Starting phenix.real_space_refine on Mon Dec 30 06:17:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d67_27219/12_2024/8d67_27219_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d67_27219/12_2024/8d67_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_27219/12_2024/8d67_27219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d67_27219/12_2024/8d67_27219.map" model { file = "/net/cci-nas-00/data/ceres_data/8d67_27219/12_2024/8d67_27219_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d67_27219/12_2024/8d67_27219_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: C, B, E, D Time building chain proxies: 5.41, per 1000 atoms: 0.43 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: 2.91 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.38 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: 3.63 Time building geometry restraints manager: 3.39 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: 0.00 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: 0.010 Normalize map: mean=0, sd=1: 0.370 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 27.460 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.930 ------------------------------------------------------------------------------- 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= 0.593 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 : 6.52 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 (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: -1.52 (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 TRP 0.035 0.003 TRP A 206 HIS 0.005 0.001 HIS D 177 PHE 0.021 0.003 PHE A 208 TYR 0.022 0.003 TYR C 248 ARG 0.004 0.001 ARG B 141 *********************** 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 : 1.450 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: 0.7360 (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: 0.7369 (ttm-80) REVERT: E 208 PHE cc_start: 0.8357 (m-10) cc_final: 0.8097 (m-80) outliers start: 5 outliers final: 5 residues processed: 155 average time/residue: 0.3440 time to fit residues: 71.1863 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 : 1.520 ------------------------------------------------------------------------------- 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 126 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 87 optimal weight: 20.0000 chunk 136 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12910 Z= 0.205 Angle : 0.556 6.283 17585 Z= 0.285 Chirality : 0.047 0.150 1945 Planarity : 0.004 0.040 2240 Dihedral : 4.791 17.580 1705 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.73 % Allowed : 5.96 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.21), residues: 1525 helix: 0.86 (0.25), residues: 460 sheet: 0.33 (0.25), residues: 455 loop : -2.52 (0.21), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 206 HIS 0.002 0.001 HIS C 177 PHE 0.015 0.001 PHE E 119 TYR 0.011 0.001 TYR D 245 ARG 0.002 0.000 ARG C 65 *********************** 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 121 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 1.321 Fit side-chains REVERT: A 252 ILE cc_start: 0.8150 (mt) cc_final: 0.7811 (pt) REVERT: B 114 MET cc_start: 0.7674 (mtt) cc_final: 0.7333 (mtt) REVERT: D 115 ASP cc_start: 0.8261 (t70) cc_final: 0.7914 (t70) outliers start: 10 outliers final: 8 residues processed: 112 average time/residue: 0.3781 time to fit residues: 56.2876 Evaluate side-chains 108 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 1.564 ------------------------------------------------------------------------------- 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 75 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 92 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN B 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12910 Z= 0.177 Angle : 0.510 5.314 17585 Z= 0.260 Chirality : 0.046 0.143 1945 Planarity : 0.003 0.032 2240 Dihedral : 4.403 17.145 1695 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.38 % Allowed : 8.00 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.53 (0.22), residues: 1525 helix: 1.43 (0.25), residues: 460 sheet: 0.34 (0.25), residues: 460 loop : -2.42 (0.22), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 206 HIS 0.002 0.000 HIS A 177 PHE 0.013 0.001 PHE A 247 TYR 0.011 0.001 TYR C 245 ARG 0.002 0.000 ARG C 255 *********************** 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 120 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 1.391 Fit side-chains REVERT: A 174 ARG cc_start: 0.8112 (tpp80) cc_final: 0.7870 (tpp80) REVERT: A 252 ILE cc_start: 0.8109 (mt) cc_final: 0.7805 (pt) REVERT: B 114 MET cc_start: 0.7622 (mtt) cc_final: 0.7385 (mtt) REVERT: B 174 ARG cc_start: 0.7982 (tpp80) cc_final: 0.7664 (tpp-160) REVERT: C 114 MET cc_start: 0.8157 (mtt) cc_final: 0.7744 (mtt) outliers start: 19 outliers final: 9 residues processed: 108 average time/residue: 0.3999 time to fit residues: 56.4333 Evaluate side-chains 109 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 1.376 ------------------------------------------------------------------------------- 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 265 MET Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain D residue 265 MET 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 134 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 144 optimal weight: 9.9990 chunk 71 optimal weight: 0.6980 chunk 129 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1598 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= 0.226 Angle : 0.523 5.335 17585 Z= 0.269 Chirality : 0.047 0.153 1945 Planarity : 0.003 0.028 2240 Dihedral : 4.443 17.584 1695 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.38 % Allowed : 9.67 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.22), residues: 1525 helix: 1.49 (0.24), residues: 490 sheet: 0.36 (0.25), residues: 460 loop : -2.64 (0.23), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 206 HIS 0.003 0.001 HIS A 177 PHE 0.013 0.001 PHE A 247 TYR 0.011 0.001 TYR D 245 ARG 0.002 0.000 ARG C 141 *********************** 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 132 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 1.410 Fit side-chains REVERT: A 59 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8310 (mm-30) REVERT: A 174 ARG cc_start: 0.8150 (tpp80) cc_final: 0.7877 (tpp80) REVERT: C 114 MET cc_start: 0.8244 (mtt) cc_final: 0.7819 (mtt) outliers start: 19 outliers final: 16 residues processed: 123 average time/residue: 0.3777 time to fit residues: 61.3630 Evaluate side-chains 111 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 1.391 ------------------------------------------------------------------------------- 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 60 ASN 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 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 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 120 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 123 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 0 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12910 Z= 0.267 Angle : 0.534 5.261 17585 Z= 0.275 Chirality : 0.047 0.148 1945 Planarity : 0.003 0.026 2240 Dihedral : 4.549 20.566 1695 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 1.53 % Allowed : 10.76 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.22), residues: 1525 helix: 1.56 (0.25), residues: 490 sheet: 0.29 (0.26), residues: 460 loop : -2.67 (0.22), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 206 HIS 0.003 0.001 HIS B 177 PHE 0.013 0.001 PHE A 247 TYR 0.011 0.002 TYR E 245 ARG 0.002 0.000 ARG A 141 *********************** 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: 21 poor density : 100 time to evaluate : 1.278 Fit side-chains REVERT: A 59 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8309 (mm-30) REVERT: A 174 ARG cc_start: 0.8092 (tpp80) cc_final: 0.7671 (tpp-160) REVERT: C 114 MET cc_start: 0.8278 (mtt) cc_final: 0.7847 (mtt) REVERT: E 90 LYS cc_start: 0.8637 (pttm) cc_final: 0.8432 (pttm) outliers start: 21 outliers final: 15 residues processed: 114 average time/residue: 0.3732 time to fit residues: 56.2307 Evaluate side-chains 109 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 1.487 ------------------------------------------------------------------------------- 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 60 ASN 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 265 MET Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 242 VAL 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 48 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 12910 Z= 0.394 Angle : 0.599 6.330 17585 Z= 0.311 Chirality : 0.050 0.156 1945 Planarity : 0.004 0.028 2240 Dihedral : 4.922 24.589 1695 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.55 % Allowed : 10.47 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.22), residues: 1525 helix: 1.47 (0.25), residues: 490 sheet: 0.17 (0.26), residues: 460 loop : -2.74 (0.22), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 206 HIS 0.004 0.001 HIS E 177 PHE 0.014 0.002 PHE C 19 TYR 0.016 0.002 TYR E 261 ARG 0.003 0.001 ARG C 141 *********************** 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 135 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 1.424 Fit side-chains REVERT: A 174 ARG cc_start: 0.8076 (tpp80) cc_final: 0.7826 (tpp80) REVERT: A 263 ASP cc_start: 0.7555 (t70) cc_final: 0.7336 (t0) REVERT: C 114 MET cc_start: 0.8341 (mtt) cc_final: 0.7924 (mtt) REVERT: E 90 LYS cc_start: 0.8723 (pttm) cc_final: 0.8522 (pttm) outliers start: 35 outliers final: 30 residues processed: 123 average time/residue: 0.3594 time to fit residues: 59.2377 Evaluate side-chains 123 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 118 LEU 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 36 ASP Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 118 LEU 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 118 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 259 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 113 ASP 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 16 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 chunk 144 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12910 Z= 0.171 Angle : 0.494 5.052 17585 Z= 0.254 Chirality : 0.046 0.149 1945 Planarity : 0.003 0.024 2240 Dihedral : 4.417 23.107 1695 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.18 % Allowed : 11.27 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.22), residues: 1525 helix: 1.59 (0.24), residues: 490 sheet: 0.35 (0.26), residues: 455 loop : -2.64 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 206 HIS 0.003 0.001 HIS C 177 PHE 0.011 0.001 PHE E 247 TYR 0.012 0.001 TYR D 245 ARG 0.002 0.000 ARG A 255 *********************** 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 127 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 1.255 Fit side-chains REVERT: A 59 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8283 (mm-30) REVERT: C 114 MET cc_start: 0.8220 (mtt) cc_final: 0.7785 (mtt) outliers start: 30 outliers final: 20 residues processed: 119 average time/residue: 0.3480 time to fit residues: 55.5388 Evaluate side-chains 113 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 145 ILE 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 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 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 Chi-restraints excluded: chain E residue 278 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 28 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2141 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= 0.145 Angle : 0.477 5.082 17585 Z= 0.245 Chirality : 0.045 0.157 1945 Planarity : 0.003 0.024 2240 Dihedral : 4.163 20.716 1695 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.75 % Allowed : 12.00 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.22), residues: 1525 helix: 1.68 (0.24), residues: 490 sheet: 0.49 (0.26), residues: 455 loop : -2.56 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 206 HIS 0.002 0.000 HIS E 177 PHE 0.011 0.001 PHE A 247 TYR 0.011 0.001 TYR E 245 ARG 0.002 0.000 ARG E 255 *********************** 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 126 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 1.299 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8257 (mm-30) REVERT: A 174 ARG cc_start: 0.8165 (tpp80) cc_final: 0.7937 (tpp80) REVERT: C 114 MET cc_start: 0.8188 (mtt) cc_final: 0.7741 (mtt) outliers start: 24 outliers final: 20 residues processed: 117 average time/residue: 0.3486 time to fit residues: 54.2133 Evaluate side-chains 115 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 145 ILE 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 118 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 146 GLN 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 252 ILE Chi-restraints excluded: chain C residue 265 MET 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 113 ASP Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 265 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 88 optimal weight: 20.0000 chunk 142 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12910 Z= 0.207 Angle : 0.502 6.707 17585 Z= 0.258 Chirality : 0.047 0.152 1945 Planarity : 0.003 0.025 2240 Dihedral : 4.283 22.390 1695 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.75 % Allowed : 12.51 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.22), residues: 1525 helix: 1.69 (0.24), residues: 490 sheet: 0.48 (0.26), residues: 455 loop : -2.58 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 206 HIS 0.002 0.001 HIS A 177 PHE 0.013 0.001 PHE A 247 TYR 0.011 0.001 TYR E 245 ARG 0.002 0.000 ARG D 163 *********************** 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 117 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 1.414 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8275 (mm-30) REVERT: C 114 MET cc_start: 0.8213 (mtt) cc_final: 0.7775 (mtt) outliers start: 24 outliers final: 24 residues processed: 110 average time/residue: 0.3622 time to fit residues: 53.5440 Evaluate side-chains 117 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 145 ILE 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 118 LEU 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 252 ILE Chi-restraints excluded: chain C residue 265 MET 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 113 ASP 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 67 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 chunk 118 optimal weight: 20.0000 chunk 12 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 126 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12910 Z= 0.158 Angle : 0.478 6.742 17585 Z= 0.245 Chirality : 0.046 0.152 1945 Planarity : 0.003 0.026 2240 Dihedral : 4.129 21.875 1695 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.82 % Allowed : 12.44 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.22), residues: 1525 helix: 1.72 (0.24), residues: 490 sheet: 0.57 (0.26), residues: 455 loop : -2.54 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 206 HIS 0.002 0.001 HIS A 177 PHE 0.016 0.001 PHE B 208 TYR 0.013 0.001 TYR B 248 ARG 0.002 0.000 ARG A 174 ********************** 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: 25 poor density : 96 time to evaluate : 1.408 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8344 (mm-30) REVERT: C 114 MET cc_start: 0.8189 (mtt) cc_final: 0.7748 (mtt) REVERT: D 144 ASP cc_start: 0.8257 (p0) cc_final: 0.7864 (p0) outliers start: 25 outliers final: 23 residues processed: 113 average time/residue: 0.3620 time to fit residues: 54.4725 Evaluate side-chains 117 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 145 ILE 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 118 LEU 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 252 ILE Chi-restraints excluded: chain C residue 265 MET 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 109 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3940 r_free = 0.3940 target = 0.174503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.132938 restraints weight = 12998.995| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.60 r_work: 0.3241 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12910 Z= 0.203 Angle : 0.498 6.244 17585 Z= 0.256 Chirality : 0.047 0.156 1945 Planarity : 0.003 0.033 2240 Dihedral : 4.255 23.543 1695 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.75 % Allowed : 12.65 % 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 (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: -0.24 (0.22), residues: 1525 helix: 1.76 (0.25), residues: 490 sheet: 0.54 (0.26), residues: 455 loop : -2.57 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 206 HIS 0.002 0.001 HIS A 177 PHE 0.012 0.001 PHE A 247 TYR 0.011 0.001 TYR E 245 ARG 0.009 0.000 ARG B 174 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2334.40 seconds wall clock time: 43 minutes 22.85 seconds (2602.85 seconds total)