Starting phenix.real_space_refine on Fri Mar 15 01:24:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofj_20047/03_2024/6ofj_20047.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofj_20047/03_2024/6ofj_20047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofj_20047/03_2024/6ofj_20047.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofj_20047/03_2024/6ofj_20047.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofj_20047/03_2024/6ofj_20047.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofj_20047/03_2024/6ofj_20047.pdb" } resolution = 4.5 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 3442 2.51 5 N 796 2.21 5 O 878 1.98 5 H 5142 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 247": "OE1" <-> "OE2" Residue "A PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 33": "OE1" <-> "OE2" Residue "B TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 247": "OE1" <-> "OE2" Residue "B PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10310 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 5155 Classifications: {'peptide': 325} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 18, 'TRANS': 306} Chain: "B" Number of atoms: 5155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 5155 Classifications: {'peptide': 325} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 18, 'TRANS': 306} Time building chain proxies: 5.11, per 1000 atoms: 0.50 Number of scatterers: 10310 At special positions: 0 Unit cell: (93.96, 52.65, 85.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 O 878 8.00 N 796 7.00 C 3442 6.00 H 5142 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 187 " distance=2.03 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: 8.47 Conformation dependent library (CDL) restraints added in 966.9 milliseconds 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1212 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 2 sheets defined 71.4% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 14 through 18 removed outlier: 3.573A pdb=" N THR A 17 " --> pdb=" O SER A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 65 removed outlier: 3.815A pdb=" N PHE A 37 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 47 " --> pdb=" O TYR A 43 " (cutoff:3.500A) Proline residue: A 53 - end of helix Processing helix chain 'A' and resid 70 through 90 removed outlier: 4.020A pdb=" N TYR A 74 " --> pdb=" O THR A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 removed outlier: 3.797A pdb=" N THR A 94 " --> pdb=" O GLY A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 141 removed outlier: 3.631A pdb=" N GLY A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 115 " --> pdb=" O ASN A 111 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N LEU A 119 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL A 130 " --> pdb=" O TRP A 126 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 168 Processing helix chain 'A' and resid 169 through 173 Processing helix chain 'A' and resid 200 through 212 removed outlier: 3.574A pdb=" N VAL A 210 " --> pdb=" O TYR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 224 removed outlier: 3.580A pdb=" N LEU A 216 " --> pdb=" O PHE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 278 Proline residue: A 267 - end of helix removed outlier: 4.156A pdb=" N ALA A 272 " --> pdb=" O TYR A 268 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 295 removed outlier: 3.809A pdb=" N MET A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE A 290 " --> pdb=" O ILE A 286 " (cutoff:3.500A) Proline residue: A 291 - end of helix removed outlier: 3.999A pdb=" N ALA A 295 " --> pdb=" O PRO A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 300 removed outlier: 5.672A pdb=" N ALA A 299 " --> pdb=" O LYS A 296 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 300 " --> pdb=" O THR A 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 296 through 300' Processing helix chain 'A' and resid 301 through 310 removed outlier: 3.825A pdb=" N ILE A 305 " --> pdb=" O TYR A 301 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR A 306 " --> pdb=" O ASN A 302 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET A 309 " --> pdb=" O ILE A 305 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN A 310 " --> pdb=" O TYR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 322 removed outlier: 4.792A pdb=" N CYS A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 18 removed outlier: 3.572A pdb=" N THR B 17 " --> pdb=" O SER B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 65 removed outlier: 3.815A pdb=" N PHE B 37 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU B 47 " --> pdb=" O TYR B 43 " (cutoff:3.500A) Proline residue: B 53 - end of helix Processing helix chain 'B' and resid 70 through 90 removed outlier: 4.020A pdb=" N TYR B 74 " --> pdb=" O THR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 101 removed outlier: 3.797A pdb=" N THR B 94 " --> pdb=" O GLY B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 141 removed outlier: 3.631A pdb=" N GLY B 114 " --> pdb=" O CYS B 110 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE B 115 " --> pdb=" O ASN B 111 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR B 118 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LEU B 119 " --> pdb=" O PHE B 115 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU B 128 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B 130 " --> pdb=" O TRP B 126 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 131 " --> pdb=" O SER B 127 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 168 Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'B' and resid 200 through 212 removed outlier: 3.574A pdb=" N VAL B 210 " --> pdb=" O TYR B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 224 removed outlier: 3.579A pdb=" N LEU B 216 " --> pdb=" O PHE B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 278 Proline residue: B 267 - end of helix removed outlier: 4.156A pdb=" N ALA B 272 " --> pdb=" O TYR B 268 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR B 274 " --> pdb=" O GLY B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 295 removed outlier: 3.808A pdb=" N MET B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE B 290 " --> pdb=" O ILE B 286 " (cutoff:3.500A) Proline residue: B 291 - end of helix removed outlier: 3.999A pdb=" N ALA B 295 " --> pdb=" O PRO B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 300 removed outlier: 5.671A pdb=" N ALA B 299 " --> pdb=" O LYS B 296 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 300 " --> pdb=" O THR B 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 296 through 300' Processing helix chain 'B' and resid 301 through 310 removed outlier: 3.824A pdb=" N ILE B 305 " --> pdb=" O TYR B 301 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR B 306 " --> pdb=" O ASN B 302 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET B 309 " --> pdb=" O ILE B 305 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN B 310 " --> pdb=" O TYR B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 322 removed outlier: 4.791A pdb=" N CYS B 322 " --> pdb=" O VAL B 318 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 179 through 181 removed outlier: 3.589A pdb=" N ILE A 179 " --> pdb=" O GLY A 188 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 179 through 181 removed outlier: 3.589A pdb=" N ILE B 179 " --> pdb=" O GLY B 188 " (cutoff:3.500A) 286 hydrogen bonds defined for protein. 834 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: 3.08 Time building geometry restraints manager: 8.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5126 1.03 - 1.23: 18 1.23 - 1.42: 2308 1.42 - 1.62: 2938 1.62 - 1.81: 84 Bond restraints: 10474 Sorted by residual: bond pdb=" N MET B 1 " pdb=" H3 MET B 1 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" N MET A 1 " pdb=" H2 MET A 1 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" N MET B 1 " pdb=" H2 MET B 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" N MET A 1 " pdb=" H3 MET A 1 " ideal model delta sigma weight residual 0.890 0.959 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" CB LYS A 325 " pdb=" CG LYS A 325 " ideal model delta sigma weight residual 1.520 1.601 -0.081 3.00e-02 1.11e+03 7.33e+00 ... (remaining 10469 not shown) Histogram of bond angle deviations from ideal: 98.72 - 105.78: 253 105.78 - 112.83: 11523 112.83 - 119.89: 3155 119.89 - 126.94: 3887 126.94 - 134.00: 76 Bond angle restraints: 18894 Sorted by residual: angle pdb=" N ALA A 169 " pdb=" CA ALA A 169 " pdb=" C ALA A 169 " ideal model delta sigma weight residual 109.81 118.10 -8.29 2.21e+00 2.05e-01 1.41e+01 angle pdb=" N ALA B 169 " pdb=" CA ALA B 169 " pdb=" C ALA B 169 " ideal model delta sigma weight residual 109.81 118.08 -8.27 2.21e+00 2.05e-01 1.40e+01 angle pdb=" N PRO A 170 " pdb=" CA PRO A 170 " pdb=" C PRO A 170 " ideal model delta sigma weight residual 110.70 114.99 -4.29 1.22e+00 6.72e-01 1.24e+01 angle pdb=" H1 MET A 1 " pdb=" N MET A 1 " pdb=" H3 MET A 1 " ideal model delta sigma weight residual 109.47 98.98 10.49 3.00e+00 1.11e-01 1.22e+01 angle pdb=" N PRO B 170 " pdb=" CA PRO B 170 " pdb=" C PRO B 170 " ideal model delta sigma weight residual 110.70 114.93 -4.23 1.22e+00 6.72e-01 1.20e+01 ... (remaining 18889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.97: 4349 15.97 - 31.94: 501 31.94 - 47.92: 130 47.92 - 63.89: 50 63.89 - 79.86: 8 Dihedral angle restraints: 5038 sinusoidal: 2580 harmonic: 2458 Sorted by residual: dihedral pdb=" CB CYS B 110 " pdb=" SG CYS B 110 " pdb=" SG CYS B 187 " pdb=" CB CYS B 187 " ideal model delta sinusoidal sigma weight residual -86.00 -120.97 34.97 1 1.00e+01 1.00e-02 1.73e+01 dihedral pdb=" CB CYS A 110 " pdb=" SG CYS A 110 " pdb=" SG CYS A 187 " pdb=" CB CYS A 187 " ideal model delta sinusoidal sigma weight residual -86.00 -120.96 34.96 1 1.00e+01 1.00e-02 1.73e+01 dihedral pdb=" CA PHE A 221 " pdb=" C PHE A 221 " pdb=" N CYS A 222 " pdb=" CA CYS A 222 " ideal model delta harmonic sigma weight residual 180.00 159.24 20.76 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 5035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 468 0.033 - 0.066: 220 0.066 - 0.099: 85 0.099 - 0.132: 26 0.132 - 0.165: 9 Chirality restraints: 808 Sorted by residual: chirality pdb=" CA ILE A 179 " pdb=" N ILE A 179 " pdb=" C ILE A 179 " pdb=" CB ILE A 179 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA ILE B 179 " pdb=" N ILE B 179 " pdb=" C ILE B 179 " pdb=" CB ILE B 179 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.81e-01 chirality pdb=" CA PRO B 71 " pdb=" N PRO B 71 " pdb=" C PRO B 71 " pdb=" CB PRO B 71 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.25e-01 ... (remaining 805 not shown) Planarity restraints: 1516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 70 " 0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO A 71 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 71 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 71 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 70 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.26e+00 pdb=" N PRO B 71 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 71 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 71 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 302 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO A 303 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 303 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 303 " 0.026 5.00e-02 4.00e+02 ... (remaining 1513 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.34: 2817 2.34 - 2.90: 22232 2.90 - 3.47: 25912 3.47 - 4.03: 32708 4.03 - 4.60: 48833 Nonbonded interactions: 132502 Sorted by model distance: nonbonded pdb=" OG1 THR A 198 " pdb="HD21 ASN A 200 " model vdw 1.773 1.850 nonbonded pdb=" OG1 THR B 198 " pdb="HD21 ASN B 200 " model vdw 1.774 1.850 nonbonded pdb=" HZ3 LYS A 245 " pdb=" OE1 GLU A 249 " model vdw 1.797 1.850 nonbonded pdb=" HZ3 LYS B 245 " pdb=" OE1 GLU B 249 " model vdw 1.797 1.850 nonbonded pdb=" OE1 GLU B 196 " pdb=" H GLU B 196 " model vdw 1.800 1.850 ... (remaining 132497 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' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.98 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: 0.350 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: 0.170 Extract box with map and model: 2.040 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 35.800 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3698 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 : 0.007 0.081 5332 Z= 0.445 Angle : 0.960 9.412 7264 Z= 0.491 Chirality : 0.046 0.165 808 Planarity : 0.006 0.045 904 Dihedral : 15.744 79.861 1846 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % 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: -4.36 (0.26), residues: 646 helix: -2.60 (0.20), residues: 382 sheet: None (None), residues: 0 loop : -3.23 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 265 HIS 0.004 0.001 HIS B 152 PHE 0.018 0.002 PHE B 159 TYR 0.020 0.002 TYR A 301 ARG 0.003 0.001 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.7455 (mm) cc_final: 0.7166 (mm) REVERT: A 126 TRP cc_start: 0.3004 (m100) cc_final: 0.2347 (m100) REVERT: A 179 ILE cc_start: 0.4059 (tt) cc_final: 0.3853 (tt) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.3078 time to fit residues: 25.0645 Evaluate side-chains 50 residues out of total 277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 37 optimal weight: 0.2980 chunk 58 optimal weight: 10.0000 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3920 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5332 Z= 0.229 Angle : 0.670 10.196 7264 Z= 0.361 Chirality : 0.040 0.120 808 Planarity : 0.005 0.037 904 Dihedral : 5.694 17.760 698 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % 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: -3.26 (0.28), residues: 646 helix: -1.63 (0.22), residues: 390 sheet: None (None), residues: 0 loop : -2.93 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 35 HIS 0.005 0.001 HIS B 278 PHE 0.041 0.002 PHE A 276 TYR 0.027 0.002 TYR A 191 ARG 0.002 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 179 ILE cc_start: 0.4517 (tt) cc_final: 0.4095 (tt) REVERT: B 181 GLU cc_start: 0.4660 (mp0) cc_final: 0.4067 (mp0) REVERT: B 256 ILE cc_start: 0.8425 (mm) cc_final: 0.7793 (tt) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.2587 time to fit residues: 18.3618 Evaluate side-chains 50 residues out of total 277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3947 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5332 Z= 0.181 Angle : 0.568 5.281 7264 Z= 0.307 Chirality : 0.037 0.135 808 Planarity : 0.004 0.032 904 Dihedral : 5.270 16.525 698 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % 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: -3.18 (0.29), residues: 646 helix: -1.40 (0.23), residues: 392 sheet: None (None), residues: 0 loop : -3.22 (0.35), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 35 HIS 0.007 0.001 HIS B 278 PHE 0.019 0.001 PHE B 276 TYR 0.013 0.002 TYR B 191 ARG 0.004 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2986 time to fit residues: 19.9816 Evaluate side-chains 51 residues out of total 277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 27 optimal weight: 0.0470 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4064 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5332 Z= 0.199 Angle : 0.582 5.268 7264 Z= 0.318 Chirality : 0.038 0.129 808 Planarity : 0.005 0.038 904 Dihedral : 5.188 16.879 698 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % 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: -3.02 (0.29), residues: 646 helix: -1.23 (0.23), residues: 388 sheet: None (None), residues: 0 loop : -3.20 (0.34), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 175 HIS 0.007 0.001 HIS B 278 PHE 0.015 0.002 PHE B 294 TYR 0.013 0.002 TYR A 274 ARG 0.006 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2719 time to fit residues: 17.7077 Evaluate side-chains 50 residues out of total 277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 0.0870 chunk 0 optimal weight: 7.9990 chunk 46 optimal weight: 0.0010 chunk 25 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 overall best weight: 2.4170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4053 moved from start: 0.5465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5332 Z= 0.175 Angle : 0.565 5.405 7264 Z= 0.306 Chirality : 0.038 0.141 808 Planarity : 0.004 0.036 904 Dihedral : 5.091 17.497 698 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % 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: -2.90 (0.29), residues: 646 helix: -1.10 (0.23), residues: 392 sheet: None (None), residues: 0 loop : -3.24 (0.35), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 161 HIS 0.006 0.002 HIS A 278 PHE 0.014 0.001 PHE A 37 TYR 0.010 0.001 TYR B 30 ARG 0.005 0.001 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 VAL cc_start: 0.7748 (p) cc_final: 0.7507 (p) REVERT: B 253 MET cc_start: 0.6299 (tpp) cc_final: 0.5502 (tpp) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2560 time to fit residues: 16.3706 Evaluate side-chains 49 residues out of total 277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 59 optimal weight: 0.0270 chunk 6 optimal weight: 9.9990 chunk 35 optimal weight: 0.3980 overall best weight: 3.6844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4178 moved from start: 0.6450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5332 Z= 0.241 Angle : 0.620 5.170 7264 Z= 0.348 Chirality : 0.039 0.124 808 Planarity : 0.005 0.040 904 Dihedral : 5.460 17.443 698 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.84 % Favored : 89.16 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % 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: -3.48 (0.28), residues: 646 helix: -1.57 (0.22), residues: 382 sheet: None (None), residues: 0 loop : -3.42 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 175 HIS 0.009 0.002 HIS B 278 PHE 0.018 0.002 PHE B 273 TYR 0.015 0.002 TYR A 274 ARG 0.004 0.001 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 183 MET cc_start: 0.6668 (pmm) cc_final: 0.6465 (mmm) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.2498 time to fit residues: 14.9547 Evaluate side-chains 45 residues out of total 277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 37 optimal weight: 0.0570 chunk 28 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4097 moved from start: 0.6529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 5332 Z= 0.164 Angle : 0.544 4.705 7264 Z= 0.296 Chirality : 0.037 0.128 808 Planarity : 0.004 0.036 904 Dihedral : 5.105 17.098 698 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.84 % Favored : 89.16 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % 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: -3.06 (0.29), residues: 646 helix: -1.20 (0.23), residues: 390 sheet: None (None), residues: 0 loop : -3.36 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 35 HIS 0.004 0.001 HIS B 278 PHE 0.012 0.001 PHE A 273 TYR 0.009 0.001 TYR A 43 ARG 0.004 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 VAL cc_start: 0.7918 (p) cc_final: 0.7649 (p) REVERT: B 207 MET cc_start: 0.1444 (mmt) cc_final: 0.0984 (mmt) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2446 time to fit residues: 15.8373 Evaluate side-chains 46 residues out of total 277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 0.2980 chunk 11 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 42 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 5 optimal weight: 0.0170 chunk 48 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 overall best weight: 1.6622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4077 moved from start: 0.6795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5332 Z= 0.149 Angle : 0.532 4.703 7264 Z= 0.286 Chirality : 0.037 0.127 808 Planarity : 0.004 0.036 904 Dihedral : 4.957 17.680 698 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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: -2.71 (0.30), residues: 646 helix: -0.96 (0.24), residues: 392 sheet: None (None), residues: 0 loop : -3.16 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 126 HIS 0.004 0.001 HIS B 278 PHE 0.012 0.001 PHE B 294 TYR 0.008 0.001 TYR A 301 ARG 0.003 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 VAL cc_start: 0.7904 (p) cc_final: 0.7657 (p) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2359 time to fit residues: 15.6082 Evaluate side-chains 45 residues out of total 277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 51 optimal weight: 0.4980 chunk 54 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 60 optimal weight: 0.0670 chunk 28 optimal weight: 0.0670 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3988 moved from start: 0.6929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5332 Z= 0.134 Angle : 0.513 4.252 7264 Z= 0.273 Chirality : 0.037 0.129 808 Planarity : 0.004 0.030 904 Dihedral : 4.732 16.215 698 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -2.46 (0.31), residues: 646 helix: -0.81 (0.24), residues: 406 sheet: None (None), residues: 0 loop : -3.06 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 126 HIS 0.003 0.001 HIS A 100 PHE 0.013 0.001 PHE B 37 TYR 0.020 0.001 TYR B 192 ARG 0.002 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2285 time to fit residues: 15.0303 Evaluate side-chains 46 residues out of total 277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 0.0040 chunk 63 optimal weight: 3.9990 chunk 58 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 5 optimal weight: 0.0970 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 46 optimal weight: 0.0980 overall best weight: 0.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3988 moved from start: 0.7123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5332 Z= 0.136 Angle : 0.508 4.260 7264 Z= 0.270 Chirality : 0.037 0.126 808 Planarity : 0.004 0.029 904 Dihedral : 4.502 15.828 698 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -2.16 (0.32), residues: 646 helix: -0.55 (0.24), residues: 406 sheet: None (None), residues: 0 loop : -2.98 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 35 HIS 0.002 0.001 HIS A 100 PHE 0.012 0.001 PHE A 45 TYR 0.016 0.001 TYR B 192 ARG 0.002 0.000 ARG B 135 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 VAL cc_start: 0.7874 (p) cc_final: 0.7641 (p) REVERT: B 238 GLN cc_start: 0.6544 (tp40) cc_final: 0.6117 (tm-30) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2445 time to fit residues: 15.9615 Evaluate side-chains 46 residues out of total 277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 0.0010 chunk 14 optimal weight: 0.0770 chunk 50 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 9 optimal weight: 0.0010 chunk 44 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 overall best weight: 0.2950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.136602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.118829 restraints weight = 53722.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.121170 restraints weight = 41481.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.122990 restraints weight = 33833.790| |-----------------------------------------------------------------------------| r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5436 moved from start: 0.7146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 5332 Z= 0.127 Angle : 0.493 4.273 7264 Z= 0.257 Chirality : 0.037 0.127 808 Planarity : 0.003 0.029 904 Dihedral : 4.315 15.712 698 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.96 (0.33), residues: 646 helix: -0.35 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -3.05 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 35 HIS 0.003 0.001 HIS A 100 PHE 0.014 0.001 PHE B 37 TYR 0.009 0.001 TYR B 192 ARG 0.002 0.001 ARG B 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1787.15 seconds wall clock time: 32 minutes 22.28 seconds (1942.28 seconds total)