Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 5 06:59:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew2_28640/10_2023/8ew2_28640.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew2_28640/10_2023/8ew2_28640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew2_28640/10_2023/8ew2_28640.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew2_28640/10_2023/8ew2_28640.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew2_28640/10_2023/8ew2_28640.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew2_28640/10_2023/8ew2_28640.pdb" } resolution = 3.1 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 ------------------------------------------------------------------------------- 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 6516 2.51 5 N 1832 2.21 5 O 1948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ASP 17": "OD1" <-> "OD2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 66": "OD1" <-> "OD2" Residue "B TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 109": "OD1" <-> "OD2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "B GLU 189": "OE1" <-> "OE2" Residue "B ASP 193": "OD1" <-> "OD2" Residue "B ASP 218": "OD1" <-> "OD2" Residue "B TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 246": "OE1" <-> "OE2" Residue "B GLU 247": "OE1" <-> "OE2" Residue "B GLU 278": "OE1" <-> "OE2" Residue "B TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "A GLU 10": "OE1" <-> "OE2" Residue "A ASP 17": "OD1" <-> "OD2" Residue "A ASP 33": "OD1" <-> "OD2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A GLU 247": "OE1" <-> "OE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "C ASP 17": "OD1" <-> "OD2" Residue "C GLU 52": "OE1" <-> "OE2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C ASP 143": "OD1" <-> "OD2" Residue "C PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C GLU 206": "OE1" <-> "OE2" Residue "C TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 14": "OE1" <-> "OE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D ASP 143": "OD1" <-> "OD2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 218": "OD1" <-> "OD2" Residue "D GLU 278": "OE1" <-> "OE2" Residue "D TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 10340 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2585 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 320} Chain breaks: 1 Chain: "A" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2585 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 320} Chain breaks: 1 Chain: "C" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2585 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 320} Chain breaks: 1 Chain: "D" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2585 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 320} Chain breaks: 1 Time building chain proxies: 5.90, per 1000 atoms: 0.57 Number of scatterers: 10340 At special positions: 0 Unit cell: (79.54, 97.58, 104.96, 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 44 16.00 O 1948 8.00 N 1832 7.00 C 6516 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: 4.42 Conformation dependent library (CDL) restraints added in 1.6 seconds 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2488 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 8 sheets defined 54.1% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'B' and resid 8 through 23 Processing helix chain 'B' and resid 35 through 47 Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 79 through 85 removed outlier: 3.968A pdb=" N TYR B 84 " --> pdb=" O HIS B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 100 Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 159 through 180 Processing helix chain 'B' and resid 197 through 219 Processing helix chain 'B' and resid 222 through 226 Processing helix chain 'B' and resid 244 through 260 removed outlier: 3.536A pdb=" N THR B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 288 Processing helix chain 'B' and resid 302 through 314 removed outlier: 6.790A pdb=" N SER B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 339 Processing helix chain 'A' and resid 8 through 23 Processing helix chain 'A' and resid 35 through 45 Processing helix chain 'A' and resid 51 through 64 removed outlier: 3.585A pdb=" N ARG A 59 " --> pdb=" O ARG A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 85 removed outlier: 3.984A pdb=" N TYR A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 100 Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 159 through 180 Processing helix chain 'A' and resid 197 through 219 Processing helix chain 'A' and resid 222 through 226 Processing helix chain 'A' and resid 244 through 260 removed outlier: 3.540A pdb=" N THR A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 288 Processing helix chain 'A' and resid 302 through 312 removed outlier: 6.840A pdb=" N SER A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ALA A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 339 Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 35 through 46 Processing helix chain 'C' and resid 51 through 64 Processing helix chain 'C' and resid 66 through 70 Processing helix chain 'C' and resid 79 through 85 Processing helix chain 'C' and resid 92 through 98 Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 159 through 180 Processing helix chain 'C' and resid 197 through 219 Processing helix chain 'C' and resid 222 through 226 Processing helix chain 'C' and resid 244 through 260 removed outlier: 3.552A pdb=" N THR C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 288 Processing helix chain 'C' and resid 302 through 314 removed outlier: 6.514A pdb=" N SER C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ALA C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 339 Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 35 through 46 removed outlier: 3.756A pdb=" N ILE D 46 " --> pdb=" O ARG D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 64 Processing helix chain 'D' and resid 79 through 85 removed outlier: 3.968A pdb=" N TYR D 84 " --> pdb=" O HIS D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 100 Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 159 through 180 Processing helix chain 'D' and resid 197 through 219 Processing helix chain 'D' and resid 222 through 226 Processing helix chain 'D' and resid 244 through 260 removed outlier: 3.525A pdb=" N THR D 259 " --> pdb=" O ALA D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 288 Processing helix chain 'D' and resid 302 through 314 removed outlier: 6.314A pdb=" N SER D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ALA D 309 " --> pdb=" O LEU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 340 Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 31 removed outlier: 6.586A pdb=" N GLY B 28 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N VAL B 76 " --> pdb=" O GLY B 28 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU B 30 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LEU B 78 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL B 104 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ALA B 145 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ILE B 106 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N TRP B 147 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ASP B 143 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILE B 185 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA B 145 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N GLU B 187 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TRP B 147 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU B 189 " --> pdb=" O TRP B 147 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N CYS B 149 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU B 191 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU B 151 " --> pdb=" O LEU B 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 112 through 114 Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 31 removed outlier: 6.805A pdb=" N GLY A 28 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N VAL A 76 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU A 30 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N LEU A 78 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL A 104 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ALA A 145 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ILE A 106 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TRP A 147 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ASP A 143 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ILE A 185 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA A 145 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N GLU A 187 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TRP A 147 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLU A 189 " --> pdb=" O TRP A 147 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N CYS A 149 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU A 191 " --> pdb=" O CYS A 149 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU A 151 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU A 228 " --> pdb=" O THR A 268 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 114 Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 31 removed outlier: 6.959A pdb=" N GLY C 28 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N VAL C 76 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU C 30 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N LEU C 78 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA C 145 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N GLU C 187 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N TRP C 147 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLU C 189 " --> pdb=" O TRP C 147 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N CYS C 149 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU C 191 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU C 151 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU C 228 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N VAL C 267 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N SER C 300 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N PHE C 269 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 114 Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 31 removed outlier: 6.310A pdb=" N GLY D 28 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ILE D 77 " --> pdb=" O GLY D 28 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU D 30 " --> pdb=" O ILE D 77 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU D 228 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N VAL D 267 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N SER D 300 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N PHE D 269 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 114 571 hydrogen bonds defined for protein. 1656 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: 3.07 Time building geometry restraints manager: 4.71 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: 3441 1.34 - 1.46: 1498 1.46 - 1.57: 5536 1.57 - 1.69: 1 1.69 - 1.81: 56 Bond restraints: 10532 Sorted by residual: bond pdb=" CB PRO D 71 " pdb=" CG PRO D 71 " ideal model delta sigma weight residual 1.492 1.600 -0.108 5.00e-02 4.00e+02 4.67e+00 bond pdb=" C ASN C 70 " pdb=" N PRO C 71 " ideal model delta sigma weight residual 1.331 1.348 -0.017 7.90e-03 1.60e+04 4.55e+00 bond pdb=" C ASN A 70 " pdb=" N PRO A 71 " ideal model delta sigma weight residual 1.335 1.350 -0.015 9.40e-03 1.13e+04 2.40e+00 bond pdb=" CG1 ILE D 77 " pdb=" CD1 ILE D 77 " ideal model delta sigma weight residual 1.513 1.458 0.055 3.90e-02 6.57e+02 2.00e+00 bond pdb=" CB GLN C 95 " pdb=" CG GLN C 95 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.64e+00 ... (remaining 10527 not shown) Histogram of bond angle deviations from ideal: 100.34 - 107.07: 340 107.07 - 113.80: 6037 113.80 - 120.52: 3955 120.52 - 127.25: 3822 127.25 - 133.98: 114 Bond angle restraints: 14268 Sorted by residual: angle pdb=" CA PRO D 71 " pdb=" N PRO D 71 " pdb=" CD PRO D 71 " ideal model delta sigma weight residual 112.00 105.58 6.42 1.40e+00 5.10e-01 2.10e+01 angle pdb=" N VAL B 23 " pdb=" CA VAL B 23 " pdb=" C VAL B 23 " ideal model delta sigma weight residual 106.21 110.54 -4.33 1.07e+00 8.73e-01 1.63e+01 angle pdb=" C THR A 51 " pdb=" N GLU A 52 " pdb=" CA GLU A 52 " ideal model delta sigma weight residual 120.82 125.63 -4.81 1.50e+00 4.44e-01 1.03e+01 angle pdb=" N GLU A 49 " pdb=" CA GLU A 49 " pdb=" C GLU A 49 " ideal model delta sigma weight residual 107.73 111.89 -4.16 1.34e+00 5.57e-01 9.63e+00 angle pdb=" N THR A 51 " pdb=" CA THR A 51 " pdb=" C THR A 51 " ideal model delta sigma weight residual 110.35 114.64 -4.29 1.40e+00 5.10e-01 9.39e+00 ... (remaining 14263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5508 17.98 - 35.97: 694 35.97 - 53.95: 167 53.95 - 71.94: 39 71.94 - 89.92: 12 Dihedral angle restraints: 6420 sinusoidal: 2540 harmonic: 3880 Sorted by residual: dihedral pdb=" CA ALA A 304 " pdb=" C ALA A 304 " pdb=" N LEU A 305 " pdb=" CA LEU A 305 " ideal model delta harmonic sigma weight residual 180.00 161.78 18.22 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CB GLU B 132 " pdb=" CG GLU B 132 " pdb=" CD GLU B 132 " pdb=" OE1 GLU B 132 " ideal model delta sinusoidal sigma weight residual 0.00 -89.92 89.92 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CA ASP C 88 " pdb=" CB ASP C 88 " pdb=" CG ASP C 88 " pdb=" OD1 ASP C 88 " ideal model delta sinusoidal sigma weight residual -30.00 -86.17 56.17 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 6417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 936 0.026 - 0.051: 393 0.051 - 0.077: 158 0.077 - 0.102: 99 0.102 - 0.128: 42 Chirality restraints: 1628 Sorted by residual: chirality pdb=" CA ILE B 190 " pdb=" N ILE B 190 " pdb=" C ILE B 190 " pdb=" CB ILE B 190 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.07e-01 chirality pdb=" CA ILE D 182 " pdb=" N ILE D 182 " pdb=" C ILE D 182 " pdb=" CB ILE D 182 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 chirality pdb=" CA TYR C 84 " pdb=" N TYR C 84 " pdb=" C TYR C 84 " pdb=" CB TYR C 84 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 1625 not shown) Planarity restraints: 1848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 70 " 0.044 5.00e-02 4.00e+02 6.38e-02 6.52e+00 pdb=" N PRO D 71 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 71 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 71 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 187 " -0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO A 188 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 188 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 188 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 8 " -0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO A 9 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 9 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 9 " -0.027 5.00e-02 4.00e+02 ... (remaining 1845 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 662 2.73 - 3.27: 10885 3.27 - 3.82: 19395 3.82 - 4.36: 23068 4.36 - 4.90: 38736 Nonbonded interactions: 92746 Sorted by model distance: nonbonded pdb=" OE1 GLU A 121 " pdb=" OG SER A 159 " model vdw 2.188 2.440 nonbonded pdb=" NZ LYS B 146 " pdb=" OE1 GLU B 187 " model vdw 2.216 2.520 nonbonded pdb=" OE1 GLU A 81 " pdb=" NE2 GLN A 85 " model vdw 2.220 2.520 nonbonded pdb=" NZ LYS C 207 " pdb=" O SER D 217 " model vdw 2.220 2.520 nonbonded pdb=" O GLN B 60 " pdb=" OG1 THR B 64 " model vdw 2.230 2.440 ... (remaining 92741 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 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: 4.180 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 30.830 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 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 : 0.004 0.108 10532 Z= 0.241 Angle : 0.626 10.619 14268 Z= 0.353 Chirality : 0.040 0.128 1628 Planarity : 0.005 0.064 1848 Dihedral : 17.049 89.921 3932 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.46 % Allowed : 21.72 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.24), residues: 1340 helix: 1.69 (0.19), residues: 696 sheet: -1.46 (0.38), residues: 192 loop : -0.61 (0.31), residues: 452 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 116 time to evaluate : 1.158 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 118 average time/residue: 0.2362 time to fit residues: 39.6006 Evaluate side-chains 109 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 1.145 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1043 time to fit residues: 2.4062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.0591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10532 Z= 0.215 Angle : 0.512 7.160 14268 Z= 0.261 Chirality : 0.039 0.125 1628 Planarity : 0.004 0.049 1848 Dihedral : 4.173 17.365 1452 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.55 % Allowed : 19.80 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.24), residues: 1340 helix: 2.01 (0.19), residues: 692 sheet: -1.26 (0.35), residues: 216 loop : -0.65 (0.31), residues: 432 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 123 time to evaluate : 1.212 Fit side-chains outliers start: 28 outliers final: 16 residues processed: 142 average time/residue: 0.2634 time to fit residues: 51.1043 Evaluate side-chains 130 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 1.230 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0969 time to fit residues: 4.5078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 0.3980 chunk 37 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 120 optimal weight: 0.6980 chunk 129 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10532 Z= 0.194 Angle : 0.481 6.176 14268 Z= 0.245 Chirality : 0.039 0.121 1628 Planarity : 0.004 0.049 1848 Dihedral : 3.973 16.374 1452 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.28 % Allowed : 19.80 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.04 (0.24), residues: 1340 helix: 2.18 (0.19), residues: 692 sheet: -1.32 (0.34), residues: 216 loop : -0.62 (0.31), residues: 432 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 135 time to evaluate : 1.169 Fit side-chains outliers start: 25 outliers final: 12 residues processed: 152 average time/residue: 0.2680 time to fit residues: 55.2170 Evaluate side-chains 127 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 1.304 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1216 time to fit residues: 4.0950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 9.9990 chunk 90 optimal weight: 0.4980 chunk 62 optimal weight: 0.0060 chunk 13 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 80 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 106 optimal weight: 10.0000 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10532 Z= 0.180 Angle : 0.486 8.483 14268 Z= 0.244 Chirality : 0.039 0.142 1628 Planarity : 0.004 0.045 1848 Dihedral : 3.823 15.710 1452 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.19 % Allowed : 20.35 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.14 (0.24), residues: 1340 helix: 2.31 (0.19), residues: 692 sheet: -1.39 (0.34), residues: 216 loop : -0.60 (0.31), residues: 432 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 1.143 Fit side-chains outliers start: 24 outliers final: 11 residues processed: 147 average time/residue: 0.2589 time to fit residues: 52.1438 Evaluate side-chains 124 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 1.279 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1028 time to fit residues: 3.7901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 108 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 11 GLN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 ASN ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 10532 Z= 0.353 Angle : 0.567 6.970 14268 Z= 0.288 Chirality : 0.042 0.147 1628 Planarity : 0.004 0.047 1848 Dihedral : 4.079 16.031 1452 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.92 % Allowed : 20.53 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.24), residues: 1340 helix: 1.98 (0.19), residues: 692 sheet: -1.43 (0.34), residues: 216 loop : -0.74 (0.31), residues: 432 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 126 time to evaluate : 1.289 Fit side-chains outliers start: 32 outliers final: 17 residues processed: 145 average time/residue: 0.2679 time to fit residues: 53.1106 Evaluate side-chains 126 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 109 time to evaluate : 1.276 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1684 time to fit residues: 5.9696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 127 optimal weight: 0.0970 chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 10 optimal weight: 0.0470 chunk 42 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 ASN C 334 ASN ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10532 Z= 0.186 Angle : 0.490 6.366 14268 Z= 0.247 Chirality : 0.039 0.132 1628 Planarity : 0.004 0.039 1848 Dihedral : 3.863 15.021 1452 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.55 % Allowed : 21.35 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.02 (0.24), residues: 1340 helix: 2.21 (0.19), residues: 692 sheet: -1.47 (0.34), residues: 216 loop : -0.65 (0.31), residues: 432 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 130 time to evaluate : 1.306 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 135 average time/residue: 0.2695 time to fit residues: 49.6277 Evaluate side-chains 119 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 115 time to evaluate : 1.156 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0931 time to fit residues: 2.2142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 77 optimal weight: 0.0670 chunk 58 optimal weight: 0.0770 chunk 78 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 GLN ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10532 Z= 0.198 Angle : 0.500 8.333 14268 Z= 0.252 Chirality : 0.039 0.130 1628 Planarity : 0.004 0.042 1848 Dihedral : 3.762 14.415 1452 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.91 % Allowed : 21.90 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.15 (0.24), residues: 1340 helix: 2.32 (0.19), residues: 692 sheet: -1.42 (0.34), residues: 216 loop : -0.59 (0.31), residues: 432 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 123 time to evaluate : 1.262 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 130 average time/residue: 0.2858 time to fit residues: 50.8296 Evaluate side-chains 122 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 1.565 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0996 time to fit residues: 2.8209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10532 Z= 0.224 Angle : 0.513 8.360 14268 Z= 0.258 Chirality : 0.040 0.173 1628 Planarity : 0.004 0.045 1848 Dihedral : 3.768 14.460 1452 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.00 % Allowed : 21.81 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.11 (0.24), residues: 1340 helix: 2.29 (0.19), residues: 692 sheet: -1.43 (0.34), residues: 216 loop : -0.62 (0.31), residues: 432 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 1.356 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 129 average time/residue: 0.2765 time to fit residues: 48.5575 Evaluate side-chains 120 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 115 time to evaluate : 1.198 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1721 time to fit residues: 3.1072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 77 optimal weight: 0.0770 chunk 125 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 10532 Z= 0.271 Angle : 0.548 7.975 14268 Z= 0.276 Chirality : 0.041 0.355 1628 Planarity : 0.004 0.045 1848 Dihedral : 3.858 14.534 1452 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.46 % Allowed : 22.63 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.00 (0.24), residues: 1340 helix: 2.18 (0.19), residues: 692 sheet: -1.43 (0.34), residues: 216 loop : -0.67 (0.31), residues: 432 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 114 time to evaluate : 1.201 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 116 average time/residue: 0.2846 time to fit residues: 44.6063 Evaluate side-chains 113 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 1.214 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0958 time to fit residues: 1.7410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 104 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10532 Z= 0.205 Angle : 0.524 7.916 14268 Z= 0.262 Chirality : 0.040 0.310 1628 Planarity : 0.004 0.044 1848 Dihedral : 3.781 14.362 1452 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.18 % Allowed : 22.90 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.06 (0.24), residues: 1340 helix: 2.25 (0.19), residues: 692 sheet: -1.45 (0.34), residues: 216 loop : -0.64 (0.31), residues: 432 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 117 time to evaluate : 1.227 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 119 average time/residue: 0.2860 time to fit residues: 46.0997 Evaluate side-chains 113 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.198 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 75 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.148552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.117463 restraints weight = 13999.800| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.88 r_work: 0.3275 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10532 Z= 0.205 Angle : 0.530 7.644 14268 Z= 0.265 Chirality : 0.040 0.228 1628 Planarity : 0.004 0.043 1848 Dihedral : 3.739 13.941 1452 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.09 % Allowed : 23.27 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.12 (0.24), residues: 1340 helix: 2.30 (0.19), residues: 692 sheet: -1.42 (0.34), residues: 216 loop : -0.63 (0.31), residues: 432 =============================================================================== Job complete usr+sys time: 2246.43 seconds wall clock time: 42 minutes 4.60 seconds (2524.60 seconds total)