Starting phenix.real_space_refine on Fri Nov 15 08:19:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fab_50271/11_2024/9fab_50271_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fab_50271/11_2024/9fab_50271.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fab_50271/11_2024/9fab_50271.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fab_50271/11_2024/9fab_50271.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fab_50271/11_2024/9fab_50271_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fab_50271/11_2024/9fab_50271_trim.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 10 5.16 5 C 2770 2.51 5 N 725 2.21 5 O 900 1.98 5 H 4190 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8595 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1705 Classifications: {'peptide': 117} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 107} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, B, E, D Time building chain proxies: 4.08, per 1000 atoms: 0.47 Number of scatterers: 8595 At special positions: 0 Unit cell: (91.567, 114.681, 44.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 O 900 8.00 N 725 7.00 C 2770 6.00 H 4190 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 87 " distance=2.04 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 Links applied NAG-ASN " NAG A 201 " - " ASN A 19 " " NAG B 201 " - " ASN B 19 " " NAG C 201 " - " ASN C 19 " " NAG D 201 " - " ASN D 19 " " NAG E 201 " - " ASN E 19 " Time building additional restraints: 2.12 Conformation dependent library (CDL) restraints added in 690.0 milliseconds 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1030 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 37.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 3 through 5 removed outlier: 6.295A pdb=" N GLU B 3 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLU A 3 " --> pdb=" O LEU B 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.378A pdb=" N SER B 9 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL D 12 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N SER B 11 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N SER A 9 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL B 12 " --> pdb=" O SER A 9 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N SER A 11 " --> pdb=" O VAL B 12 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 17 through 23 removed outlier: 6.872A pdb=" N THR B 17 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ILE D 20 " --> pdb=" O THR B 17 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ASN B 19 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N CYS D 22 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR B 21 " --> pdb=" O CYS D 22 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR A 17 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ILE B 20 " --> pdb=" O THR A 17 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASN A 19 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N CYS B 22 " --> pdb=" O ASN A 19 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N THR A 21 " --> pdb=" O CYS B 22 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA A 18 " --> pdb=" O ASN C 19 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N THR C 21 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE A 20 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N SER C 23 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N CYS A 22 " --> pdb=" O SER C 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 26 through 30 removed outlier: 6.181A pdb=" N TYR B 26 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N GLU D 29 " --> pdb=" O TYR B 26 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY B 28 " --> pdb=" O GLU D 29 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N TYR A 26 " --> pdb=" O LEU B 27 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N GLU B 29 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLY A 28 " --> pdb=" O GLU B 29 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 33 through 37 removed outlier: 6.266A pdb=" N SER B 33 " --> pdb=" O TRP D 34 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N GLN D 36 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N TYR B 35 " --> pdb=" O GLN D 36 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N SER A 33 " --> pdb=" O TRP B 34 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N GLN B 36 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR A 35 " --> pdb=" O GLN B 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 44 through 52 removed outlier: 6.787A pdb=" N VAL B 44 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N ILE D 47 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL B 46 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N GLN D 49 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TYR B 48 " --> pdb=" O GLN D 49 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N SER D 51 " --> pdb=" O TYR B 48 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER B 50 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL A 44 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N ILE B 47 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL A 46 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N GLN B 49 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N TYR A 48 " --> pdb=" O GLN B 49 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N SER B 51 " --> pdb=" O TYR A 48 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N SER A 50 " --> pdb=" O SER B 51 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 72 through 75 removed outlier: 6.507A pdb=" N THR B 73 " --> pdb=" O ILE D 74 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR A 73 " --> pdb=" O ILE B 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 83 through 86 removed outlier: 6.879A pdb=" N ALA B 83 " --> pdb=" O ASP D 84 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N PHE D 86 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TYR B 85 " --> pdb=" O PHE D 86 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA A 83 " --> pdb=" O ASP B 84 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N PHE B 86 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TYR A 85 " --> pdb=" O PHE B 86 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 89 through 97 removed outlier: 7.095A pdb=" N PHE B 97 " --> pdb=" O VAL D 96 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N PHE A 97 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N TRP A 90 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N THR C 93 " --> pdb=" O TRP A 90 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHE A 92 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N VAL C 95 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER A 94 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N PHE C 97 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N VAL A 96 " --> pdb=" O PHE C 97 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TRP C 90 " --> pdb=" O ASP E 91 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N THR E 93 " --> pdb=" O TRP C 90 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N PHE C 92 " --> pdb=" O THR E 93 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL E 95 " --> pdb=" O PHE C 92 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N SER C 94 " --> pdb=" O VAL E 95 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N PHE E 97 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N VAL C 96 " --> pdb=" O PHE E 97 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 102 through 103 removed outlier: 6.183A pdb=" N LYS B 102 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LYS A 102 " --> pdb=" O LEU B 103 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 114 through 116 removed outlier: 6.315A pdb=" N VAL A 115 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL C 115 " --> pdb=" O THR E 116 " (cutoff:3.500A) 82 hydrogen bonds defined for protein. 243 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.97 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.04: 4190 1.04 - 1.24: 655 1.24 - 1.45: 1368 1.45 - 1.65: 2482 1.65 - 1.86: 10 Bond restraints: 8705 Sorted by residual: bond pdb=" CA THR A 21 " pdb=" C THR A 21 " ideal model delta sigma weight residual 1.521 1.542 -0.021 1.26e-02 6.30e+03 2.70e+00 bond pdb=" CA THR B 21 " pdb=" C THR B 21 " ideal model delta sigma weight residual 1.521 1.541 -0.021 1.26e-02 6.30e+03 2.65e+00 bond pdb=" CA THR C 21 " pdb=" C THR C 21 " ideal model delta sigma weight residual 1.521 1.541 -0.020 1.26e-02 6.30e+03 2.61e+00 bond pdb=" CA THR D 21 " pdb=" C THR D 21 " ideal model delta sigma weight residual 1.521 1.541 -0.020 1.26e-02 6.30e+03 2.60e+00 bond pdb=" CA THR E 21 " pdb=" C THR E 21 " ideal model delta sigma weight residual 1.521 1.541 -0.020 1.26e-02 6.30e+03 2.56e+00 ... (remaining 8700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 14274 1.95 - 3.89: 1141 3.89 - 5.84: 185 5.84 - 7.78: 40 7.78 - 9.73: 10 Bond angle restraints: 15650 Sorted by residual: angle pdb=" N THR B 77 " pdb=" CA THR B 77 " pdb=" C THR B 77 " ideal model delta sigma weight residual 111.07 116.38 -5.31 1.07e+00 8.73e-01 2.46e+01 angle pdb=" N THR A 77 " pdb=" CA THR A 77 " pdb=" C THR A 77 " ideal model delta sigma weight residual 111.07 116.35 -5.28 1.07e+00 8.73e-01 2.44e+01 angle pdb=" N THR C 77 " pdb=" CA THR C 77 " pdb=" C THR C 77 " ideal model delta sigma weight residual 111.07 116.34 -5.27 1.07e+00 8.73e-01 2.43e+01 angle pdb=" N THR E 77 " pdb=" CA THR E 77 " pdb=" C THR E 77 " ideal model delta sigma weight residual 111.07 116.31 -5.24 1.07e+00 8.73e-01 2.40e+01 angle pdb=" N THR D 77 " pdb=" CA THR D 77 " pdb=" C THR D 77 " ideal model delta sigma weight residual 111.07 116.30 -5.23 1.07e+00 8.73e-01 2.39e+01 ... (remaining 15645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.68: 3759 14.68 - 29.37: 309 29.37 - 44.05: 90 44.05 - 58.73: 95 58.73 - 73.42: 30 Dihedral angle restraints: 4283 sinusoidal: 2363 harmonic: 1920 Sorted by residual: dihedral pdb=" CA THR A 69 " pdb=" C THR A 69 " pdb=" N ALA A 70 " pdb=" CA ALA A 70 " ideal model delta harmonic sigma weight residual -180.00 -162.76 -17.24 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA THR C 69 " pdb=" C THR C 69 " pdb=" N ALA C 70 " pdb=" CA ALA C 70 " ideal model delta harmonic sigma weight residual -180.00 -162.76 -17.24 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA THR D 69 " pdb=" C THR D 69 " pdb=" N ALA D 70 " pdb=" CA ALA D 70 " ideal model delta harmonic sigma weight residual -180.00 -162.77 -17.23 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 4280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 309 0.038 - 0.076: 209 0.076 - 0.113: 94 0.113 - 0.151: 58 0.151 - 0.189: 30 Chirality restraints: 700 Sorted by residual: chirality pdb=" C1 NAG D 201 " pdb=" ND2 ASN D 19 " pdb=" C2 NAG D 201 " pdb=" O5 NAG D 201 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" C1 NAG C 201 " pdb=" ND2 ASN C 19 " pdb=" C2 NAG C 201 " pdb=" O5 NAG C 201 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" C1 NAG A 201 " pdb=" ND2 ASN A 19 " pdb=" C2 NAG A 201 " pdb=" O5 NAG A 201 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.76e-01 ... (remaining 697 not shown) Planarity restraints: 1335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 90 " -0.005 2.00e-02 2.50e+03 1.78e-02 1.27e+01 pdb=" CG TRP E 90 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP E 90 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP E 90 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP E 90 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 TRP E 90 " 0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP E 90 " -0.017 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 90 " 0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 90 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP E 90 " 0.015 2.00e-02 2.50e+03 pdb=" HD1 TRP E 90 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 TRP E 90 " -0.022 2.00e-02 2.50e+03 pdb=" HE3 TRP E 90 " 0.011 2.00e-02 2.50e+03 pdb=" HZ2 TRP E 90 " -0.022 2.00e-02 2.50e+03 pdb=" HZ3 TRP E 90 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP E 90 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 90 " -0.005 2.00e-02 2.50e+03 1.78e-02 1.26e+01 pdb=" CG TRP C 90 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP C 90 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP C 90 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 90 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 TRP C 90 " 0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP C 90 " -0.017 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 90 " 0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 90 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP C 90 " 0.014 2.00e-02 2.50e+03 pdb=" HD1 TRP C 90 " 0.013 2.00e-02 2.50e+03 pdb=" HE1 TRP C 90 " -0.022 2.00e-02 2.50e+03 pdb=" HE3 TRP C 90 " 0.011 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 90 " -0.022 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 90 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP C 90 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 90 " -0.005 2.00e-02 2.50e+03 1.77e-02 1.26e+01 pdb=" CG TRP D 90 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP D 90 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP D 90 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP D 90 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 TRP D 90 " 0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP D 90 " -0.017 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 90 " 0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 90 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP D 90 " 0.014 2.00e-02 2.50e+03 pdb=" HD1 TRP D 90 " 0.013 2.00e-02 2.50e+03 pdb=" HE1 TRP D 90 " -0.022 2.00e-02 2.50e+03 pdb=" HE3 TRP D 90 " 0.010 2.00e-02 2.50e+03 pdb=" HZ2 TRP D 90 " -0.022 2.00e-02 2.50e+03 pdb=" HZ3 TRP D 90 " -0.000 2.00e-02 2.50e+03 pdb=" HH2 TRP D 90 " -0.020 2.00e-02 2.50e+03 ... (remaining 1332 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.38: 3589 2.38 - 2.93: 18474 2.93 - 3.49: 19251 3.49 - 4.04: 28985 4.04 - 4.60: 40178 Nonbonded interactions: 110477 Sorted by model distance: nonbonded pdb=" O THR B 104 " pdb=" HG1 THR B 104 " model vdw 1.824 2.450 nonbonded pdb=" O THR D 104 " pdb=" HG1 THR D 104 " model vdw 1.825 2.450 nonbonded pdb=" O THR A 104 " pdb=" HG1 THR A 104 " model vdw 1.825 2.450 nonbonded pdb=" O THR C 104 " pdb=" HG1 THR C 104 " model vdw 1.825 2.450 nonbonded pdb=" O THR E 104 " pdb=" HG1 THR E 104 " model vdw 1.825 2.450 ... (remaining 110472 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.500 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: 0.160 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.740 Find NCS groups from input model: 0.240 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: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 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 : 0.010 0.058 4515 Z= 0.690 Angle : 1.566 9.728 6160 Z= 0.923 Chirality : 0.070 0.189 700 Planarity : 0.007 0.051 795 Dihedral : 11.241 73.418 1675 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.50 (0.24), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.18), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.009 TRP A 90 PHE 0.022 0.005 PHE A 2 TYR 0.040 0.008 TYR B 85 ARG 0.005 0.002 ARG E 60 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.8487 (mt) cc_final: 0.8181 (mt) REVERT: A 78 GLN cc_start: 0.7987 (tt0) cc_final: 0.7777 (tt0) REVERT: A 110 LYS cc_start: 0.7916 (tptm) cc_final: 0.7643 (mptt) REVERT: A 115 VAL cc_start: 0.6206 (t) cc_final: 0.5965 (t) REVERT: C 88 GLN cc_start: 0.7501 (tm-30) cc_final: 0.7249 (tm-30) REVERT: C 110 LYS cc_start: 0.8031 (tptm) cc_final: 0.7584 (mptt) REVERT: D 38 LYS cc_start: 0.8618 (mtmt) cc_final: 0.8316 (mmtt) REVERT: D 78 GLN cc_start: 0.8016 (tt0) cc_final: 0.7484 (tp-100) REVERT: E 36 GLN cc_start: 0.7393 (tt0) cc_final: 0.7024 (pm20) REVERT: E 61 PHE cc_start: 0.5374 (p90) cc_final: 0.5058 (t80) REVERT: E 72 LEU cc_start: 0.8601 (tp) cc_final: 0.8397 (pp) REVERT: E 86 PHE cc_start: 0.6696 (m-80) cc_final: 0.6025 (p90) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.3153 time to fit residues: 54.9516 Evaluate side-chains 66 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4515 Z= 0.269 Angle : 0.721 4.946 6160 Z= 0.389 Chirality : 0.049 0.217 700 Planarity : 0.005 0.040 795 Dihedral : 6.109 19.381 725 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.68 % Allowed : 9.07 % Favored : 88.25 % 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: -4.59 (0.22), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.17), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 34 PHE 0.017 0.002 PHE C 2 TYR 0.029 0.003 TYR A 31 ARG 0.004 0.001 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.7969 (tptm) cc_final: 0.7667 (mptt) REVERT: C 110 LYS cc_start: 0.7999 (tptm) cc_final: 0.7570 (mptt) REVERT: D 38 LYS cc_start: 0.8594 (mtmt) cc_final: 0.7993 (mmtt) REVERT: E 36 GLN cc_start: 0.7854 (tt0) cc_final: 0.7600 (pm20) REVERT: E 86 PHE cc_start: 0.6475 (m-80) cc_final: 0.5759 (p90) outliers start: 13 outliers final: 8 residues processed: 90 average time/residue: 0.2847 time to fit residues: 33.7951 Evaluate side-chains 65 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 88 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 54 optimal weight: 0.4980 chunk 44 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 40 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 68 ASN A 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4515 Z= 0.165 Angle : 0.573 3.935 6160 Z= 0.302 Chirality : 0.046 0.189 700 Planarity : 0.005 0.039 795 Dihedral : 5.242 20.753 725 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.06 % Allowed : 10.72 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.64 (0.22), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.17), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 34 PHE 0.011 0.001 PHE A 2 TYR 0.011 0.001 TYR A 31 ARG 0.002 0.000 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: A 110 LYS cc_start: 0.7854 (tptm) cc_final: 0.7589 (mptt) REVERT: B 38 LYS cc_start: 0.8738 (mtpp) cc_final: 0.8487 (mtpp) REVERT: C 110 LYS cc_start: 0.7931 (tptm) cc_final: 0.7597 (mptt) REVERT: D 2 PHE cc_start: 0.3231 (t80) cc_final: 0.3003 (t80) REVERT: D 36 GLN cc_start: 0.8141 (tt0) cc_final: 0.7845 (tt0) REVERT: D 38 LYS cc_start: 0.8513 (mtmt) cc_final: 0.8136 (mmtt) REVERT: E 86 PHE cc_start: 0.6256 (m-80) cc_final: 0.5645 (p90) outliers start: 10 outliers final: 7 residues processed: 77 average time/residue: 0.2729 time to fit residues: 28.0100 Evaluate side-chains 68 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain D residue 61 PHE Chi-restraints excluded: chain D residue 87 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 5 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 50 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN D 41 GLN D 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4515 Z= 0.179 Angle : 0.539 3.844 6160 Z= 0.284 Chirality : 0.046 0.180 700 Planarity : 0.005 0.038 795 Dihedral : 5.415 21.507 725 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.86 % Allowed : 11.13 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.70 (0.22), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.57 (0.17), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 34 PHE 0.009 0.001 PHE B 61 TYR 0.009 0.001 TYR C 85 ARG 0.001 0.000 ARG E 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.7891 (tptm) cc_final: 0.7635 (mptt) REVERT: C 110 LYS cc_start: 0.7927 (tptm) cc_final: 0.7601 (mptt) REVERT: D 38 LYS cc_start: 0.8515 (mtmt) cc_final: 0.8048 (mmtt) REVERT: E 86 PHE cc_start: 0.6432 (m-80) cc_final: 0.5601 (p90) outliers start: 9 outliers final: 9 residues processed: 67 average time/residue: 0.2914 time to fit residues: 25.9477 Evaluate side-chains 66 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain D residue 61 PHE Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain E residue 87 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 GLN E 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 4515 Z= 0.419 Angle : 0.723 4.352 6160 Z= 0.390 Chirality : 0.049 0.205 700 Planarity : 0.006 0.051 795 Dihedral : 8.194 49.518 725 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 3.51 % Allowed : 11.75 % Favored : 84.74 % 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: -5.31 (0.22), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.04 (0.17), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 90 PHE 0.012 0.002 PHE B 61 TYR 0.020 0.003 TYR C 85 ARG 0.006 0.001 ARG D 60 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.676 Fit side-chains REVERT: C 110 LYS cc_start: 0.8000 (tptm) cc_final: 0.7683 (mptt) REVERT: D 38 LYS cc_start: 0.8645 (mtmt) cc_final: 0.8257 (mmtt) REVERT: E 86 PHE cc_start: 0.6609 (m-80) cc_final: 0.5520 (p90) outliers start: 17 outliers final: 16 residues processed: 59 average time/residue: 0.3304 time to fit residues: 25.3515 Evaluate side-chains 64 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 PHE Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 61 PHE Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain E residue 87 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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: 0.7063 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4515 Z= 0.345 Angle : 0.661 4.867 6160 Z= 0.352 Chirality : 0.049 0.216 700 Planarity : 0.006 0.053 795 Dihedral : 7.498 43.501 725 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 3.09 % Allowed : 13.40 % Favored : 83.51 % 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: -5.51 (0.22), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.19 (0.17), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 90 PHE 0.009 0.002 PHE B 61 TYR 0.016 0.002 TYR C 85 ARG 0.004 0.000 ARG D 60 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.759 Fit side-chains REVERT: C 110 LYS cc_start: 0.8099 (tptm) cc_final: 0.7715 (mptt) REVERT: D 38 LYS cc_start: 0.8639 (mtmt) cc_final: 0.8199 (mmtt) REVERT: D 61 PHE cc_start: 0.6983 (OUTLIER) cc_final: 0.6654 (p90) REVERT: E 86 PHE cc_start: 0.6666 (m-80) cc_final: 0.5382 (p90) REVERT: E 88 GLN cc_start: 0.6481 (pp30) cc_final: 0.6112 (tm-30) outliers start: 15 outliers final: 14 residues processed: 61 average time/residue: 0.3216 time to fit residues: 25.6276 Evaluate side-chains 64 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 PHE Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain D residue 61 PHE Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 87 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4515 Z= 0.236 Angle : 0.581 4.499 6160 Z= 0.306 Chirality : 0.047 0.187 700 Planarity : 0.005 0.048 795 Dihedral : 6.938 38.814 725 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.43 % Favored : 89.57 % Rotamer: Outliers : 3.09 % Allowed : 14.64 % Favored : 82.27 % 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: -5.47 (0.22), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.16 (0.17), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 90 PHE 0.008 0.001 PHE B 2 TYR 0.012 0.002 TYR C 85 ARG 0.002 0.000 ARG D 60 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.626 Fit side-chains REVERT: A 88 GLN cc_start: 0.7537 (tm-30) cc_final: 0.7331 (tm-30) REVERT: C 110 LYS cc_start: 0.8071 (tptm) cc_final: 0.7670 (mptt) REVERT: D 38 LYS cc_start: 0.8563 (mtmt) cc_final: 0.8181 (mmtt) REVERT: D 61 PHE cc_start: 0.7022 (OUTLIER) cc_final: 0.6522 (p90) REVERT: E 86 PHE cc_start: 0.6493 (m-80) cc_final: 0.5285 (p90) outliers start: 15 outliers final: 12 residues processed: 59 average time/residue: 0.3413 time to fit residues: 25.5938 Evaluate side-chains 58 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 PHE Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain D residue 61 PHE Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 87 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.5615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4515 Z= 0.175 Angle : 0.535 4.004 6160 Z= 0.278 Chirality : 0.046 0.164 700 Planarity : 0.005 0.044 795 Dihedral : 6.254 33.125 725 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 2.47 % Allowed : 14.85 % Favored : 82.68 % 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: -5.36 (0.22), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.08 (0.17), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 90 PHE 0.006 0.001 PHE D 61 TYR 0.009 0.001 TYR C 85 ARG 0.001 0.000 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.658 Fit side-chains REVERT: C 110 LYS cc_start: 0.8040 (tptm) cc_final: 0.7708 (mptt) REVERT: D 38 LYS cc_start: 0.8539 (mtmt) cc_final: 0.8119 (mmtt) REVERT: D 61 PHE cc_start: 0.6937 (OUTLIER) cc_final: 0.6507 (p90) REVERT: E 86 PHE cc_start: 0.6441 (m-80) cc_final: 0.5158 (p90) outliers start: 12 outliers final: 11 residues processed: 58 average time/residue: 0.2932 time to fit residues: 22.5186 Evaluate side-chains 58 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 PHE Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 61 PHE Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 87 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.5768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4515 Z= 0.231 Angle : 0.568 4.276 6160 Z= 0.298 Chirality : 0.046 0.174 700 Planarity : 0.005 0.045 795 Dihedral : 6.763 38.312 725 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 3.30 % Allowed : 14.43 % Favored : 82.27 % 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: -5.40 (0.23), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.11 (0.17), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 34 PHE 0.011 0.001 PHE C 86 TYR 0.012 0.002 TYR A 85 ARG 0.001 0.000 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.588 Fit side-chains REVERT: A 72 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8121 (tp) REVERT: C 110 LYS cc_start: 0.8031 (tptm) cc_final: 0.7650 (mptt) REVERT: D 38 LYS cc_start: 0.8610 (mtmt) cc_final: 0.8225 (mmtt) REVERT: D 61 PHE cc_start: 0.6979 (OUTLIER) cc_final: 0.6645 (p90) REVERT: E 86 PHE cc_start: 0.6494 (m-80) cc_final: 0.5189 (p90) outliers start: 16 outliers final: 13 residues processed: 58 average time/residue: 0.2950 time to fit residues: 22.7126 Evaluate side-chains 60 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 61 PHE Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 87 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 chunk 54 optimal weight: 0.8980 chunk 50 optimal weight: 8.9990 chunk 43 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.5810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4515 Z= 0.158 Angle : 0.523 4.161 6160 Z= 0.270 Chirality : 0.045 0.152 700 Planarity : 0.005 0.041 795 Dihedral : 5.909 30.649 725 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 2.68 % Allowed : 14.64 % Favored : 82.68 % 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: -5.28 (0.23), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.02 (0.17), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 34 PHE 0.009 0.001 PHE C 86 TYR 0.007 0.001 TYR C 85 ARG 0.001 0.000 ARG A 60 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.532 Fit side-chains REVERT: C 110 LYS cc_start: 0.8017 (tptm) cc_final: 0.7663 (mptt) REVERT: D 38 LYS cc_start: 0.8557 (mtmt) cc_final: 0.8130 (mmtt) REVERT: D 61 PHE cc_start: 0.6875 (OUTLIER) cc_final: 0.6440 (p90) REVERT: E 86 PHE cc_start: 0.6466 (m-80) cc_final: 0.5166 (p90) outliers start: 13 outliers final: 10 residues processed: 55 average time/residue: 0.2959 time to fit residues: 21.5496 Evaluate side-chains 59 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 61 PHE Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain E residue 87 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** 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 = 0.4485 r_free = 0.4485 target = 0.151074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.134218 restraints weight = 25050.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.138465 restraints weight = 11044.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.141077 restraints weight = 6082.843| |-----------------------------------------------------------------------------| r_work (final): 0.4362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.5874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4515 Z= 0.185 Angle : 0.532 4.179 6160 Z= 0.276 Chirality : 0.045 0.157 700 Planarity : 0.005 0.041 795 Dihedral : 6.145 33.725 725 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 2.89 % Allowed : 14.64 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.27 (0.23), residues: 575 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.01 (0.18), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 34 PHE 0.007 0.001 PHE C 86 TYR 0.011 0.001 TYR C 85 ARG 0.001 0.000 ARG A 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2690.48 seconds wall clock time: 48 minutes 41.66 seconds (2921.66 seconds total)