Starting phenix.real_space_refine on Thu Mar 6 01:05:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pkg_17738/03_2025/8pkg_17738.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pkg_17738/03_2025/8pkg_17738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pkg_17738/03_2025/8pkg_17738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pkg_17738/03_2025/8pkg_17738.map" model { file = "/net/cci-nas-00/data/ceres_data/8pkg_17738/03_2025/8pkg_17738.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pkg_17738/03_2025/8pkg_17738.cif" } resolution = 2.99 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: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2796 2.51 5 N 708 2.21 5 O 804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4314 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 2.11, per 1000 atoms: 0.49 Number of scatterers: 4314 At special positions: 0 Unit cell: (78, 82.16, 46.8, 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 6 16.00 O 804 8.00 N 708 7.00 C 2796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 522.7 milliseconds 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1044 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 45.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 26 removed outlier: 6.331A pdb=" N ALA A 25 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA B 25 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA C 25 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA D 25 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA E 25 " --> pdb=" O ILE F 26 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 29 through 34 Processing sheet with id=AA5, first strand: chain 'A' and resid 59 through 65 removed outlier: 6.566A pdb=" N THR A 60 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N GLU B 63 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N GLU A 62 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL B 65 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N PHE A 64 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR B 60 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N GLU C 63 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N GLU B 62 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL C 65 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N PHE B 64 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR C 60 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N GLU D 63 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N GLU C 62 " --> pdb=" O GLU D 63 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL D 65 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N PHE C 64 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR D 60 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N GLU E 63 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N GLU D 62 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL E 65 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N PHE D 64 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR E 60 " --> pdb=" O GLU F 61 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N GLU F 63 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N GLU E 62 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL F 65 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N PHE E 64 " --> pdb=" O VAL F 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 71 through 80 removed outlier: 6.759A pdb=" N THR A 75 " --> pdb=" O ASP B 74 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS B 76 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N SER A 77 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR B 78 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR B 75 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS C 76 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N SER B 77 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR C 78 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR C 75 " --> pdb=" O ASP D 74 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS D 76 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N SER C 77 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR D 78 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR D 75 " --> pdb=" O ASP E 74 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS E 76 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N SER D 77 " --> pdb=" O LYS E 76 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR E 78 " --> pdb=" O SER D 77 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR E 75 " --> pdb=" O ASP F 74 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LYS F 76 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N SER E 77 " --> pdb=" O LYS F 76 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR F 78 " --> pdb=" O SER E 77 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 92 through 99 removed outlier: 6.478A pdb=" N VAL A 93 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N THR B 96 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE A 95 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ASN B 98 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA A 97 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL B 93 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N THR C 96 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE B 95 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ASN C 98 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA B 97 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL C 93 " --> pdb=" O VAL D 94 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N THR D 96 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE C 95 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ASN D 98 " --> pdb=" O PHE C 95 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA C 97 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL D 93 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N THR E 96 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE D 95 " --> pdb=" O THR E 96 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ASN E 98 " --> pdb=" O PHE D 95 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA D 97 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL E 93 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N THR F 96 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE E 95 " --> pdb=" O THR F 96 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ASN F 98 " --> pdb=" O PHE E 95 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA E 97 " --> pdb=" O ASN F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 104 through 106 removed outlier: 6.800A pdb=" N TYR A 105 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TYR B 105 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TYR C 105 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TYR D 105 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TYR E 105 " --> pdb=" O THR F 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AB1, first strand: chain 'A' and resid 114 through 115 Processing sheet with id=AB2, first strand: chain 'A' and resid 118 through 122 removed outlier: 5.720A pdb=" N THR A 118 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL B 121 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA A 120 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N THR B 118 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL C 121 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA B 120 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N THR C 118 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL D 121 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA C 120 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N THR D 118 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL E 121 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA D 120 " --> pdb=" O VAL E 121 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N THR E 118 " --> pdb=" O THR F 119 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL F 121 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA E 120 " --> pdb=" O VAL F 121 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 90 hydrogen bonds defined for protein. 270 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.10 Time building geometry restraints manager: 1.25 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: 778 1.33 - 1.45: 1124 1.45 - 1.57: 2502 1.57 - 1.69: 0 1.69 - 1.81: 12 Bond restraints: 4416 Sorted by residual: bond pdb=" N SER C 85 " pdb=" CA SER C 85 " ideal model delta sigma weight residual 1.457 1.491 -0.034 9.10e-03 1.21e+04 1.40e+01 bond pdb=" N SER B 85 " pdb=" CA SER B 85 " ideal model delta sigma weight residual 1.457 1.490 -0.034 9.10e-03 1.21e+04 1.38e+01 bond pdb=" N SER A 85 " pdb=" CA SER A 85 " ideal model delta sigma weight residual 1.457 1.490 -0.034 9.10e-03 1.21e+04 1.37e+01 bond pdb=" N SER D 85 " pdb=" CA SER D 85 " ideal model delta sigma weight residual 1.457 1.490 -0.034 9.10e-03 1.21e+04 1.37e+01 bond pdb=" N SER E 85 " pdb=" CA SER E 85 " ideal model delta sigma weight residual 1.457 1.490 -0.034 9.10e-03 1.21e+04 1.36e+01 ... (remaining 4411 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 4009 1.46 - 2.93: 1538 2.93 - 4.39: 375 4.39 - 5.86: 72 5.86 - 7.32: 12 Bond angle restraints: 6006 Sorted by residual: angle pdb=" CA SER F 85 " pdb=" C SER F 85 " pdb=" N PRO F 86 " ideal model delta sigma weight residual 118.16 121.70 -3.54 7.00e-01 2.04e+00 2.56e+01 angle pdb=" CA SER C 85 " pdb=" C SER C 85 " pdb=" N PRO C 86 " ideal model delta sigma weight residual 118.16 121.70 -3.54 7.00e-01 2.04e+00 2.55e+01 angle pdb=" CA SER D 85 " pdb=" C SER D 85 " pdb=" N PRO D 86 " ideal model delta sigma weight residual 118.16 121.69 -3.53 7.00e-01 2.04e+00 2.55e+01 angle pdb=" CA SER A 85 " pdb=" C SER A 85 " pdb=" N PRO A 86 " ideal model delta sigma weight residual 118.16 121.69 -3.53 7.00e-01 2.04e+00 2.54e+01 angle pdb=" CA SER B 85 " pdb=" C SER B 85 " pdb=" N PRO B 86 " ideal model delta sigma weight residual 118.16 121.68 -3.52 7.00e-01 2.04e+00 2.53e+01 ... (remaining 6001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.01: 2166 8.01 - 16.02: 234 16.02 - 24.04: 114 24.04 - 32.05: 54 32.05 - 40.06: 36 Dihedral angle restraints: 2604 sinusoidal: 990 harmonic: 1614 Sorted by residual: dihedral pdb=" C TYR D 116 " pdb=" N TYR D 116 " pdb=" CA TYR D 116 " pdb=" CB TYR D 116 " ideal model delta harmonic sigma weight residual -122.60 -129.60 7.00 0 2.50e+00 1.60e-01 7.84e+00 dihedral pdb=" C TYR A 116 " pdb=" N TYR A 116 " pdb=" CA TYR A 116 " pdb=" CB TYR A 116 " ideal model delta harmonic sigma weight residual -122.60 -129.60 7.00 0 2.50e+00 1.60e-01 7.84e+00 dihedral pdb=" C TYR E 116 " pdb=" N TYR E 116 " pdb=" CA TYR E 116 " pdb=" CB TYR E 116 " ideal model delta harmonic sigma weight residual -122.60 -129.59 6.99 0 2.50e+00 1.60e-01 7.82e+00 ... (remaining 2601 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.058: 203 0.058 - 0.115: 247 0.115 - 0.173: 164 0.173 - 0.230: 76 0.230 - 0.287: 18 Chirality restraints: 708 Sorted by residual: chirality pdb=" CA ILE F 107 " pdb=" N ILE F 107 " pdb=" C ILE F 107 " pdb=" CB ILE F 107 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA ILE A 107 " pdb=" N ILE A 107 " pdb=" C ILE A 107 " pdb=" CB ILE A 107 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA ILE E 107 " pdb=" N ILE E 107 " pdb=" C ILE E 107 " pdb=" CB ILE E 107 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 705 not shown) Planarity restraints: 738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR F 114 " 0.012 2.00e-02 2.50e+03 2.51e-02 6.32e+00 pdb=" C TYR F 114 " -0.043 2.00e-02 2.50e+03 pdb=" O TYR F 114 " 0.016 2.00e-02 2.50e+03 pdb=" N SER F 115 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 90 " 0.012 2.00e-02 2.50e+03 2.51e-02 6.29e+00 pdb=" C HIS B 90 " -0.043 2.00e-02 2.50e+03 pdb=" O HIS B 90 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA B 91 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 90 " 0.012 2.00e-02 2.50e+03 2.51e-02 6.29e+00 pdb=" C HIS D 90 " -0.043 2.00e-02 2.50e+03 pdb=" O HIS D 90 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA D 91 " 0.015 2.00e-02 2.50e+03 ... (remaining 735 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 1739 2.90 - 3.40: 3766 3.40 - 3.90: 7659 3.90 - 4.40: 8773 4.40 - 4.90: 16883 Nonbonded interactions: 38820 Sorted by model distance: nonbonded pdb=" O ASN A 27 " pdb=" OH TYR B 69 " model vdw 2.394 3.040 nonbonded pdb=" O ASN B 27 " pdb=" OH TYR C 69 " model vdw 2.395 3.040 nonbonded pdb=" O ASN C 27 " pdb=" OH TYR D 69 " model vdw 2.395 3.040 nonbonded pdb=" O ASN D 27 " pdb=" OH TYR E 69 " model vdw 2.395 3.040 nonbonded pdb=" O ASN E 27 " pdb=" OH TYR F 69 " model vdw 2.395 3.040 ... (remaining 38815 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 13.890 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:10.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 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 : 0.012 0.041 4416 Z= 0.848 Angle : 1.652 7.321 6006 Z= 1.222 Chirality : 0.117 0.287 708 Planarity : 0.007 0.034 738 Dihedral : 10.764 40.059 1560 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 0.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.30), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 79 HIS 0.006 0.002 HIS F 31 PHE 0.013 0.002 PHE E 64 TYR 0.007 0.002 TYR B 116 ARG 0.003 0.001 ARG F 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.6384 (ttm) cc_final: 0.6072 (ttt) REVERT: A 27 ASN cc_start: 0.7847 (m-40) cc_final: 0.7536 (m110) REVERT: A 34 ARG cc_start: 0.7483 (ttt-90) cc_final: 0.6969 (pmt170) REVERT: A 63 GLU cc_start: 0.7419 (mt-10) cc_final: 0.6692 (tp30) REVERT: A 72 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7139 (pm20) REVERT: A 75 THR cc_start: 0.8487 (m) cc_final: 0.8273 (p) REVERT: A 76 LYS cc_start: 0.8108 (mptt) cc_final: 0.7083 (mmpt) REVERT: A 89 GLU cc_start: 0.7364 (mt-10) cc_final: 0.7038 (pm20) REVERT: B 89 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7021 (mt-10) REVERT: C 13 MET cc_start: 0.6786 (ttm) cc_final: 0.6435 (ttt) REVERT: C 89 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6898 (mt-10) REVERT: D 15 LYS cc_start: 0.7726 (mtpt) cc_final: 0.7513 (mtpp) REVERT: D 63 GLU cc_start: 0.7546 (mt-10) cc_final: 0.6997 (tm-30) REVERT: E 63 GLU cc_start: 0.7509 (mt-10) cc_final: 0.6371 (tp30) REVERT: F 35 LYS cc_start: 0.7428 (tttt) cc_final: 0.6929 (pmtt) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.9586 time to fit residues: 207.3194 Evaluate side-chains 127 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 0.0980 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.129393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.110975 restraints weight = 6358.647| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 2.90 r_work: 0.3952 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4416 Z= 0.264 Angle : 0.671 8.511 6006 Z= 0.356 Chirality : 0.052 0.202 708 Planarity : 0.005 0.035 738 Dihedral : 5.225 15.881 594 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 4.06 % Allowed : 18.59 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.31), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 79 HIS 0.003 0.001 HIS E 31 PHE 0.014 0.002 PHE F 87 TYR 0.027 0.003 TYR C 114 ARG 0.008 0.001 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.492 Fit side-chains REVERT: A 13 MET cc_start: 0.6644 (ttm) cc_final: 0.5966 (ttt) REVERT: A 27 ASN cc_start: 0.8165 (m-40) cc_final: 0.7877 (m-40) REVERT: A 34 ARG cc_start: 0.8203 (ttt-90) cc_final: 0.6620 (pmt170) REVERT: A 72 GLU cc_start: 0.8584 (mt-10) cc_final: 0.7240 (pm20) REVERT: A 76 LYS cc_start: 0.8486 (mptt) cc_final: 0.6734 (mmpt) REVERT: A 89 GLU cc_start: 0.7836 (mt-10) cc_final: 0.6783 (pm20) REVERT: A 110 LEU cc_start: 0.8142 (tp) cc_final: 0.7881 (tt) REVERT: B 13 MET cc_start: 0.6899 (OUTLIER) cc_final: 0.6437 (tmm) REVERT: B 26 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8146 (mt) REVERT: B 27 ASN cc_start: 0.8592 (m110) cc_final: 0.8381 (m110) REVERT: B 89 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7021 (mt-10) REVERT: C 13 MET cc_start: 0.6974 (ttm) cc_final: 0.6104 (tmm) REVERT: C 18 ASP cc_start: 0.7723 (p0) cc_final: 0.7330 (p0) REVERT: C 21 ARG cc_start: 0.6586 (tpp80) cc_final: 0.5909 (tpp-160) REVERT: C 69 TYR cc_start: 0.8767 (m-80) cc_final: 0.8541 (m-80) REVERT: C 89 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7069 (mt-10) REVERT: D 15 LYS cc_start: 0.7394 (mtpt) cc_final: 0.7135 (mtpp) REVERT: D 89 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7085 (mt-10) REVERT: D 95 PHE cc_start: 0.8331 (t80) cc_final: 0.7836 (t80) REVERT: D 110 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8618 (tp) REVERT: D 117 SER cc_start: 0.9148 (m) cc_final: 0.8915 (m) REVERT: E 13 MET cc_start: 0.7015 (ttp) cc_final: 0.6691 (ttp) REVERT: E 69 TYR cc_start: 0.8831 (m-80) cc_final: 0.8597 (m-80) REVERT: E 99 ASP cc_start: 0.6471 (t0) cc_final: 0.6210 (t0) REVERT: F 12 LEU cc_start: 0.8325 (mt) cc_final: 0.7983 (tm) REVERT: F 21 ARG cc_start: 0.5884 (ttt180) cc_final: 0.5022 (pmt-80) REVERT: F 35 LYS cc_start: 0.7839 (tttt) cc_final: 0.6975 (pmtt) REVERT: F 82 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7911 (mt) outliers start: 19 outliers final: 7 residues processed: 139 average time/residue: 0.9967 time to fit residues: 144.3807 Evaluate side-chains 116 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 112 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 46 optimal weight: 0.0470 chunk 17 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 15 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 14 optimal weight: 0.0980 overall best weight: 1.1480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.124790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.106946 restraints weight = 6664.941| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 2.83 r_work: 0.3907 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4416 Z= 0.278 Angle : 0.619 5.024 6006 Z= 0.331 Chirality : 0.051 0.142 708 Planarity : 0.004 0.028 738 Dihedral : 5.168 17.426 594 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 4.49 % Allowed : 20.09 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.31), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 79 HIS 0.003 0.001 HIS F 31 PHE 0.011 0.002 PHE A 87 TYR 0.015 0.002 TYR F 114 ARG 0.005 0.001 ARG E 104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.423 Fit side-chains REVERT: A 13 MET cc_start: 0.6658 (ttm) cc_final: 0.6039 (ttm) REVERT: A 34 ARG cc_start: 0.8108 (ttt-90) cc_final: 0.6774 (pmt170) REVERT: A 76 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.6678 (mmpt) REVERT: B 12 LEU cc_start: 0.8497 (tt) cc_final: 0.8169 (tm) REVERT: B 13 MET cc_start: 0.7053 (OUTLIER) cc_final: 0.6661 (tmm) REVERT: B 89 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7151 (mt-10) REVERT: C 13 MET cc_start: 0.6950 (ttm) cc_final: 0.5942 (tmt) REVERT: C 18 ASP cc_start: 0.7807 (p0) cc_final: 0.7500 (p0) REVERT: C 21 ARG cc_start: 0.6790 (tpp80) cc_final: 0.6053 (tpp-160) REVERT: C 89 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6953 (mt-10) REVERT: D 15 LYS cc_start: 0.7475 (mtpt) cc_final: 0.7209 (mtpp) REVERT: D 89 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7169 (mt-10) REVERT: E 12 LEU cc_start: 0.8482 (tp) cc_final: 0.7974 (tm) REVERT: E 13 MET cc_start: 0.7337 (ttp) cc_final: 0.6951 (ttp) REVERT: E 69 TYR cc_start: 0.8895 (m-80) cc_final: 0.8632 (m-80) REVERT: E 76 LYS cc_start: 0.8475 (mttt) cc_final: 0.8160 (mptt) REVERT: E 99 ASP cc_start: 0.6396 (t0) cc_final: 0.6124 (t0) REVERT: F 12 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8198 (tm) REVERT: F 21 ARG cc_start: 0.6002 (ttt180) cc_final: 0.5136 (pmt-80) REVERT: F 35 LYS cc_start: 0.8133 (tttt) cc_final: 0.6981 (pmtt) REVERT: F 76 LYS cc_start: 0.8597 (mppt) cc_final: 0.6698 (pmtt) REVERT: F 112 SER cc_start: 0.6386 (OUTLIER) cc_final: 0.6185 (m) outliers start: 21 outliers final: 10 residues processed: 125 average time/residue: 1.7334 time to fit residues: 224.0984 Evaluate side-chains 121 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 43 optimal weight: 0.1980 chunk 11 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 37 optimal weight: 0.2980 chunk 13 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.124642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.106320 restraints weight = 6447.402| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 2.85 r_work: 0.3922 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4416 Z= 0.201 Angle : 0.577 6.922 6006 Z= 0.304 Chirality : 0.050 0.133 708 Planarity : 0.004 0.044 738 Dihedral : 5.054 17.155 594 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 4.27 % Allowed : 22.01 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.31), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 79 HIS 0.002 0.001 HIS E 31 PHE 0.008 0.001 PHE D 64 TYR 0.022 0.002 TYR E 114 ARG 0.009 0.001 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 1.015 Fit side-chains REVERT: A 13 MET cc_start: 0.6648 (ttm) cc_final: 0.6067 (ttm) REVERT: A 34 ARG cc_start: 0.8265 (ttt-90) cc_final: 0.6814 (pmt170) REVERT: A 63 GLU cc_start: 0.8032 (mt-10) cc_final: 0.6827 (tp30) REVERT: A 76 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.6724 (mmpt) REVERT: B 13 MET cc_start: 0.7008 (ttm) cc_final: 0.6625 (tmm) REVERT: B 89 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7320 (mt-10) REVERT: C 13 MET cc_start: 0.6973 (ttm) cc_final: 0.6279 (tmm) REVERT: C 18 ASP cc_start: 0.7855 (p0) cc_final: 0.7601 (p0) REVERT: C 21 ARG cc_start: 0.6981 (tpp80) cc_final: 0.6166 (tpp-160) REVERT: C 89 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7145 (mt-10) REVERT: C 99 ASP cc_start: 0.6888 (OUTLIER) cc_final: 0.6446 (t0) REVERT: D 15 LYS cc_start: 0.7548 (mtpt) cc_final: 0.7253 (mtpp) REVERT: D 89 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7234 (mt-10) REVERT: E 13 MET cc_start: 0.7492 (ttp) cc_final: 0.7035 (ttp) REVERT: E 21 ARG cc_start: 0.7085 (tpp80) cc_final: 0.6838 (tpp80) REVERT: E 76 LYS cc_start: 0.8510 (mttt) cc_final: 0.8195 (mptt) REVERT: F 12 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8015 (tm) REVERT: F 18 ASP cc_start: 0.7215 (p0) cc_final: 0.6922 (p0) REVERT: F 21 ARG cc_start: 0.6074 (ttt180) cc_final: 0.5093 (ppt90) REVERT: F 26 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.6893 (tp) REVERT: F 35 LYS cc_start: 0.8103 (tttt) cc_final: 0.7125 (pmtt) REVERT: F 76 LYS cc_start: 0.8567 (mppt) cc_final: 0.6693 (pmtt) REVERT: F 112 SER cc_start: 0.6481 (OUTLIER) cc_final: 0.6274 (m) outliers start: 20 outliers final: 6 residues processed: 125 average time/residue: 1.1220 time to fit residues: 146.4168 Evaluate side-chains 118 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 27 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 0.0770 chunk 48 optimal weight: 0.0270 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.122192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.104243 restraints weight = 6625.291| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 2.79 r_work: 0.3892 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 4416 Z= 0.249 Angle : 0.595 7.482 6006 Z= 0.309 Chirality : 0.050 0.130 708 Planarity : 0.004 0.029 738 Dihedral : 5.037 16.489 594 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 4.06 % Allowed : 22.86 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.32), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 79 HIS 0.003 0.001 HIS F 31 PHE 0.012 0.002 PHE A 87 TYR 0.018 0.002 TYR E 114 ARG 0.004 0.001 ARG F 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.458 Fit side-chains REVERT: A 13 MET cc_start: 0.6641 (ttm) cc_final: 0.6040 (ttm) REVERT: A 34 ARG cc_start: 0.8301 (ttt-90) cc_final: 0.6803 (pmt170) REVERT: A 63 GLU cc_start: 0.8014 (mt-10) cc_final: 0.6832 (tp30) REVERT: A 76 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.6692 (mmpt) REVERT: B 13 MET cc_start: 0.7120 (OUTLIER) cc_final: 0.6717 (tmm) REVERT: B 89 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7528 (mt-10) REVERT: C 13 MET cc_start: 0.6921 (ttm) cc_final: 0.6204 (tmm) REVERT: C 18 ASP cc_start: 0.7870 (p0) cc_final: 0.7637 (p0) REVERT: C 21 ARG cc_start: 0.7032 (tpp80) cc_final: 0.6226 (tpp-160) REVERT: C 99 ASP cc_start: 0.7051 (OUTLIER) cc_final: 0.6478 (t0) REVERT: D 15 LYS cc_start: 0.7614 (mtpt) cc_final: 0.7322 (mtpp) REVERT: D 89 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7253 (mt-10) REVERT: E 13 MET cc_start: 0.7240 (ttp) cc_final: 0.6779 (ttp) REVERT: E 76 LYS cc_start: 0.8509 (mttt) cc_final: 0.8206 (mptt) REVERT: F 12 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8029 (tm) REVERT: F 18 ASP cc_start: 0.7240 (p0) cc_final: 0.6920 (p0) REVERT: F 21 ARG cc_start: 0.6346 (ttt180) cc_final: 0.5349 (ppt90) REVERT: F 26 ILE cc_start: 0.7831 (OUTLIER) cc_final: 0.6900 (tp) REVERT: F 35 LYS cc_start: 0.8186 (tttt) cc_final: 0.7042 (pmtt) REVERT: F 76 LYS cc_start: 0.8587 (mppt) cc_final: 0.6687 (pmtt) REVERT: F 112 SER cc_start: 0.6470 (OUTLIER) cc_final: 0.6216 (m) outliers start: 19 outliers final: 8 residues processed: 117 average time/residue: 1.2379 time to fit residues: 149.5638 Evaluate side-chains 114 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 46 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 HIS ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.123030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.105108 restraints weight = 6561.773| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 2.79 r_work: 0.3900 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 4416 Z= 0.223 Angle : 0.591 9.671 6006 Z= 0.303 Chirality : 0.050 0.130 708 Planarity : 0.004 0.039 738 Dihedral : 4.987 16.696 594 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.21 % Allowed : 23.72 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.32), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 79 HIS 0.002 0.001 HIS E 31 PHE 0.009 0.001 PHE A 87 TYR 0.017 0.002 TYR E 114 ARG 0.009 0.001 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.480 Fit side-chains REVERT: A 13 MET cc_start: 0.6612 (ttm) cc_final: 0.6035 (ttm) REVERT: A 34 ARG cc_start: 0.8297 (ttt-90) cc_final: 0.6807 (pmt170) REVERT: A 63 GLU cc_start: 0.8036 (mt-10) cc_final: 0.6864 (tp30) REVERT: A 76 LYS cc_start: 0.8552 (mptt) cc_final: 0.6714 (mmpt) REVERT: B 13 MET cc_start: 0.7150 (OUTLIER) cc_final: 0.6755 (tmm) REVERT: B 89 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7536 (mt-10) REVERT: C 13 MET cc_start: 0.6950 (ttm) cc_final: 0.6263 (tmm) REVERT: C 21 ARG cc_start: 0.6952 (tpp80) cc_final: 0.6161 (tpp-160) REVERT: C 34 ARG cc_start: 0.7779 (ttt-90) cc_final: 0.7466 (ttt-90) REVERT: C 99 ASP cc_start: 0.7043 (OUTLIER) cc_final: 0.6446 (t0) REVERT: D 15 LYS cc_start: 0.7650 (mtpt) cc_final: 0.7360 (mtpp) REVERT: D 89 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7218 (mt-10) REVERT: E 76 LYS cc_start: 0.8515 (mttt) cc_final: 0.8217 (mptt) REVERT: E 89 GLU cc_start: 0.8052 (tt0) cc_final: 0.7767 (mt-10) REVERT: F 12 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8045 (tm) REVERT: F 18 ASP cc_start: 0.7236 (p0) cc_final: 0.6913 (p0) REVERT: F 21 ARG cc_start: 0.6535 (ttt180) cc_final: 0.5462 (ppt90) REVERT: F 26 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.6906 (tp) REVERT: F 35 LYS cc_start: 0.8167 (tttt) cc_final: 0.7093 (pmtt) REVERT: F 76 LYS cc_start: 0.8537 (mppt) cc_final: 0.6716 (pmtt) REVERT: F 112 SER cc_start: 0.6411 (OUTLIER) cc_final: 0.6136 (m) outliers start: 15 outliers final: 7 residues processed: 117 average time/residue: 1.2902 time to fit residues: 155.8365 Evaluate side-chains 111 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 25 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 HIS ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.119722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.101788 restraints weight = 6755.683| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.82 r_work: 0.3849 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 4416 Z= 0.318 Angle : 0.644 9.055 6006 Z= 0.334 Chirality : 0.051 0.257 708 Planarity : 0.005 0.039 738 Dihedral : 5.245 16.289 594 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.42 % Allowed : 23.93 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.32), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 79 HIS 0.003 0.001 HIS F 31 PHE 0.013 0.002 PHE A 87 TYR 0.017 0.002 TYR E 114 ARG 0.009 0.001 ARG E 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.490 Fit side-chains REVERT: A 13 MET cc_start: 0.6695 (ttm) cc_final: 0.6108 (ttm) REVERT: A 34 ARG cc_start: 0.8120 (ttt-90) cc_final: 0.6705 (pmt170) REVERT: A 63 GLU cc_start: 0.8104 (mt-10) cc_final: 0.6923 (tp30) REVERT: B 13 MET cc_start: 0.7179 (OUTLIER) cc_final: 0.6791 (tmm) REVERT: B 89 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7543 (mt-10) REVERT: C 13 MET cc_start: 0.7054 (ttm) cc_final: 0.6563 (ttt) REVERT: C 21 ARG cc_start: 0.7049 (tpp80) cc_final: 0.6187 (tpp-160) REVERT: C 34 ARG cc_start: 0.7829 (ttt-90) cc_final: 0.7486 (ttt-90) REVERT: C 99 ASP cc_start: 0.7119 (OUTLIER) cc_final: 0.6502 (t0) REVERT: D 15 LYS cc_start: 0.7692 (mtpt) cc_final: 0.7430 (mtpp) REVERT: D 21 ARG cc_start: 0.6775 (tpp80) cc_final: 0.6512 (ttp80) REVERT: D 89 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7255 (mt-10) REVERT: E 13 MET cc_start: 0.7269 (ttp) cc_final: 0.6854 (ttp) REVERT: E 76 LYS cc_start: 0.8471 (mttt) cc_final: 0.8141 (mptt) REVERT: E 89 GLU cc_start: 0.8143 (tt0) cc_final: 0.7843 (mt-10) REVERT: F 12 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8107 (tm) REVERT: F 18 ASP cc_start: 0.6923 (p0) cc_final: 0.6552 (p0) REVERT: F 21 ARG cc_start: 0.6579 (ttt180) cc_final: 0.5392 (ppt90) REVERT: F 26 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7279 (tp) REVERT: F 35 LYS cc_start: 0.8224 (tttt) cc_final: 0.7030 (pmtt) REVERT: F 76 LYS cc_start: 0.8553 (mppt) cc_final: 0.6771 (pmtt) REVERT: F 112 SER cc_start: 0.6513 (OUTLIER) cc_final: 0.6144 (m) outliers start: 16 outliers final: 8 residues processed: 109 average time/residue: 1.3928 time to fit residues: 156.2851 Evaluate side-chains 104 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 43 optimal weight: 0.1980 chunk 41 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.136370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.113676 restraints weight = 6746.719| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 2.73 r_work: 0.3874 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.5295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4416 Z= 0.252 Angle : 0.624 11.486 6006 Z= 0.319 Chirality : 0.050 0.165 708 Planarity : 0.004 0.033 738 Dihedral : 5.175 18.027 594 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.42 % Allowed : 24.57 % Favored : 72.01 % 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: -2.35 (0.33), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 79 HIS 0.002 0.001 HIS E 31 PHE 0.010 0.001 PHE A 87 TYR 0.015 0.002 TYR E 114 ARG 0.008 0.001 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.562 Fit side-chains REVERT: A 13 MET cc_start: 0.6753 (ttm) cc_final: 0.6171 (ttm) REVERT: A 34 ARG cc_start: 0.8150 (ttt-90) cc_final: 0.6708 (pmt170) REVERT: A 63 GLU cc_start: 0.8097 (mt-10) cc_final: 0.6955 (tp30) REVERT: A 76 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.6551 (mmpt) REVERT: B 13 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6778 (tmm) REVERT: B 89 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7667 (mt-10) REVERT: C 13 MET cc_start: 0.7041 (ttm) cc_final: 0.6153 (tmt) REVERT: C 18 ASP cc_start: 0.7456 (p0) cc_final: 0.6876 (p0) REVERT: C 21 ARG cc_start: 0.7039 (tpp80) cc_final: 0.6155 (tpp-160) REVERT: C 34 ARG cc_start: 0.7840 (ttt-90) cc_final: 0.7482 (ttt-90) REVERT: C 99 ASP cc_start: 0.7109 (OUTLIER) cc_final: 0.6506 (t0) REVERT: D 15 LYS cc_start: 0.7730 (mtpt) cc_final: 0.7442 (mtpp) REVERT: D 21 ARG cc_start: 0.6821 (tpp80) cc_final: 0.6564 (ttp80) REVERT: D 89 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7361 (mt-10) REVERT: E 13 MET cc_start: 0.7327 (ttp) cc_final: 0.6930 (ttp) REVERT: E 76 LYS cc_start: 0.8521 (mttt) cc_final: 0.8167 (mptt) REVERT: E 89 GLU cc_start: 0.8130 (tt0) cc_final: 0.7879 (mt-10) REVERT: F 12 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8091 (tm) REVERT: F 18 ASP cc_start: 0.6923 (p0) cc_final: 0.6557 (p0) REVERT: F 21 ARG cc_start: 0.6677 (ttt180) cc_final: 0.5490 (ppt90) REVERT: F 26 ILE cc_start: 0.7883 (OUTLIER) cc_final: 0.6947 (tp) REVERT: F 35 LYS cc_start: 0.8249 (tttt) cc_final: 0.7045 (pmtt) REVERT: F 76 LYS cc_start: 0.8543 (mppt) cc_final: 0.6755 (pmtt) REVERT: F 112 SER cc_start: 0.6480 (OUTLIER) cc_final: 0.6131 (m) outliers start: 16 outliers final: 7 residues processed: 104 average time/residue: 1.4491 time to fit residues: 155.0284 Evaluate side-chains 105 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.6980 chunk 11 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.133436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.111101 restraints weight = 6884.851| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 2.77 r_work: 0.3857 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 4416 Z= 0.312 Angle : 0.669 13.223 6006 Z= 0.339 Chirality : 0.052 0.274 708 Planarity : 0.005 0.042 738 Dihedral : 5.305 21.852 594 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.78 % Allowed : 25.00 % Favored : 72.22 % 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: -2.39 (0.33), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 79 HIS 0.003 0.001 HIS E 31 PHE 0.012 0.002 PHE A 87 TYR 0.015 0.002 TYR E 114 ARG 0.010 0.001 ARG E 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.6819 (ttm) cc_final: 0.6168 (ttm) REVERT: A 34 ARG cc_start: 0.8137 (ttt-90) cc_final: 0.6711 (pmt170) REVERT: B 13 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6730 (tmm) REVERT: B 89 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7674 (mt-10) REVERT: C 13 MET cc_start: 0.6996 (ttm) cc_final: 0.6016 (tmt) REVERT: C 21 ARG cc_start: 0.6944 (tpp80) cc_final: 0.6170 (tpp-160) REVERT: C 99 ASP cc_start: 0.7074 (OUTLIER) cc_final: 0.6469 (t0) REVERT: D 15 LYS cc_start: 0.7767 (mtpt) cc_final: 0.7496 (mtpp) REVERT: D 21 ARG cc_start: 0.6882 (tpp80) cc_final: 0.6628 (ttp80) REVERT: D 89 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7345 (mt-10) REVERT: E 26 ILE cc_start: 0.8780 (pt) cc_final: 0.8486 (pp) REVERT: E 34 ARG cc_start: 0.7897 (ttt-90) cc_final: 0.7565 (ttt-90) REVERT: E 76 LYS cc_start: 0.8516 (mttt) cc_final: 0.8157 (mptt) REVERT: E 89 GLU cc_start: 0.8191 (tt0) cc_final: 0.7929 (mt-10) REVERT: F 12 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8147 (tm) REVERT: F 18 ASP cc_start: 0.7052 (p0) cc_final: 0.6714 (p0) REVERT: F 21 ARG cc_start: 0.6916 (ttt180) cc_final: 0.5575 (ppt90) REVERT: F 26 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.6897 (tp) REVERT: F 35 LYS cc_start: 0.8247 (tttt) cc_final: 0.6992 (pmtt) REVERT: F 76 LYS cc_start: 0.8549 (mppt) cc_final: 0.6775 (pmtt) REVERT: F 112 SER cc_start: 0.6530 (OUTLIER) cc_final: 0.6136 (m) outliers start: 13 outliers final: 9 residues processed: 100 average time/residue: 1.3558 time to fit residues: 139.7999 Evaluate side-chains 102 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 5 optimal weight: 0.0010 chunk 12 optimal weight: 2.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.135849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.113565 restraints weight = 6666.516| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 2.75 r_work: 0.3884 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4416 Z= 0.229 Angle : 0.650 15.463 6006 Z= 0.324 Chirality : 0.052 0.404 708 Planarity : 0.004 0.043 738 Dihedral : 5.218 24.548 594 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.78 % Allowed : 25.43 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.33), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 79 HIS 0.002 0.000 HIS E 31 PHE 0.009 0.001 PHE A 87 TYR 0.015 0.002 TYR E 114 ARG 0.009 0.001 ARG E 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.6829 (ttm) cc_final: 0.6173 (ttm) REVERT: A 34 ARG cc_start: 0.8153 (ttt-90) cc_final: 0.6694 (pmt170) REVERT: A 63 GLU cc_start: 0.8085 (mt-10) cc_final: 0.6932 (tp30) REVERT: A 76 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.6506 (mmpt) REVERT: B 13 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6737 (tmm) REVERT: B 89 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7692 (mt-10) REVERT: C 13 MET cc_start: 0.7036 (ttm) cc_final: 0.6107 (tmm) REVERT: C 21 ARG cc_start: 0.6943 (tpp80) cc_final: 0.6177 (tpp-160) REVERT: C 99 ASP cc_start: 0.6991 (OUTLIER) cc_final: 0.6364 (t0) REVERT: D 15 LYS cc_start: 0.7784 (mtpt) cc_final: 0.7500 (mtpp) REVERT: D 89 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7293 (mt-10) REVERT: E 26 ILE cc_start: 0.8769 (pt) cc_final: 0.8499 (pp) REVERT: E 76 LYS cc_start: 0.8567 (mttt) cc_final: 0.8262 (mptt) REVERT: E 89 GLU cc_start: 0.8149 (tt0) cc_final: 0.7914 (mt-10) REVERT: F 12 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8079 (tm) REVERT: F 18 ASP cc_start: 0.6984 (p0) cc_final: 0.6655 (p0) REVERT: F 21 ARG cc_start: 0.6928 (ttt180) cc_final: 0.5596 (ppt90) REVERT: F 26 ILE cc_start: 0.7619 (OUTLIER) cc_final: 0.6761 (tp) REVERT: F 35 LYS cc_start: 0.8238 (tttt) cc_final: 0.7012 (pmtt) REVERT: F 76 LYS cc_start: 0.8544 (mppt) cc_final: 0.6755 (pmtt) REVERT: F 112 SER cc_start: 0.6472 (OUTLIER) cc_final: 0.6139 (m) outliers start: 13 outliers final: 7 residues processed: 100 average time/residue: 1.4874 time to fit residues: 153.1286 Evaluate side-chains 102 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 33 optimal weight: 0.0020 chunk 30 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.135242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.113042 restraints weight = 6793.838| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.77 r_work: 0.3892 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.5550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4416 Z= 0.252 Angle : 0.659 17.716 6006 Z= 0.324 Chirality : 0.050 0.131 708 Planarity : 0.004 0.031 738 Dihedral : 5.100 22.225 594 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.56 % Allowed : 25.43 % Favored : 72.01 % 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: -2.32 (0.33), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 79 HIS 0.003 0.001 HIS E 31 PHE 0.010 0.001 PHE A 87 TYR 0.014 0.002 TYR E 114 ARG 0.009 0.001 ARG C 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3781.44 seconds wall clock time: 66 minutes 2.23 seconds (3962.23 seconds total)