Starting phenix.real_space_refine (version: dev) on Sun Feb 19 09:54:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4j_31713/02_2023/7v4j_31713.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4j_31713/02_2023/7v4j_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_31713/02_2023/7v4j_31713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4j_31713/02_2023/7v4j_31713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4j_31713/02_2023/7v4j_31713.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4j_31713/02_2023/7v4j_31713.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 6.02, per 1000 atoms: 0.61 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: 4.33 Conformation dependent library (CDL) restraints added in 1.5 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: 0.69 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: 2.63 Time building geometry restraints manager: 4.61 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 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. 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: 8.790 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: 27.570 Check model and map are aligned: 0.150 Process input model: 28.220 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.090 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5240 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 % 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 *********************** 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 : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2170 time to fit residues: 51.1745 Evaluate side-chains 135 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.132 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5135 ------------------------------------------------------------------------------- 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: 4.9990 chunk 94 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 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: 1.6384 ------------------------------------------------------------------------------- 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** A 201 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5359 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 10090 Z= 0.226 Angle : 0.635 6.640 13705 Z= 0.331 Chirality : 0.047 0.226 1470 Planarity : 0.006 0.070 1775 Dihedral : 4.686 24.105 1365 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 20.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer Outliers : 0.85 % 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: -1.40 (0.25), residues: 1225 helix: 1.17 (0.27), residues: 340 sheet: -2.23 (0.28), residues: 325 loop : -1.36 (0.28), residues: 560 *********************** 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 149 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 140 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 145 average time/residue: 0.2011 time to fit residues: 42.4247 Evaluate side-chains 126 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 123 time to evaluate : 1.218 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1103 time to fit residues: 2.5837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 0.0270 chunk 94 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 chunk 112 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 overall best weight: 1.1440 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5329 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 10090 Z= 0.187 Angle : 0.605 8.406 13705 Z= 0.310 Chirality : 0.046 0.165 1470 Planarity : 0.006 0.068 1775 Dihedral : 4.554 25.054 1365 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.25), residues: 1225 helix: 1.37 (0.27), residues: 340 sheet: -2.22 (0.27), residues: 325 loop : -1.31 (0.28), residues: 560 *********************** 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 148 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 134 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 143 average time/residue: 0.2097 time to fit residues: 43.9137 Evaluate side-chains 133 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 123 time to evaluate : 1.066 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1226 time to fit residues: 3.5439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 54 optimal weight: 0.0020 chunk 76 optimal weight: 0.0870 chunk 114 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 overall best weight: 2.0172 ------------------------------------------------------------------------------- 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 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 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** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5447 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 10090 Z= 0.247 Angle : 0.656 8.175 13705 Z= 0.338 Chirality : 0.047 0.165 1470 Planarity : 0.006 0.067 1775 Dihedral : 4.798 26.716 1365 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 23.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer Outliers : 1.70 % 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: -1.43 (0.25), residues: 1225 helix: 1.26 (0.27), residues: 340 sheet: -2.34 (0.27), residues: 325 loop : -1.39 (0.28), residues: 560 *********************** 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 151 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 133 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 146 average time/residue: 0.2157 time to fit residues: 44.9632 Evaluate side-chains 136 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 128 time to evaluate : 1.142 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1220 time to fit residues: 3.2721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 89 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 108 optimal weight: 0.0980 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 249 HIS C 9 ASN ** 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 105 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5370 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 10090 Z= 0.189 Angle : 0.623 9.488 13705 Z= 0.315 Chirality : 0.046 0.174 1470 Planarity : 0.006 0.066 1775 Dihedral : 4.538 24.427 1365 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer Outliers : 0.85 % 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: -1.32 (0.25), residues: 1225 helix: 1.36 (0.28), residues: 340 sheet: -2.32 (0.27), residues: 325 loop : -1.30 (0.28), residues: 560 *********************** 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 147 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 138 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 145 average time/residue: 0.2114 time to fit residues: 44.1435 Evaluate side-chains 130 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 126 time to evaluate : 1.135 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1045 time to fit residues: 2.7178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.3980 chunk 23 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 120 optimal weight: 0.8980 chunk 100 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 10 optimal weight: 0.0070 chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.4602 ------------------------------------------------------------------------------- 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** A 201 GLN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 105 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5409 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 10090 Z= 0.209 Angle : 0.659 12.264 13705 Z= 0.327 Chirality : 0.046 0.183 1470 Planarity : 0.006 0.065 1775 Dihedral : 4.595 24.287 1365 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 22.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer Outliers : 1.42 % 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: -1.38 (0.25), residues: 1225 helix: 1.35 (0.28), residues: 340 sheet: -2.46 (0.27), residues: 325 loop : -1.29 (0.28), residues: 560 *********************** 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 146 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 142 average time/residue: 0.2173 time to fit residues: 44.7430 Evaluate side-chains 132 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 125 time to evaluate : 1.162 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1172 time to fit residues: 3.0182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 88 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 73 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- 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 ** 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 105 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: 0.5485 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 10090 Z= 0.269 Angle : 0.701 10.869 13705 Z= 0.354 Chirality : 0.048 0.175 1470 Planarity : 0.006 0.069 1775 Dihedral : 4.880 24.528 1365 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 24.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer Outliers : 1.60 % 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: -1.57 (0.24), residues: 1225 helix: 1.08 (0.27), residues: 340 sheet: -2.28 (0.29), residues: 275 loop : -1.66 (0.26), residues: 610 *********************** 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 151 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 134 time to evaluate : 1.162 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 148 average time/residue: 0.2167 time to fit residues: 46.7396 Evaluate side-chains 136 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 128 time to evaluate : 1.193 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1398 time to fit residues: 3.4987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 76 optimal weight: 0.0970 chunk 82 optimal weight: 0.7980 chunk 59 optimal weight: 0.0010 chunk 11 optimal weight: 6.9990 chunk 94 optimal weight: 0.0270 chunk 109 optimal weight: 6.9990 chunk 115 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 overall best weight: 0.3442 ------------------------------------------------------------------------------- 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** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS C 52 GLN ** 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 105 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: 0.5281 moved from start: 0.2652 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= 0.171 Angle : 0.661 11.375 13705 Z= 0.324 Chirality : 0.046 0.201 1470 Planarity : 0.006 0.068 1775 Dihedral : 4.433 22.964 1365 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer Outliers : 0.38 % 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: -1.23 (0.25), residues: 1225 helix: 1.44 (0.28), residues: 340 sheet: -2.31 (0.27), residues: 330 loop : -1.20 (0.29), residues: 555 *********************** 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 145 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 141 time to evaluate : 1.200 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 143 average time/residue: 0.1863 time to fit residues: 39.2688 Evaluate side-chains 134 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 132 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1244 time to fit residues: 1.8057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 111 optimal weight: 0.0000 chunk 73 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- 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** B 249 HIS C 52 GLN ** 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 105 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: 0.5466 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 10090 Z= 0.271 Angle : 0.720 11.557 13705 Z= 0.363 Chirality : 0.048 0.186 1470 Planarity : 0.006 0.072 1775 Dihedral : 4.813 23.801 1365 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 25.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer Outliers : 0.57 % 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: -1.42 (0.24), residues: 1225 helix: 1.15 (0.27), residues: 340 sheet: -2.18 (0.29), residues: 275 loop : -1.54 (0.26), residues: 610 *********************** 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 137 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 131 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 134 average time/residue: 0.2085 time to fit residues: 40.4957 Evaluate side-chains 128 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 1.165 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0956 time to fit residues: 1.7288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 8.9990 chunk 56 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 78 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 136 GLN ** 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 105 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: 0.5529 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 10090 Z= 0.315 Angle : 0.782 12.929 13705 Z= 0.394 Chirality : 0.050 0.179 1470 Planarity : 0.007 0.073 1775 Dihedral : 5.161 26.088 1365 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 27.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer Outliers : 0.47 % 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: -1.74 (0.24), residues: 1225 helix: 0.80 (0.27), residues: 340 sheet: -2.61 (0.26), residues: 325 loop : -1.36 (0.27), residues: 560 ********************** 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 136 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 133 average time/residue: 0.2100 time to fit residues: 40.7385 Evaluate side-chains 129 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 126 time to evaluate : 1.171 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1449 time to fit residues: 2.7230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 14 optimal weight: 0.0770 chunk 27 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 41 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 87 optimal weight: 0.0980 chunk 5 optimal weight: 6.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS D 9 ASN ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN E 62 GLN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5260 r_free = 0.5260 target = 0.210311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.165632 restraints weight = 14672.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.168444 restraints weight = 11980.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.170563 restraints weight = 10457.513| |-----------------------------------------------------------------------------| r_work (final): 0.4831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5653 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 10090 Z= 0.186 Angle : 0.683 12.082 13705 Z= 0.338 Chirality : 0.047 0.197 1470 Planarity : 0.006 0.072 1775 Dihedral : 4.622 24.805 1365 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer Outliers : 0.19 % 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: -1.29 (0.25), residues: 1225 helix: 1.34 (0.28), residues: 340 sheet: -2.19 (0.29), residues: 275 loop : -1.46 (0.27), residues: 610 =============================================================================== Job complete usr+sys time: 2264.83 seconds wall clock time: 42 minutes 35.87 seconds (2555.87 seconds total)