GLN C 197 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N GLN C 197 " --> pdb=" O GLY C 191 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS C 249 " --> pdb=" O GLU C 129 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 33 through 37 removed outlier: 3.763A pdb=" N ARG D 34 " --> pdb=" O TRP D 25 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS D 36 " --> pdb=" O TYR D 23 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 187 through 190 removed outlier: 4.493A pdb=" N ILE D 189 " --> pdb=" O GLU D 199 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLU D 199 " --> pdb=" O ILE D 189 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN D 130 " --> pdb=" O PHE D 200 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 33 through 38 removed outlier: 3.741A pdb=" N ARG E 34 " --> pdb=" O TRP E 25 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TRP E 25 " --> pdb=" O ARG E 34 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS E 36 " --> pdb=" O TYR E 23 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 72 through 73 removed outlier: 4.189A pdb=" N TYR E 73 " --> pdb=" O ASP E 93 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASP E 93 " --> pdb=" O TYR E 73 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 188 through 191 removed outlier: 3.564A pdb=" N GLY E 188 " --> pdb=" O GLN E 201 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN E 130 " --> pdb=" O PHE E 200 " (cutoff:3.500A) 320 hydrogen bonds defined for protein. 915 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: 2.64 Time building geometry restraints manager: 4.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3147 1.34 - 1.46: 1594 1.46 - 1.57: 5248 1.57 - 1.69: 1 1.69 - 1.81: 100 Bond restraints: 10090 Sorted by residual: bond pdb=" CB PRO E 101 " pdb=" CG PRO E 101 " ideal model delta sigma weight residual 1.492 1.584 -0.092 5.00e-02 4.00e+02 3.35e+00 bond pdb=" CG PRO E 101 " pdb=" CD PRO E 101 " ideal model delta sigma weight residual 1.503 1.472 0.031 3.40e-02 8.65e+02 8.21e-01 bond pdb=" CA GLU D 123 " pdb=" CB GLU D 123 " ideal model delta sigma weight residual 1.530 1.543 -0.014 1.58e-02 4.01e+03 7.33e-01 bond pdb=" C LYS D 237 " pdb=" O LYS D 237 " ideal model delta sigma weight residual 1.238 1.249 -0.011 1.28e-02 6.10e+03 7.30e-01 bond pdb=" N GLN E 136 " pdb=" CA GLN E 136 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.29e-02 6.01e+03 6.64e-01 ... (remaining 10085 not shown) Histogram of bond angle deviations from ideal: 98.51 - 105.61: 317 105.61 - 112.71: 5076 112.71 - 119.81: 3462 119.81 - 126.92: 4686 126.92 - 134.02: 164 Bond angle restraints: 13705 Sorted by residual: angle pdb=" N MET C 31 " pdb=" CA MET C 31 " pdb=" C MET C 31 " ideal model delta sigma weight residual 114.56 109.11 5.45 1.27e+00 6.20e-01 1.84e+01 angle pdb=" CA PRO E 101 " pdb=" N PRO E 101 " pdb=" CD PRO E 101 " ideal model delta sigma weight residual 112.00 106.92 5.08 1.40e+00 5.10e-01 1.32e+01 angle pdb=" N GLY D 188 " pdb=" CA GLY D 188 " pdb=" C GLY D 188 " ideal model delta sigma weight residual 112.65 116.97 -4.32 1.30e+00 5.92e-01 1.10e+01 angle pdb=" N ARG C 107 " pdb=" CA ARG C 107 " pdb=" C ARG C 107 " ideal model delta sigma weight residual 113.18 108.84 4.34 1.33e+00 5.65e-01 1.06e+01 angle pdb=" CA TRP C 53 " pdb=" CB TRP C 53 " pdb=" CG TRP C 53 " ideal model delta sigma weight residual 113.60 119.57 -5.97 1.90e+00 2.77e-01 9.87e+00 ... (remaining 13700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 5369 17.54 - 35.07: 520 35.07 - 52.61: 72 52.61 - 70.15: 14 70.15 - 87.68: 10 Dihedral angle restraints: 5985 sinusoidal: 2355 harmonic: 3630 Sorted by residual: dihedral pdb=" CA GLN E 136 " pdb=" C GLN E 136 " pdb=" N LYS E 137 " pdb=" CA LYS E 137 " ideal model delta harmonic sigma weight residual 180.00 153.64 26.36 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA GLN B 136 " pdb=" C GLN B 136 " pdb=" N LYS B 137 " pdb=" CA LYS B 137 " ideal model delta harmonic sigma weight residual 180.00 154.90 25.10 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA TYR D 95 " pdb=" C TYR D 95 " pdb=" N THR D 96 " pdb=" CA THR D 96 " ideal model delta harmonic sigma weight residual 180.00 159.42 20.58 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 5982 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 941 0.041 - 0.082: 394 0.082 - 0.122: 112 0.122 - 0.163: 18 0.163 - 0.204: 5 Chirality restraints: 1470 Sorted by residual: chirality pdb=" CB ILE E 24 " pdb=" CA ILE E 24 " pdb=" CG1 ILE E 24 " pdb=" CG2 ILE E 24 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB ILE D 24 " pdb=" CA ILE D 24 " pdb=" CG1 ILE D 24 " pdb=" CG2 ILE D 24 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB ILE A 24 " pdb=" CA ILE A 24 " pdb=" CG1 ILE A 24 " pdb=" CG2 ILE A 24 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.80e-01 ... (remaining 1467 not shown) Planarity restraints: 1775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU E 100 " 0.070 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO E 101 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO E 101 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO E 101 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 102 " -0.048 5.00e-02 4.00e+02 7.23e-02 8.36e+00 pdb=" N PRO D 103 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 102 " 0.047 5.00e-02 4.00e+02 7.21e-02 8.32e+00 pdb=" N PRO A 103 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 103 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 103 " 0.040 5.00e-02 4.00e+02 ... (remaining 1772 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 236 2.65 - 3.22: 9801 3.22 - 3.78: 16131 3.78 - 4.34: 21550 4.34 - 4.90: 34287 Nonbonded interactions: 82005 Sorted by model distance: nonbonded pdb=" NZ LYS A 137 " pdb=" O GLY A 229 " model vdw 2.092 2.520 nonbonded pdb=" OG SER C 205 " pdb=" OG SER C 209 " model vdw 2.119 2.440 nonbonded pdb=" NE2 GLN D 52 " pdb=" O LEU D 72 " model vdw 2.175 2.520 nonbonded pdb=" O TYR B 181 " pdb=" OG SER E 15 " model vdw 2.207 2.440 nonbonded pdb=" OH TYR D 55 " pdb=" OE1 GLN D 62 " model vdw 2.215 2.440 ... (remaining 82000 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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 group one per residue 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: 5.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 27.560 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 28.940 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5235 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 10090 Z= 0.219 Angle : 0.670 6.894 13705 Z= 0.354 Chirality : 0.048 0.204 1470 Planarity : 0.007 0.104 1775 Dihedral : 13.953 87.681 3675 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.24), residues: 1225 helix: 0.49 (0.25), residues: 395 sheet: -2.13 (0.30), residues: 275 loop : -1.56 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 53 HIS 0.006 0.001 HIS A 249 PHE 0.014 0.002 PHE B 82 TYR 0.019 0.001 TYR C 181 ARG 0.008 0.001 ARG D 107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 LEU cc_start: 0.7145 (mt) cc_final: 0.6942 (mt) REVERT: C 216 MET cc_start: 0.5703 (mtm) cc_final: 0.5491 (mtp) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2097 time to fit residues: 49.5666 Evaluate side-chains 135 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 59 optimal weight: 0.5980 chunk 72 optimal weight: 20.0000 chunk 113 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 HIS ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5391 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10090 Z= 0.249 Angle : 0.651 6.677 13705 Z= 0.341 Chirality : 0.048 0.231 1470 Planarity : 0.007 0.070 1775 Dihedral : 4.765 24.587 1365 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 22.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 0.75 % Allowed : 10.57 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.25), residues: 1225 helix: 1.12 (0.27), residues: 340 sheet: -2.29 (0.28), residues: 330 loop : -1.36 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 198 HIS 0.005 0.001 HIS B 249 PHE 0.015 0.002 PHE B 167 TYR 0.020 0.002 TYR D 176 ARG 0.006 0.001 ARG D 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 140 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LEU cc_start: 0.7162 (mt) cc_final: 0.6794 (mt) outliers start: 8 outliers final: 3 residues processed: 145 average time/residue: 0.1918 time to fit residues: 40.5958 Evaluate side-chains 132 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 129 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 254 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 0.3980 chunk 35 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5313 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10090 Z= 0.179 Angle : 0.603 8.490 13705 Z= 0.309 Chirality : 0.046 0.165 1470 Planarity : 0.006 0.068 1775 Dihedral : 4.540 25.179 1365 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 1.51 % Allowed : 13.40 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.25), residues: 1225 helix: 1.40 (0.27), residues: 340 sheet: -2.26 (0.27), residues: 330 loop : -1.27 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 198 HIS 0.005 0.001 HIS B 249 PHE 0.013 0.002 PHE A 200 TYR 0.016 0.001 TYR D 176 ARG 0.004 0.000 ARG D 107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 133 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 LEU cc_start: 0.3886 (mt) cc_final: 0.3565 (mp) REVERT: E 70 VAL cc_start: 0.6676 (OUTLIER) cc_final: 0.5221 (t) outliers start: 16 outliers final: 12 residues processed: 145 average time/residue: 0.1882 time to fit residues: 40.0408 Evaluate side-chains 137 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 213 GLN Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 213 GLN Chi-restraints excluded: chain E residue 254 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 chunk 114 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 ASN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5597 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 10090 Z= 0.373 Angle : 0.761 8.218 13705 Z= 0.398 Chirality : 0.051 0.189 1470 Planarity : 0.007 0.068 1775 Dihedral : 5.448 29.161 1365 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 29.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.33 % Favored : 87.67 % Rotamer: Outliers : 2.64 % Allowed : 16.98 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.24), residues: 1225 helix: 0.61 (0.25), residues: 370 sheet: -2.31 (0.29), residues: 275 loop : -1.87 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 198 HIS 0.005 0.001 HIS B 249 PHE 0.017 0.003 PHE B 167 TYR 0.020 0.002 TYR D 176 ARG 0.004 0.001 ARG C 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 SER cc_start: 0.6952 (t) cc_final: 0.6667 (t) REVERT: B 53 TRP cc_start: 0.6730 (t60) cc_final: 0.6371 (t60) REVERT: C 250 THR cc_start: 0.5656 (OUTLIER) cc_final: 0.5447 (t) REVERT: D 112 LYS cc_start: 0.7003 (pptt) cc_final: 0.6664 (pptt) REVERT: E 70 VAL cc_start: 0.6965 (OUTLIER) cc_final: 0.5418 (t) REVERT: E 194 MET cc_start: 0.2513 (tmm) cc_final: 0.2287 (tpp) outliers start: 28 outliers final: 16 residues processed: 157 average time/residue: 0.2121 time to fit residues: 48.3445 Evaluate side-chains 145 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 127 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain C residue 9 ASN Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 53 TRP Chi-restraints excluded: chain C residue 198 TRP Chi-restraints excluded: chain C residue 213 GLN Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain E residue 53 TRP Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 213 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 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 62 GLN ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5567 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10090 Z= 0.307 Angle : 0.707 7.407 13705 Z= 0.368 Chirality : 0.049 0.161 1470 Planarity : 0.007 0.067 1775 Dihedral : 5.282 26.449 1365 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 27.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 3.58 % Allowed : 18.49 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.24), residues: 1225 helix: 0.63 (0.25), residues: 370 sheet: -2.38 (0.29), residues: 275 loop : -1.85 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 198 HIS 0.016 0.001 HIS B 249 PHE 0.014 0.002 PHE B 167 TYR 0.018 0.002 TYR A 158 ARG 0.003 0.001 ARG C 169 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 137 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 SER cc_start: 0.6931 (t) cc_final: 0.6285 (p) REVERT: A 194 MET cc_start: 0.2827 (tpp) cc_final: 0.2481 (mtp) REVERT: B 106 LYS cc_start: 0.7306 (mppt) cc_final: 0.7096 (mttp) REVERT: D 112 LYS cc_start: 0.7075 (pptt) cc_final: 0.6655 (pptt) REVERT: E 70 VAL cc_start: 0.6931 (OUTLIER) cc_final: 0.5384 (t) outliers start: 38 outliers final: 19 residues processed: 169 average time/residue: 0.2094 time to fit residues: 50.3580 Evaluate side-chains 150 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 53 TRP Chi-restraints excluded: chain C residue 198 TRP Chi-restraints excluded: chain C residue 213 GLN Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain E residue 53 TRP Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 87 ASN Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 213 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 0.1980 chunk 116 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS C 9 ASN ** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5406 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10090 Z= 0.184 Angle : 0.622 8.641 13705 Z= 0.317 Chirality : 0.046 0.190 1470 Planarity : 0.006 0.065 1775 Dihedral : 4.688 24.771 1365 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 20.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.02 % Allowed : 20.75 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.24), residues: 1225 helix: 1.23 (0.27), residues: 340 sheet: -2.28 (0.29), residues: 275 loop : -1.62 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 53 HIS 0.003 0.001 HIS B 249 PHE 0.015 0.002 PHE A 200 TYR 0.022 0.001 TYR D 176 ARG 0.003 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 132 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 SER cc_start: 0.6858 (t) cc_final: 0.6554 (p) REVERT: A 194 MET cc_start: 0.2776 (tpp) cc_final: 0.2360 (mtp) REVERT: B 53 TRP cc_start: 0.6617 (t60) cc_final: 0.6212 (t60) REVERT: C 91 MET cc_start: 0.5513 (tpt) cc_final: 0.5069 (tpt) REVERT: C 133 THR cc_start: 0.6586 (OUTLIER) cc_final: 0.6295 (p) REVERT: D 112 LYS cc_start: 0.7060 (pptt) cc_final: 0.6855 (pptt) REVERT: E 70 VAL cc_start: 0.6779 (OUTLIER) cc_final: 0.5260 (t) outliers start: 32 outliers final: 18 residues processed: 158 average time/residue: 0.1897 time to fit residues: 43.9042 Evaluate side-chains 145 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain C residue 9 ASN Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 53 TRP Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 198 TRP Chi-restraints excluded: chain C residue 213 GLN Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain E residue 53 TRP Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 213 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 88 optimal weight: 0.5980 chunk 101 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 75 optimal weight: 0.3980 chunk 73 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS ** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5411 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10090 Z= 0.196 Angle : 0.649 11.612 13705 Z= 0.326 Chirality : 0.046 0.183 1470 Planarity : 0.006 0.068 1775 Dihedral : 4.641 24.142 1365 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 20.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 2.45 % Allowed : 22.08 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.25), residues: 1225 helix: 1.29 (0.27), residues: 340 sheet: -2.27 (0.29), residues: 275 loop : -1.56 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 53 HIS 0.004 0.001 HIS B 249 PHE 0.015 0.002 PHE A 200 TYR 0.019 0.001 TYR D 176 ARG 0.002 0.000 ARG C 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 128 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 SER cc_start: 0.6852 (t) cc_final: 0.6549 (p) REVERT: A 194 MET cc_start: 0.2790 (tpp) cc_final: 0.2408 (mtp) REVERT: C 91 MET cc_start: 0.5548 (tpt) cc_final: 0.5201 (pmm) REVERT: E 70 VAL cc_start: 0.6807 (OUTLIER) cc_final: 0.5345 (t) outliers start: 26 outliers final: 21 residues processed: 148 average time/residue: 0.1953 time to fit residues: 42.9922 Evaluate side-chains 146 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 53 TRP Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 198 TRP Chi-restraints excluded: chain C residue 213 GLN Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 53 TRP Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 213 GLN Chi-restraints excluded: chain E residue 254 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 20.0000 chunk 76 optimal weight: 1.9990 chunk 82 optimal weight: 0.0670 chunk 59 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 94 optimal weight: 8.9990 chunk 109 optimal weight: 0.1980 chunk 115 optimal weight: 0.4980 chunk 105 optimal weight: 7.9990 overall best weight: 0.5120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5298 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10090 Z= 0.169 Angle : 0.640 11.544 13705 Z= 0.318 Chirality : 0.046 0.195 1470 Planarity : 0.006 0.068 1775 Dihedral : 4.390 23.498 1365 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.26 % Allowed : 23.30 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.25), residues: 1225 helix: 1.40 (0.27), residues: 340 sheet: -2.18 (0.29), residues: 275 loop : -1.44 (0.27), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 53 HIS 0.003 0.001 HIS E 175 PHE 0.015 0.001 PHE A 200 TYR 0.018 0.001 TYR D 176 ARG 0.004 0.000 ARG D 107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 137 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 TRP cc_start: 0.6541 (t60) cc_final: 0.6175 (t60) REVERT: C 133 THR cc_start: 0.6604 (OUTLIER) cc_final: 0.6321 (p) REVERT: E 70 VAL cc_start: 0.6718 (OUTLIER) cc_final: 0.5306 (t) outliers start: 24 outliers final: 18 residues processed: 157 average time/residue: 0.1859 time to fit residues: 43.1404 Evaluate side-chains 149 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 129 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 53 TRP Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 198 TRP Chi-restraints excluded: chain C residue 213 GLN Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 213 GLN Chi-restraints excluded: chain E residue 254 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 10.0000 chunk 115 optimal weight: 0.9990 chunk 67 optimal weight: 0.0170 chunk 48 optimal weight: 20.0000 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 chunk 111 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 118 optimal weight: 0.7980 overall best weight: 1.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5462 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10090 Z= 0.256 Angle : 0.719 12.381 13705 Z= 0.363 Chirality : 0.048 0.175 1470 Planarity : 0.006 0.071 1775 Dihedral : 4.782 24.479 1365 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 23.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 2.26 % Allowed : 24.62 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.24), residues: 1225 helix: 1.13 (0.27), residues: 340 sheet: -2.21 (0.29), residues: 275 loop : -1.57 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 53 HIS 0.003 0.001 HIS C 249 PHE 0.014 0.002 PHE A 200 TYR 0.024 0.002 TYR D 176 ARG 0.003 0.000 ARG C 223 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 MET cc_start: 0.5467 (tpt) cc_final: 0.5079 (pmm) REVERT: D 35 SER cc_start: 0.6950 (t) cc_final: 0.6056 (p) REVERT: E 70 VAL cc_start: 0.6868 (OUTLIER) cc_final: 0.5406 (t) REVERT: E 194 MET cc_start: 0.2393 (tmm) cc_final: 0.2023 (tpp) outliers start: 24 outliers final: 19 residues processed: 146 average time/residue: 0.1897 time to fit residues: 40.9388 Evaluate side-chains 145 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 53 TRP Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 198 TRP Chi-restraints excluded: chain C residue 213 GLN Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 213 GLN Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 0.7980 chunk 56 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 ASN ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5655 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 10090 Z= 0.417 Angle : 0.858 12.238 13705 Z= 0.444 Chirality : 0.052 0.197 1470 Planarity : 0.007 0.073 1775 Dihedral : 5.826 27.323 1365 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 33.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Rotamer: Outliers : 2.55 % Allowed : 24.72 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.24), residues: 1225 helix: 0.21 (0.25), residues: 370 sheet: -2.80 (0.26), residues: 325 loop : -1.54 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 53 HIS 0.005 0.002 HIS A 249 PHE 0.023 0.003 PHE C 108 TYR 0.016 0.003 TYR D 176 ARG 0.004 0.001 ARG A 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 123 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 252 TYR cc_start: 0.4314 (t80) cc_final: 0.3556 (m-80) REVERT: C 128 ILE cc_start: 0.6516 (mm) cc_final: 0.6298 (mt) REVERT: E 70 VAL cc_start: 0.6945 (OUTLIER) cc_final: 0.5370 (t) outliers start: 27 outliers final: 22 residues processed: 145 average time/residue: 0.1918 time to fit residues: 40.6114 Evaluate side-chains 145 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 122 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain C residue 53 TRP Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 198 TRP Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 213 GLN Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain D residue 9 ASN Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain E residue 53 TRP Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 213 GLN Chi-restraints excluded: chain E residue 352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 99 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 ASN ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5275 r_free = 0.5275 target = 0.209482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.165890 restraints weight = 14475.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.166663 restraints weight = 11470.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.168368 restraints weight = 10599.503| |-----------------------------------------------------------------------------| r_work (final): 0.4817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5735 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10090 Z= 0.215 Angle : 0.708 11.376 13705 Z= 0.358 Chirality : 0.048 0.192 1470 Planarity : 0.006 0.072 1775 Dihedral : 4.945 24.421 1365 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 22.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.17 % Allowed : 25.38 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.24), residues: 1225 helix: 0.97 (0.27), residues: 340 sheet: -2.38 (0.28), residues: 300 loop : -1.58 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 53 HIS 0.003 0.001 HIS E 175 PHE 0.015 0.002 PHE A 200 TYR 0.027 0.001 TYR B 95 ARG 0.003 0.001 ARG A 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2275.99 seconds wall clock time: 42 minutes 1.41 seconds (2521.41 seconds total)