Starting phenix.real_space_refine on Wed Mar 4 09:06:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d67_27219/03_2026/8d67_27219_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d67_27219/03_2026/8d67_27219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d67_27219/03_2026/8d67_27219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d67_27219/03_2026/8d67_27219.map" model { file = "/net/cci-nas-00/data/ceres_data/8d67_27219/03_2026/8d67_27219_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d67_27219/03_2026/8d67_27219_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.012 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 35 5.16 5 C 8195 2.51 5 N 2085 2.21 5 O 2255 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12570 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2510 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'DHL': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E Time building chain proxies: 2.25, per 1000 atoms: 0.18 Number of scatterers: 12570 At special positions: 0 Unit cell: (89.1, 89.1, 125.4, 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 35 16.00 O 2255 8.00 N 2085 7.00 C 8195 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 - 3.00 Amino acid : True - 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: 1.00 Conformation dependent library (CDL) restraints added in 602.3 milliseconds 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2910 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 20 sheets defined 31.8% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 63 through 68 Processing helix chain 'A' and resid 201 through 209 removed outlier: 3.802A pdb=" N ILE A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 221 Processing helix chain 'A' and resid 222 through 225 removed outlier: 3.579A pdb=" N LEU A 225 " --> pdb=" O VAL A 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 222 through 225' Processing helix chain 'A' and resid 228 through 251 removed outlier: 3.626A pdb=" N TYR A 245 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 246 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE A 247 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASN A 251 " --> pdb=" O PHE A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 285 Processing helix chain 'A' and resid 302 through 317 removed outlier: 3.841A pdb=" N LEU A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 68 Processing helix chain 'B' and resid 201 through 209 removed outlier: 3.802A pdb=" N ILE B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 221 Processing helix chain 'B' and resid 222 through 225 removed outlier: 3.580A pdb=" N LEU B 225 " --> pdb=" O VAL B 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 222 through 225' Processing helix chain 'B' and resid 228 through 251 removed outlier: 3.626A pdb=" N TYR B 245 " --> pdb=" O THR B 241 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA B 246 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE B 247 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN B 251 " --> pdb=" O PHE B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 285 Processing helix chain 'B' and resid 302 through 317 removed outlier: 3.842A pdb=" N LEU B 306 " --> pdb=" O LEU B 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 68 Processing helix chain 'C' and resid 201 through 209 removed outlier: 3.802A pdb=" N ILE C 209 " --> pdb=" O LEU C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 221 Processing helix chain 'C' and resid 222 through 225 removed outlier: 3.580A pdb=" N LEU C 225 " --> pdb=" O VAL C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 222 through 225' Processing helix chain 'C' and resid 228 through 251 removed outlier: 3.626A pdb=" N TYR C 245 " --> pdb=" O THR C 241 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE C 247 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASN C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 285 Processing helix chain 'C' and resid 302 through 317 removed outlier: 3.842A pdb=" N LEU C 306 " --> pdb=" O LEU C 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 68 Processing helix chain 'D' and resid 201 through 209 removed outlier: 3.803A pdb=" N ILE D 209 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 221 Processing helix chain 'D' and resid 222 through 225 removed outlier: 3.579A pdb=" N LEU D 225 " --> pdb=" O VAL D 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 222 through 225' Processing helix chain 'D' and resid 228 through 251 removed outlier: 3.625A pdb=" N TYR D 245 " --> pdb=" O THR D 241 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA D 246 " --> pdb=" O VAL D 242 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE D 247 " --> pdb=" O VAL D 243 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN D 251 " --> pdb=" O PHE D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 285 Processing helix chain 'D' and resid 302 through 317 removed outlier: 3.842A pdb=" N LEU D 306 " --> pdb=" O LEU D 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 68 Processing helix chain 'E' and resid 201 through 209 removed outlier: 3.802A pdb=" N ILE E 209 " --> pdb=" O LEU E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 221 Processing helix chain 'E' and resid 222 through 225 removed outlier: 3.580A pdb=" N LEU E 225 " --> pdb=" O VAL E 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 222 through 225' Processing helix chain 'E' and resid 228 through 251 removed outlier: 3.626A pdb=" N TYR E 245 " --> pdb=" O THR E 241 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA E 246 " --> pdb=" O VAL E 242 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE E 247 " --> pdb=" O VAL E 243 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN E 251 " --> pdb=" O PHE E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 285 Processing helix chain 'E' and resid 302 through 317 removed outlier: 3.842A pdb=" N LEU E 306 " --> pdb=" O LEU E 302 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 5.724A pdb=" N VAL A 12 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N SER A 143 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N VAL A 14 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE A 145 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL A 16 " --> pdb=" O ILE A 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 24 removed outlier: 5.174A pdb=" N ILE A 20 " --> pdb=" O TYR A 38 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TYR A 38 " --> pdb=" O ILE A 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.572A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.572A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 12 through 16 removed outlier: 5.724A pdb=" N VAL B 12 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER B 143 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N VAL B 14 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE B 145 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL B 16 " --> pdb=" O ILE B 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 19 through 24 removed outlier: 5.174A pdb=" N ILE B 20 " --> pdb=" O TYR B 38 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TYR B 38 " --> pdb=" O ILE B 20 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.572A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.572A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 12 through 16 removed outlier: 5.724A pdb=" N VAL C 12 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N SER C 143 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL C 14 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE C 145 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL C 16 " --> pdb=" O ILE C 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 19 through 24 removed outlier: 5.174A pdb=" N ILE C 20 " --> pdb=" O TYR C 38 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TYR C 38 " --> pdb=" O ILE C 20 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.572A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.572A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 12 through 16 removed outlier: 5.724A pdb=" N VAL D 12 " --> pdb=" O ARG D 141 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N SER D 143 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL D 14 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE D 145 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL D 16 " --> pdb=" O ILE D 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 19 through 24 removed outlier: 5.174A pdb=" N ILE D 20 " --> pdb=" O TYR D 38 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TYR D 38 " --> pdb=" O ILE D 20 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.572A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.572A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 12 through 16 removed outlier: 5.724A pdb=" N VAL E 12 " --> pdb=" O ARG E 141 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER E 143 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N VAL E 14 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE E 145 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL E 16 " --> pdb=" O ILE E 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 19 through 24 removed outlier: 5.174A pdb=" N ILE E 20 " --> pdb=" O TYR E 38 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TYR E 38 " --> pdb=" O ILE E 20 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.572A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.572A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) 590 hydrogen bonds defined for protein. 1740 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: 1.51 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2765 1.33 - 1.45: 3066 1.45 - 1.57: 7024 1.57 - 1.69: 0 1.69 - 1.81: 55 Bond restraints: 12910 Sorted by residual: bond pdb=" C GLU C 59 " pdb=" O GLU C 59 " ideal model delta sigma weight residual 1.234 1.205 0.029 1.07e-02 8.73e+03 7.30e+00 bond pdb=" CA GLN A 62 " pdb=" C GLN A 62 " ideal model delta sigma weight residual 1.521 1.486 0.035 1.31e-02 5.83e+03 7.25e+00 bond pdb=" CA GLN E 62 " pdb=" C GLN E 62 " ideal model delta sigma weight residual 1.521 1.486 0.035 1.31e-02 5.83e+03 7.23e+00 bond pdb=" CA GLN C 62 " pdb=" C GLN C 62 " ideal model delta sigma weight residual 1.521 1.486 0.035 1.31e-02 5.83e+03 7.18e+00 bond pdb=" C GLU E 59 " pdb=" O GLU E 59 " ideal model delta sigma weight residual 1.234 1.206 0.029 1.07e-02 8.73e+03 7.13e+00 ... (remaining 12905 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 17064 2.45 - 4.90: 441 4.90 - 7.35: 65 7.35 - 9.80: 0 9.80 - 12.25: 15 Bond angle restraints: 17585 Sorted by residual: angle pdb=" N GLN B 62 " pdb=" CA GLN B 62 " pdb=" C GLN B 62 " ideal model delta sigma weight residual 113.61 101.36 12.25 1.50e+00 4.44e-01 6.67e+01 angle pdb=" N GLN D 62 " pdb=" CA GLN D 62 " pdb=" C GLN D 62 " ideal model delta sigma weight residual 113.61 101.36 12.25 1.50e+00 4.44e-01 6.67e+01 angle pdb=" N GLN A 62 " pdb=" CA GLN A 62 " pdb=" C GLN A 62 " ideal model delta sigma weight residual 113.61 101.40 12.21 1.50e+00 4.44e-01 6.63e+01 angle pdb=" N GLN C 62 " pdb=" CA GLN C 62 " pdb=" C GLN C 62 " ideal model delta sigma weight residual 113.61 101.40 12.21 1.50e+00 4.44e-01 6.63e+01 angle pdb=" N GLN E 62 " pdb=" CA GLN E 62 " pdb=" C GLN E 62 " ideal model delta sigma weight residual 113.61 101.40 12.21 1.50e+00 4.44e-01 6.62e+01 ... (remaining 17580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 6784 17.66 - 35.33: 631 35.33 - 52.99: 105 52.99 - 70.66: 10 70.66 - 88.32: 10 Dihedral angle restraints: 7540 sinusoidal: 3030 harmonic: 4510 Sorted by residual: dihedral pdb=" CA SER A 250 " pdb=" C SER A 250 " pdb=" N ASN A 251 " pdb=" CA ASN A 251 " ideal model delta harmonic sigma weight residual -180.00 -159.02 -20.98 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA SER C 250 " pdb=" C SER C 250 " pdb=" N ASN C 251 " pdb=" CA ASN C 251 " ideal model delta harmonic sigma weight residual -180.00 -159.04 -20.96 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA SER E 250 " pdb=" C SER E 250 " pdb=" N ASN E 251 " pdb=" CA ASN E 251 " ideal model delta harmonic sigma weight residual 180.00 -159.05 -20.95 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 7537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1654 0.087 - 0.175: 251 0.175 - 0.262: 20 0.262 - 0.350: 15 0.350 - 0.437: 5 Chirality restraints: 1945 Sorted by residual: chirality pdb=" CA PHE A 119 " pdb=" N PHE A 119 " pdb=" C PHE A 119 " pdb=" CB PHE A 119 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" CA PHE C 119 " pdb=" N PHE C 119 " pdb=" C PHE C 119 " pdb=" CB PHE C 119 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.68e+00 chirality pdb=" CA PHE D 119 " pdb=" N PHE D 119 " pdb=" C PHE D 119 " pdb=" CB PHE D 119 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.68e+00 ... (remaining 1942 not shown) Planarity restraints: 2240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 206 " 0.014 2.00e-02 2.50e+03 1.50e-02 5.63e+00 pdb=" CG TRP A 206 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 206 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP A 206 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 206 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 206 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 206 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 206 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 206 " 0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP A 206 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 206 " -0.014 2.00e-02 2.50e+03 1.49e-02 5.58e+00 pdb=" CG TRP D 206 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP D 206 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP D 206 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 206 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 206 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 206 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 206 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 206 " -0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP D 206 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 206 " -0.013 2.00e-02 2.50e+03 1.49e-02 5.57e+00 pdb=" CG TRP C 206 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP C 206 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP C 206 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 206 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 206 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 206 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 206 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 206 " -0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP C 206 " 0.003 2.00e-02 2.50e+03 ... (remaining 2237 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2999 2.79 - 3.32: 10644 3.32 - 3.84: 19850 3.84 - 4.37: 23606 4.37 - 4.90: 41997 Nonbonded interactions: 99096 Sorted by model distance: nonbonded pdb=" OG SER A 84 " pdb=" OD2 ASP B 86 " model vdw 2.261 3.040 nonbonded pdb=" O SER B 221 " pdb=" OG SER B 221 " model vdw 2.290 3.040 nonbonded pdb=" O SER A 221 " pdb=" OG SER A 221 " model vdw 2.290 3.040 nonbonded pdb=" O SER C 221 " pdb=" OG SER C 221 " model vdw 2.290 3.040 nonbonded pdb=" O SER E 221 " pdb=" OG SER E 221 " model vdw 2.290 3.040 ... (remaining 99091 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.570 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 10.980 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 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 : 0.009 0.063 12910 Z= 0.397 Angle : 0.968 12.253 17585 Z= 0.560 Chirality : 0.070 0.437 1945 Planarity : 0.006 0.057 2240 Dihedral : 13.901 88.320 4630 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 0.36 % Allowed : 0.73 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.21), residues: 1525 helix: -0.17 (0.24), residues: 460 sheet: -0.05 (0.25), residues: 480 loop : -2.52 (0.22), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 141 TYR 0.022 0.003 TYR C 248 PHE 0.021 0.003 PHE A 208 TRP 0.035 0.003 TRP A 206 HIS 0.005 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00932 (12910) covalent geometry : angle 0.96773 (17585) hydrogen bonds : bond 0.07198 ( 540) hydrogen bonds : angle 5.29909 ( 1740) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 150 time to evaluate : 0.453 Fit side-chains REVERT: A 90 LYS cc_start: 0.8876 (pttm) cc_final: 0.8515 (pttm) REVERT: A 123 ARG cc_start: 0.7668 (ttm110) cc_final: 0.7361 (ttm-80) REVERT: A 176 ASP cc_start: 0.7592 (m-30) cc_final: 0.7245 (m-30) REVERT: B 86 ASP cc_start: 0.8073 (t70) cc_final: 0.7643 (t70) REVERT: B 90 LYS cc_start: 0.8862 (pttm) cc_final: 0.8647 (pttm) REVERT: C 124 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7748 (mm110) REVERT: D 86 ASP cc_start: 0.8197 (t70) cc_final: 0.7983 (t70) REVERT: D 124 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7495 (mm-40) REVERT: E 86 ASP cc_start: 0.8117 (t70) cc_final: 0.7556 (t70) REVERT: E 90 LYS cc_start: 0.8788 (pttm) cc_final: 0.8533 (pttm) REVERT: E 123 ARG cc_start: 0.7583 (ttm110) cc_final: 0.7370 (ttm-80) REVERT: E 208 PHE cc_start: 0.8357 (m-10) cc_final: 0.8092 (m-80) outliers start: 5 outliers final: 5 residues processed: 155 average time/residue: 0.1573 time to fit residues: 32.2508 Evaluate side-chains 117 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 112 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 118 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.0040 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 10.0000 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN B 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.178253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.136326 restraints weight = 12945.945| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.63 r_work: 0.3232 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12910 Z= 0.105 Angle : 0.520 5.324 17585 Z= 0.267 Chirality : 0.046 0.152 1945 Planarity : 0.004 0.039 2240 Dihedral : 4.640 17.803 1705 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.73 % Allowed : 5.89 % Favored : 93.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.21), residues: 1525 helix: 0.87 (0.24), residues: 460 sheet: 0.12 (0.25), residues: 480 loop : -2.39 (0.22), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 255 TYR 0.012 0.001 TYR D 245 PHE 0.010 0.001 PHE E 247 TRP 0.011 0.001 TRP E 206 HIS 0.001 0.000 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00226 (12910) covalent geometry : angle 0.52025 (17585) hydrogen bonds : bond 0.03370 ( 540) hydrogen bonds : angle 4.19255 ( 1740) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.455 Fit side-chains REVERT: A 176 ASP cc_start: 0.8137 (m-30) cc_final: 0.7797 (m-30) REVERT: A 252 ILE cc_start: 0.8060 (mt) cc_final: 0.7778 (pt) REVERT: B 86 ASP cc_start: 0.8623 (t70) cc_final: 0.8198 (t70) REVERT: B 114 MET cc_start: 0.7940 (mtt) cc_final: 0.7619 (mtt) REVERT: C 86 ASP cc_start: 0.8562 (t70) cc_final: 0.8334 (t70) REVERT: C 176 ASP cc_start: 0.8394 (m-30) cc_final: 0.8113 (m-30) REVERT: D 115 ASP cc_start: 0.8439 (t70) cc_final: 0.8119 (t70) REVERT: E 86 ASP cc_start: 0.8393 (t70) cc_final: 0.8186 (t70) outliers start: 10 outliers final: 8 residues processed: 130 average time/residue: 0.1494 time to fit residues: 26.2881 Evaluate side-chains 111 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain E residue 113 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 47 optimal weight: 4.9990 chunk 100 optimal weight: 0.0270 chunk 122 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 17 optimal weight: 0.0670 chunk 143 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN B 89 ASN ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.172408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.130106 restraints weight = 13211.115| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.62 r_work: 0.3222 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12910 Z= 0.153 Angle : 0.545 5.547 17585 Z= 0.280 Chirality : 0.047 0.147 1945 Planarity : 0.003 0.032 2240 Dihedral : 4.589 17.881 1695 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.45 % Allowed : 7.49 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.22), residues: 1525 helix: 1.38 (0.25), residues: 460 sheet: 0.30 (0.26), residues: 460 loop : -2.42 (0.22), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 199 TYR 0.011 0.001 TYR B 245 PHE 0.013 0.001 PHE D 119 TRP 0.017 0.001 TRP A 161 HIS 0.003 0.001 HIS E 177 Details of bonding type rmsd covalent geometry : bond 0.00371 (12910) covalent geometry : angle 0.54534 (17585) hydrogen bonds : bond 0.03713 ( 540) hydrogen bonds : angle 4.12771 ( 1740) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.453 Fit side-chains REVERT: B 86 ASP cc_start: 0.8661 (t70) cc_final: 0.8443 (t70) REVERT: B 163 ARG cc_start: 0.8080 (mmt180) cc_final: 0.7758 (mmp80) REVERT: C 86 ASP cc_start: 0.8512 (t70) cc_final: 0.8270 (t70) REVERT: E 44 THR cc_start: 0.9039 (t) cc_final: 0.8794 (m) REVERT: E 86 ASP cc_start: 0.8513 (t70) cc_final: 0.8288 (t70) outliers start: 20 outliers final: 13 residues processed: 123 average time/residue: 0.1656 time to fit residues: 26.8135 Evaluate side-chains 110 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 278 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 26 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 103 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 = 0.3938 r_free = 0.3938 target = 0.174133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.132002 restraints weight = 13069.068| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.62 r_work: 0.3213 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12910 Z= 0.157 Angle : 0.528 5.388 17585 Z= 0.272 Chirality : 0.047 0.153 1945 Planarity : 0.003 0.029 2240 Dihedral : 4.515 17.681 1695 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.60 % Allowed : 9.82 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.22), residues: 1525 helix: 1.44 (0.24), residues: 490 sheet: 0.32 (0.26), residues: 460 loop : -2.66 (0.22), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 174 TYR 0.012 0.001 TYR D 245 PHE 0.014 0.001 PHE A 247 TRP 0.018 0.001 TRP E 206 HIS 0.003 0.001 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00383 (12910) covalent geometry : angle 0.52786 (17585) hydrogen bonds : bond 0.03662 ( 540) hydrogen bonds : angle 4.07712 ( 1740) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.497 Fit side-chains REVERT: A 86 ASP cc_start: 0.8556 (t70) cc_final: 0.8224 (t70) REVERT: B 86 ASP cc_start: 0.8514 (t70) cc_final: 0.8311 (t70) REVERT: E 44 THR cc_start: 0.8966 (t) cc_final: 0.8749 (m) REVERT: E 86 ASP cc_start: 0.8338 (t70) cc_final: 0.7743 (t70) outliers start: 22 outliers final: 17 residues processed: 117 average time/residue: 0.1547 time to fit residues: 23.8612 Evaluate side-chains 115 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain E residue 278 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 59 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 64 optimal weight: 20.0000 chunk 17 optimal weight: 0.1980 chunk 8 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.176823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.134914 restraints weight = 13133.708| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.62 r_work: 0.3268 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12910 Z= 0.108 Angle : 0.480 5.215 17585 Z= 0.246 Chirality : 0.045 0.145 1945 Planarity : 0.003 0.025 2240 Dihedral : 4.266 17.272 1695 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.24 % Allowed : 10.76 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.22), residues: 1525 helix: 1.60 (0.24), residues: 490 sheet: 0.47 (0.26), residues: 455 loop : -2.59 (0.22), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 255 TYR 0.011 0.001 TYR C 245 PHE 0.012 0.001 PHE A 247 TRP 0.017 0.001 TRP A 206 HIS 0.002 0.000 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00248 (12910) covalent geometry : angle 0.48027 (17585) hydrogen bonds : bond 0.03199 ( 540) hydrogen bonds : angle 3.89225 ( 1740) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.447 Fit side-chains REVERT: A 86 ASP cc_start: 0.8581 (t70) cc_final: 0.8329 (t70) REVERT: A 265 MET cc_start: 0.7826 (ttp) cc_final: 0.7276 (ttt) REVERT: B 86 ASP cc_start: 0.8433 (t70) cc_final: 0.8232 (t70) REVERT: B 163 ARG cc_start: 0.8005 (mmt180) cc_final: 0.7757 (mmp80) REVERT: C 86 ASP cc_start: 0.8329 (t70) cc_final: 0.8052 (t70) REVERT: C 114 MET cc_start: 0.8407 (mtt) cc_final: 0.8004 (mtt) REVERT: C 137 ASN cc_start: 0.8252 (p0) cc_final: 0.7993 (p0) REVERT: D 44 THR cc_start: 0.8929 (t) cc_final: 0.8724 (m) REVERT: E 86 ASP cc_start: 0.8256 (t70) cc_final: 0.7839 (t70) outliers start: 17 outliers final: 11 residues processed: 113 average time/residue: 0.1694 time to fit residues: 25.0570 Evaluate side-chains 109 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 265 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 97 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.169820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.127475 restraints weight = 13181.556| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.62 r_work: 0.3174 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 12910 Z= 0.284 Angle : 0.625 6.848 17585 Z= 0.324 Chirality : 0.052 0.160 1945 Planarity : 0.004 0.028 2240 Dihedral : 4.947 22.383 1695 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.04 % Allowed : 10.84 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.22), residues: 1525 helix: 1.48 (0.25), residues: 490 sheet: 0.19 (0.26), residues: 460 loop : -2.74 (0.22), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 99 TYR 0.016 0.002 TYR E 261 PHE 0.016 0.002 PHE C 19 TRP 0.019 0.002 TRP B 206 HIS 0.004 0.001 HIS A 177 Details of bonding type rmsd covalent geometry : bond 0.00716 (12910) covalent geometry : angle 0.62524 (17585) hydrogen bonds : bond 0.04549 ( 540) hydrogen bonds : angle 4.21093 ( 1740) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.424 Fit side-chains REVERT: A 86 ASP cc_start: 0.8519 (t70) cc_final: 0.8196 (t70) REVERT: B 86 ASP cc_start: 0.8410 (t70) cc_final: 0.7914 (t70) REVERT: C 86 ASP cc_start: 0.8410 (t70) cc_final: 0.8135 (t70) REVERT: C 114 MET cc_start: 0.8539 (mtt) cc_final: 0.8143 (mtt) REVERT: E 86 ASP cc_start: 0.8290 (t70) cc_final: 0.8062 (t70) outliers start: 28 outliers final: 24 residues processed: 123 average time/residue: 0.1499 time to fit residues: 24.8602 Evaluate side-chains 120 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain E residue 278 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 138 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 146 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN D 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.175107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.133563 restraints weight = 13032.175| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.59 r_work: 0.3238 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12910 Z= 0.110 Angle : 0.490 5.007 17585 Z= 0.252 Chirality : 0.046 0.149 1945 Planarity : 0.003 0.024 2240 Dihedral : 4.398 21.605 1695 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.75 % Allowed : 11.64 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.22), residues: 1525 helix: 1.64 (0.24), residues: 490 sheet: 0.36 (0.26), residues: 455 loop : -2.60 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 255 TYR 0.012 0.001 TYR C 245 PHE 0.012 0.001 PHE A 247 TRP 0.016 0.001 TRP A 206 HIS 0.002 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00248 (12910) covalent geometry : angle 0.49029 (17585) hydrogen bonds : bond 0.03356 ( 540) hydrogen bonds : angle 3.94450 ( 1740) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.458 Fit side-chains REVERT: A 86 ASP cc_start: 0.8445 (t70) cc_final: 0.8121 (t70) REVERT: B 86 ASP cc_start: 0.8368 (t70) cc_final: 0.7982 (t70) REVERT: B 163 ARG cc_start: 0.8012 (mmt180) cc_final: 0.7746 (mmp80) REVERT: C 86 ASP cc_start: 0.8363 (t70) cc_final: 0.7802 (t70) REVERT: C 114 MET cc_start: 0.8460 (mtt) cc_final: 0.8058 (mtt) REVERT: C 137 ASN cc_start: 0.8247 (p0) cc_final: 0.7978 (p0) REVERT: E 86 ASP cc_start: 0.8225 (t70) cc_final: 0.8024 (t70) outliers start: 24 outliers final: 15 residues processed: 116 average time/residue: 0.1523 time to fit residues: 23.5261 Evaluate side-chains 108 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 265 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 112 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 4 optimal weight: 0.4980 chunk 76 optimal weight: 6.9990 chunk 29 optimal weight: 20.0000 chunk 131 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 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 = 0.3891 r_free = 0.3891 target = 0.169138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.127125 restraints weight = 13156.021| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.60 r_work: 0.3172 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 12910 Z= 0.278 Angle : 0.621 6.878 17585 Z= 0.322 Chirality : 0.052 0.160 1945 Planarity : 0.004 0.025 2240 Dihedral : 5.004 27.628 1695 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.04 % Allowed : 11.93 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.22), residues: 1525 helix: 1.49 (0.25), residues: 490 sheet: 0.08 (0.26), residues: 460 loop : -2.73 (0.23), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 99 TYR 0.015 0.002 TYR E 261 PHE 0.016 0.002 PHE C 19 TRP 0.022 0.002 TRP B 206 HIS 0.004 0.001 HIS A 177 Details of bonding type rmsd covalent geometry : bond 0.00703 (12910) covalent geometry : angle 0.62149 (17585) hydrogen bonds : bond 0.04560 ( 540) hydrogen bonds : angle 4.23026 ( 1740) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.510 Fit side-chains REVERT: A 86 ASP cc_start: 0.8592 (t70) cc_final: 0.8241 (t70) REVERT: A 263 ASP cc_start: 0.8138 (t70) cc_final: 0.7699 (t0) REVERT: B 86 ASP cc_start: 0.8539 (t70) cc_final: 0.8303 (t70) REVERT: C 86 ASP cc_start: 0.8601 (t70) cc_final: 0.8324 (t70) REVERT: C 114 MET cc_start: 0.8622 (mtt) cc_final: 0.8233 (mtt) REVERT: E 86 ASP cc_start: 0.8414 (t70) cc_final: 0.8171 (t70) outliers start: 28 outliers final: 26 residues processed: 119 average time/residue: 0.1474 time to fit residues: 23.7977 Evaluate side-chains 125 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain E residue 278 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 128 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 143 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 44 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 46 optimal weight: 0.0970 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.175639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.134422 restraints weight = 13005.324| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.58 r_work: 0.3261 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12910 Z= 0.102 Angle : 0.486 5.030 17585 Z= 0.250 Chirality : 0.046 0.154 1945 Planarity : 0.003 0.025 2240 Dihedral : 4.327 24.213 1695 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.60 % Allowed : 12.51 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.22), residues: 1525 helix: 1.66 (0.24), residues: 490 sheet: 0.37 (0.26), residues: 455 loop : -2.58 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 174 TYR 0.012 0.001 TYR A 245 PHE 0.011 0.001 PHE A 247 TRP 0.015 0.001 TRP C 206 HIS 0.002 0.001 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00224 (12910) covalent geometry : angle 0.48619 (17585) hydrogen bonds : bond 0.03256 ( 540) hydrogen bonds : angle 3.91549 ( 1740) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.434 Fit side-chains REVERT: A 86 ASP cc_start: 0.8402 (t70) cc_final: 0.8042 (t70) REVERT: B 163 ARG cc_start: 0.8068 (mmt180) cc_final: 0.7808 (mmp80) REVERT: C 86 ASP cc_start: 0.8408 (t70) cc_final: 0.8164 (t70) REVERT: C 114 MET cc_start: 0.8405 (mtt) cc_final: 0.7994 (mtt) REVERT: D 44 THR cc_start: 0.8925 (t) cc_final: 0.8701 (m) REVERT: E 86 ASP cc_start: 0.8213 (t70) cc_final: 0.7998 (t70) outliers start: 22 outliers final: 17 residues processed: 116 average time/residue: 0.1481 time to fit residues: 23.1648 Evaluate side-chains 108 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 265 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 45 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 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 = 0.3904 r_free = 0.3904 target = 0.170900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.129091 restraints weight = 13166.158| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.61 r_work: 0.3182 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12910 Z= 0.167 Angle : 0.532 5.095 17585 Z= 0.274 Chirality : 0.048 0.163 1945 Planarity : 0.003 0.025 2240 Dihedral : 4.551 26.052 1695 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.53 % Allowed : 12.87 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.22), residues: 1525 helix: 1.69 (0.25), residues: 490 sheet: 0.27 (0.26), residues: 460 loop : -2.64 (0.23), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 174 TYR 0.012 0.002 TYR B 248 PHE 0.013 0.001 PHE A 247 TRP 0.021 0.001 TRP B 206 HIS 0.003 0.001 HIS A 177 Details of bonding type rmsd covalent geometry : bond 0.00410 (12910) covalent geometry : angle 0.53153 (17585) hydrogen bonds : bond 0.03719 ( 540) hydrogen bonds : angle 3.98317 ( 1740) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.442 Fit side-chains REVERT: A 86 ASP cc_start: 0.8501 (t70) cc_final: 0.8161 (t70) REVERT: B 163 ARG cc_start: 0.8124 (mmt180) cc_final: 0.7849 (mmp80) REVERT: C 86 ASP cc_start: 0.8366 (t70) cc_final: 0.8103 (t70) REVERT: C 114 MET cc_start: 0.8473 (mtt) cc_final: 0.8070 (mtt) REVERT: E 86 ASP cc_start: 0.8162 (t70) cc_final: 0.7949 (t70) outliers start: 21 outliers final: 21 residues processed: 112 average time/residue: 0.1574 time to fit residues: 23.5818 Evaluate side-chains 116 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 265 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 1 optimal weight: 0.0070 chunk 10 optimal weight: 0.3980 chunk 63 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.174238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.132989 restraints weight = 13051.545| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.58 r_work: 0.3273 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12910 Z= 0.102 Angle : 0.479 5.072 17585 Z= 0.247 Chirality : 0.046 0.158 1945 Planarity : 0.003 0.025 2240 Dihedral : 4.194 23.454 1695 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.45 % Allowed : 13.16 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.22), residues: 1525 helix: 1.72 (0.24), residues: 490 sheet: 0.64 (0.28), residues: 380 loop : -2.44 (0.22), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 255 TYR 0.012 0.001 TYR A 245 PHE 0.011 0.001 PHE B 208 TRP 0.016 0.001 TRP C 206 HIS 0.002 0.001 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00231 (12910) covalent geometry : angle 0.47918 (17585) hydrogen bonds : bond 0.03152 ( 540) hydrogen bonds : angle 3.83370 ( 1740) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2611.28 seconds wall clock time: 45 minutes 20.07 seconds (2720.07 seconds total)