Starting phenix.real_space_refine on Fri Aug 22 14:40:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pkg_17738/08_2025/8pkg_17738.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pkg_17738/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8pkg_17738/08_2025/8pkg_17738.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pkg_17738/08_2025/8pkg_17738.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pkg_17738/08_2025/8pkg_17738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pkg_17738/08_2025/8pkg_17738.map" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: B, C, D, E, F Time building chain proxies: 0.63, per 1000 atoms: 0.15 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: 0.32 Conformation dependent library (CDL) restraints added in 157.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.12 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: 0.54 Time building geometry restraints manager: 0.43 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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: 0.970 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: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 4.870 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 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:6.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.290 ------------------------------------------------------------------------------- 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= 0.949 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.001 ARG F 34 TYR 0.007 0.002 TYR B 116 PHE 0.013 0.002 PHE E 64 TRP 0.002 0.001 TRP B 79 HIS 0.006 0.002 HIS F 31 Details of bonding type rmsd covalent geometry : bond 0.01248 ( 4416) covalent geometry : angle 1.65219 ( 6006) hydrogen bonds : bond 0.13524 ( 90) hydrogen bonds : angle 8.47633 ( 270) *********************** 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 : 0.101 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: 0.4274 time to fit residues: 92.2775 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 : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.0050 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.146826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.119786 restraints weight = 6480.653| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 2.99 r_work: 0.3958 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4416 Z= 0.142 Angle : 0.660 8.128 6006 Z= 0.350 Chirality : 0.053 0.202 708 Planarity : 0.005 0.034 738 Dihedral : 5.198 16.234 594 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 4.27 % Allowed : 18.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.70 (0.31), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 34 TYR 0.028 0.003 TYR F 114 PHE 0.014 0.002 PHE F 87 TRP 0.009 0.002 TRP E 79 HIS 0.003 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 4416) covalent geometry : angle 0.65953 ( 6006) hydrogen bonds : bond 0.04156 ( 90) hydrogen bonds : angle 6.45002 ( 270) *********************** 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 151 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.167 Fit side-chains REVERT: A 13 MET cc_start: 0.6631 (ttm) cc_final: 0.5933 (ttt) REVERT: A 27 ASN cc_start: 0.8131 (m-40) cc_final: 0.7824 (m-40) REVERT: A 34 ARG cc_start: 0.8151 (ttt-90) cc_final: 0.6612 (pmt170) REVERT: A 72 GLU cc_start: 0.8600 (mt-10) cc_final: 0.7237 (pm20) REVERT: A 76 LYS cc_start: 0.8441 (mptt) cc_final: 0.6704 (mmpt) REVERT: A 89 GLU cc_start: 0.7817 (mt-10) cc_final: 0.6763 (pm20) REVERT: A 110 LEU cc_start: 0.8166 (tp) cc_final: 0.7843 (tt) REVERT: B 13 MET cc_start: 0.6866 (OUTLIER) cc_final: 0.6389 (tmm) REVERT: B 27 ASN cc_start: 0.8504 (m110) cc_final: 0.8282 (m110) REVERT: B 89 GLU cc_start: 0.7600 (mt-10) cc_final: 0.6977 (mt-10) REVERT: C 13 MET cc_start: 0.6939 (ttm) cc_final: 0.6041 (tmm) REVERT: C 18 ASP cc_start: 0.7731 (p0) cc_final: 0.7328 (p0) REVERT: C 89 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7039 (mt-10) REVERT: D 15 LYS cc_start: 0.7360 (mtpt) cc_final: 0.7098 (mtpp) REVERT: D 89 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7061 (mt-10) REVERT: D 95 PHE cc_start: 0.8250 (t80) cc_final: 0.7724 (t80) REVERT: D 110 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8630 (tp) REVERT: D 117 SER cc_start: 0.9155 (m) cc_final: 0.8928 (m) REVERT: E 13 MET cc_start: 0.6978 (ttp) cc_final: 0.6638 (ttp) REVERT: E 69 TYR cc_start: 0.8784 (m-80) cc_final: 0.8571 (m-80) REVERT: E 99 ASP cc_start: 0.6389 (t0) cc_final: 0.6119 (t0) REVERT: F 12 LEU cc_start: 0.8286 (mt) cc_final: 0.7913 (tm) REVERT: F 21 ARG cc_start: 0.5951 (ttt180) cc_final: 0.5040 (pmt-80) REVERT: F 35 LYS cc_start: 0.7821 (tttt) cc_final: 0.6929 (pmtt) REVERT: F 82 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7854 (mt) outliers start: 20 outliers final: 9 residues processed: 138 average time/residue: 0.3953 time to fit residues: 56.7751 Evaluate side-chains 118 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 61 GLU 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 2 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 49 optimal weight: 0.0050 chunk 51 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 0.0870 chunk 47 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.5972 ------------------------------------------------------------------------------- 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 = 0.4196 r_free = 0.4196 target = 0.128832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.110941 restraints weight = 6499.638| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 2.85 r_work: 0.3949 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4416 Z= 0.123 Angle : 0.575 4.479 6006 Z= 0.309 Chirality : 0.050 0.134 708 Planarity : 0.004 0.026 738 Dihedral : 5.026 16.570 594 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 5.13 % Allowed : 18.59 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.57 (0.31), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 21 TYR 0.024 0.002 TYR C 114 PHE 0.009 0.001 PHE D 64 TRP 0.011 0.002 TRP B 79 HIS 0.003 0.001 HIS F 31 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 4416) covalent geometry : angle 0.57541 ( 6006) hydrogen bonds : bond 0.03448 ( 90) hydrogen bonds : angle 5.93057 ( 270) *********************** 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 148 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.179 Fit side-chains REVERT: A 13 MET cc_start: 0.6553 (ttm) cc_final: 0.5905 (ttt) REVERT: A 27 ASN cc_start: 0.8333 (m-40) cc_final: 0.8024 (m-40) REVERT: A 34 ARG cc_start: 0.8243 (ttt-90) cc_final: 0.6692 (pmt170) REVERT: A 63 GLU cc_start: 0.8117 (mt-10) cc_final: 0.6767 (tp30) REVERT: A 76 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.6655 (mmpt) REVERT: A 89 GLU cc_start: 0.7903 (mt-10) cc_final: 0.6772 (pm20) REVERT: B 12 LEU cc_start: 0.8587 (tt) cc_final: 0.8249 (tm) REVERT: B 13 MET cc_start: 0.6900 (OUTLIER) cc_final: 0.6526 (tmm) REVERT: B 89 GLU cc_start: 0.7579 (mt-10) cc_final: 0.6972 (mt-10) REVERT: C 13 MET cc_start: 0.6846 (ttm) cc_final: 0.5838 (tmt) REVERT: C 18 ASP cc_start: 0.7832 (p0) cc_final: 0.7567 (p0) REVERT: C 89 GLU cc_start: 0.7318 (mt-10) cc_final: 0.6950 (mt-10) REVERT: C 93 VAL cc_start: 0.8931 (t) cc_final: 0.8645 (m) REVERT: C 99 ASP cc_start: 0.6610 (OUTLIER) cc_final: 0.6147 (t0) REVERT: D 15 LYS cc_start: 0.7383 (mtpt) cc_final: 0.7115 (mtpp) REVERT: D 72 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7491 (mt-10) REVERT: D 89 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7130 (mt-10) REVERT: D 95 PHE cc_start: 0.8373 (t80) cc_final: 0.7891 (t80) REVERT: D 117 SER cc_start: 0.9150 (m) cc_final: 0.8926 (m) REVERT: E 12 LEU cc_start: 0.8515 (tp) cc_final: 0.7906 (tm) REVERT: E 13 MET cc_start: 0.7258 (ttp) cc_final: 0.6870 (ttp) REVERT: E 76 LYS cc_start: 0.8512 (mttt) cc_final: 0.8272 (mptt) REVERT: F 12 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.7838 (tm) REVERT: F 21 ARG cc_start: 0.5901 (ttt180) cc_final: 0.4939 (pmt-80) REVERT: F 35 LYS cc_start: 0.7945 (tttt) cc_final: 0.6992 (pmtt) REVERT: F 76 LYS cc_start: 0.8730 (mppt) cc_final: 0.6787 (pmtt) outliers start: 24 outliers final: 8 residues processed: 133 average time/residue: 0.4326 time to fit residues: 59.7021 Evaluate side-chains 121 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.167 ------------------------------------------------------------------------------- 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 B residue 13 MET Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain E residue 26 ILE 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 117 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 32 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 46 optimal weight: 0.0570 chunk 30 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.8302 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.117835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.099654 restraints weight = 6729.467| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 2.80 r_work: 0.3818 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 4416 Z= 0.215 Angle : 0.680 6.645 6006 Z= 0.362 Chirality : 0.052 0.142 708 Planarity : 0.005 0.035 738 Dihedral : 5.564 19.205 594 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 4.70 % Allowed : 21.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.45 (0.32), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 104 TYR 0.020 0.003 TYR E 114 PHE 0.017 0.002 PHE A 87 TRP 0.012 0.002 TRP B 79 HIS 0.005 0.001 HIS F 31 Details of bonding type rmsd covalent geometry : bond 0.00516 ( 4416) covalent geometry : angle 0.67967 ( 6006) hydrogen bonds : bond 0.03556 ( 90) hydrogen bonds : angle 5.78494 ( 270) *********************** 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 134 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.119 Fit side-chains REVERT: A 13 MET cc_start: 0.6692 (ttm) cc_final: 0.6110 (ttm) REVERT: A 34 ARG cc_start: 0.8207 (ttt-90) cc_final: 0.6775 (pmt170) REVERT: A 63 GLU cc_start: 0.8002 (mt-10) cc_final: 0.6803 (tp30) REVERT: A 76 LYS cc_start: 0.8558 (mptt) cc_final: 0.6537 (mmpt) REVERT: B 13 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6808 (tmm) REVERT: B 89 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7593 (mt-10) REVERT: B 110 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8460 (tp) REVERT: C 13 MET cc_start: 0.6954 (ttm) cc_final: 0.6276 (tmm) REVERT: C 21 ARG cc_start: 0.7046 (tpp80) cc_final: 0.6121 (tpp-160) REVERT: C 34 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7645 (ttt-90) REVERT: D 15 LYS cc_start: 0.7571 (mtpt) cc_final: 0.7304 (mtpp) REVERT: D 89 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7272 (mt-10) REVERT: E 26 ILE cc_start: 0.8707 (pt) cc_final: 0.8371 (mp) REVERT: E 69 TYR cc_start: 0.8890 (m-80) cc_final: 0.8649 (m-80) REVERT: E 76 LYS cc_start: 0.8428 (mttt) cc_final: 0.8205 (mptt) REVERT: F 12 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.7963 (tm) REVERT: F 18 ASP cc_start: 0.6919 (p0) cc_final: 0.6586 (p0) REVERT: F 21 ARG cc_start: 0.6422 (ttt180) cc_final: 0.5400 (ppt90) REVERT: F 26 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7402 (tp) REVERT: F 35 LYS cc_start: 0.8269 (tttt) cc_final: 0.7024 (pmtt) outliers start: 22 outliers final: 7 residues processed: 125 average time/residue: 0.5076 time to fit residues: 65.5109 Evaluate side-chains 113 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 84 ILE 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 117 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 53 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 26 optimal weight: 0.2980 chunk 14 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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** C 88 HIS ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.116467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.098353 restraints weight = 6802.426| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 2.82 r_work: 0.3826 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 4416 Z= 0.204 Angle : 0.643 6.476 6006 Z= 0.338 Chirality : 0.051 0.137 708 Planarity : 0.004 0.035 738 Dihedral : 5.484 17.795 594 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.85 % Allowed : 22.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.48 (0.32), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 104 TYR 0.021 0.002 TYR C 114 PHE 0.012 0.002 PHE A 87 TRP 0.009 0.002 TRP D 79 HIS 0.004 0.001 HIS F 31 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 4416) covalent geometry : angle 0.64322 ( 6006) hydrogen bonds : bond 0.03543 ( 90) hydrogen bonds : angle 5.66617 ( 270) *********************** 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 118 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.171 Fit side-chains REVERT: A 13 MET cc_start: 0.6698 (ttm) cc_final: 0.6104 (ttm) REVERT: A 34 ARG cc_start: 0.8121 (ttt-90) cc_final: 0.6693 (pmt170) REVERT: A 76 LYS cc_start: 0.8507 (mptt) cc_final: 0.6561 (mmpt) REVERT: B 13 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.6768 (tmm) REVERT: B 74 ASP cc_start: 0.9067 (t0) cc_final: 0.8826 (t0) REVERT: B 89 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7549 (mt-10) REVERT: C 13 MET cc_start: 0.6961 (ttm) cc_final: 0.6283 (tmm) REVERT: C 18 ASP cc_start: 0.7747 (p0) cc_final: 0.7501 (p0) REVERT: C 21 ARG cc_start: 0.7200 (tpp80) cc_final: 0.6207 (tpp-160) REVERT: C 34 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7618 (ttt-90) REVERT: C 99 ASP cc_start: 0.7109 (OUTLIER) cc_final: 0.6542 (t0) REVERT: D 15 LYS cc_start: 0.7680 (mtpt) cc_final: 0.7409 (mtpp) REVERT: D 21 ARG cc_start: 0.6733 (tpp80) cc_final: 0.6495 (ttp80) REVERT: D 89 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7225 (mt-10) REVERT: E 13 MET cc_start: 0.7264 (ttp) cc_final: 0.6855 (ttp) REVERT: E 26 ILE cc_start: 0.8725 (pt) cc_final: 0.8428 (mt) REVERT: E 69 TYR cc_start: 0.8851 (m-80) cc_final: 0.8625 (m-80) REVERT: E 89 GLU cc_start: 0.8167 (tt0) cc_final: 0.7779 (mt-10) REVERT: F 12 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8087 (tm) REVERT: F 18 ASP cc_start: 0.6835 (p0) cc_final: 0.6505 (p0) REVERT: F 21 ARG cc_start: 0.6596 (ttt180) cc_final: 0.5487 (ppt90) REVERT: F 26 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7281 (tp) REVERT: F 35 LYS cc_start: 0.8284 (tttt) cc_final: 0.7005 (pmtt) outliers start: 18 outliers final: 5 residues processed: 108 average time/residue: 0.5816 time to fit residues: 64.7345 Evaluate side-chains 103 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 99 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 117 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 3 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 15 optimal weight: 0.0170 chunk 41 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 5 optimal weight: 0.0770 chunk 40 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- 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** F 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.121062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.103150 restraints weight = 6770.774| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.82 r_work: 0.3888 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4416 Z= 0.109 Angle : 0.577 7.632 6006 Z= 0.298 Chirality : 0.050 0.135 708 Planarity : 0.004 0.043 738 Dihedral : 5.139 17.828 594 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.35 % Allowed : 23.50 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.45 (0.32), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 34 TYR 0.018 0.001 TYR C 114 PHE 0.007 0.001 PHE B 64 TRP 0.006 0.001 TRP F 79 HIS 0.002 0.000 HIS D 31 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 4416) covalent geometry : angle 0.57691 ( 6006) hydrogen bonds : bond 0.03101 ( 90) hydrogen bonds : angle 5.62761 ( 270) *********************** 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 117 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.157 Fit side-chains REVERT: A 13 MET cc_start: 0.6664 (ttm) cc_final: 0.6090 (ttm) REVERT: A 34 ARG cc_start: 0.8111 (ttt-90) cc_final: 0.6704 (pmt170) REVERT: A 63 GLU cc_start: 0.8052 (mt-10) cc_final: 0.6889 (tp30) REVERT: A 70 LYS cc_start: 0.6342 (pmtt) cc_final: 0.6086 (pptt) REVERT: A 76 LYS cc_start: 0.8487 (mptt) cc_final: 0.6558 (mmpt) REVERT: B 13 MET cc_start: 0.7107 (OUTLIER) cc_final: 0.6720 (tmm) REVERT: B 74 ASP cc_start: 0.9068 (t0) cc_final: 0.8795 (t0) REVERT: B 89 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7608 (mt-10) REVERT: C 13 MET cc_start: 0.6969 (ttm) cc_final: 0.6323 (tmm) REVERT: C 15 LYS cc_start: 0.7804 (mtpt) cc_final: 0.7548 (ttmm) REVERT: C 21 ARG cc_start: 0.7090 (tpp80) cc_final: 0.6155 (tpp-160) REVERT: C 99 ASP cc_start: 0.7035 (OUTLIER) cc_final: 0.6390 (t0) REVERT: D 13 MET cc_start: 0.7359 (ttp) cc_final: 0.6912 (ttm) REVERT: D 15 LYS cc_start: 0.7690 (mtpt) cc_final: 0.7417 (mtpp) REVERT: D 21 ARG cc_start: 0.6731 (tpp80) cc_final: 0.6484 (ttp80) REVERT: D 89 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7274 (mt-10) REVERT: E 76 LYS cc_start: 0.8570 (mttt) cc_final: 0.8350 (mptt) REVERT: E 89 GLU cc_start: 0.8087 (tt0) cc_final: 0.7826 (mt-10) REVERT: F 12 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8058 (tm) REVERT: F 18 ASP cc_start: 0.6878 (p0) cc_final: 0.6539 (p0) REVERT: F 21 ARG cc_start: 0.6585 (ttt180) cc_final: 0.5467 (ppt90) REVERT: F 26 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.6893 (tp) REVERT: F 35 LYS cc_start: 0.8232 (tttt) cc_final: 0.6990 (pmtt) REVERT: F 76 LYS cc_start: 0.8557 (mppt) cc_final: 0.6775 (pmtt) outliers start: 11 outliers final: 3 residues processed: 112 average time/residue: 0.6050 time to fit residues: 69.6403 Evaluate side-chains 104 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain C residue 99 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 117 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 49 optimal weight: 0.0050 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.0980 chunk 53 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 = 0.4177 r_free = 0.4177 target = 0.139728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.114802 restraints weight = 6782.792| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 2.82 r_work: 0.3894 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.5224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4416 Z= 0.110 Angle : 0.583 10.479 6006 Z= 0.298 Chirality : 0.050 0.131 708 Planarity : 0.004 0.042 738 Dihedral : 4.995 16.281 594 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.14 % Allowed : 23.50 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.40 (0.33), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 34 TYR 0.019 0.002 TYR C 114 PHE 0.006 0.001 PHE A 87 TRP 0.005 0.001 TRP F 79 HIS 0.002 0.000 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 4416) covalent geometry : angle 0.58306 ( 6006) hydrogen bonds : bond 0.03108 ( 90) hydrogen bonds : angle 5.45824 ( 270) *********************** 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 111 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.119 Fit side-chains REVERT: A 13 MET cc_start: 0.6704 (ttm) cc_final: 0.6046 (ttm) REVERT: A 34 ARG cc_start: 0.8160 (ttt-90) cc_final: 0.6667 (pmt170) REVERT: A 63 GLU cc_start: 0.8027 (mt-10) cc_final: 0.6856 (tp30) REVERT: A 76 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.6585 (mmpt) REVERT: B 13 MET cc_start: 0.7004 (OUTLIER) cc_final: 0.6598 (tmm) REVERT: B 74 ASP cc_start: 0.9005 (t0) cc_final: 0.8739 (t0) REVERT: B 89 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7619 (mt-10) REVERT: C 13 MET cc_start: 0.6899 (ttm) cc_final: 0.6369 (tmm) REVERT: C 21 ARG cc_start: 0.7141 (tpp80) cc_final: 0.6205 (tpp-160) REVERT: D 13 MET cc_start: 0.7205 (ttp) cc_final: 0.6681 (ttm) REVERT: D 15 LYS cc_start: 0.7665 (mtpt) cc_final: 0.7391 (mtpp) REVERT: D 21 ARG cc_start: 0.6656 (tpp80) cc_final: 0.6425 (ttp80) REVERT: D 89 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7225 (mt-10) REVERT: E 76 LYS cc_start: 0.8605 (mttt) cc_final: 0.8400 (mptt) REVERT: E 89 GLU cc_start: 0.8063 (tt0) cc_final: 0.7796 (mt-10) REVERT: E 112 SER cc_start: 0.8905 (m) cc_final: 0.8522 (m) REVERT: F 12 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8036 (tm) REVERT: F 18 ASP cc_start: 0.6818 (p0) cc_final: 0.6460 (p0) REVERT: F 21 ARG cc_start: 0.6674 (ttt180) cc_final: 0.5466 (ppt90) REVERT: F 26 ILE cc_start: 0.7641 (OUTLIER) cc_final: 0.6757 (tp) REVERT: F 35 LYS cc_start: 0.8227 (tttt) cc_final: 0.6989 (pmtt) REVERT: F 76 LYS cc_start: 0.8611 (mppt) cc_final: 0.6774 (pmtt) outliers start: 10 outliers final: 3 residues processed: 106 average time/residue: 0.5843 time to fit residues: 63.7590 Evaluate side-chains 102 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain B residue 13 MET 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 117 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 33 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 50 optimal weight: 0.0050 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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 = 0.4183 r_free = 0.4183 target = 0.138547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.114347 restraints weight = 6719.425| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 2.78 r_work: 0.3937 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4416 Z= 0.114 Angle : 0.588 9.849 6006 Z= 0.301 Chirality : 0.049 0.132 708 Planarity : 0.004 0.044 738 Dihedral : 4.944 16.214 594 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.92 % Allowed : 24.79 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.010 0.001 ARG E 34 TYR 0.018 0.002 TYR C 114 PHE 0.008 0.001 PHE A 87 TRP 0.004 0.001 TRP F 79 HIS 0.003 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 4416) covalent geometry : angle 0.58795 ( 6006) hydrogen bonds : bond 0.03088 ( 90) hydrogen bonds : angle 5.37954 ( 270) *********************** 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 104 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.221 Fit side-chains REVERT: A 13 MET cc_start: 0.6706 (ttm) cc_final: 0.6108 (ttm) REVERT: A 34 ARG cc_start: 0.8258 (ttt-90) cc_final: 0.6702 (pmt170) REVERT: A 63 GLU cc_start: 0.8028 (mt-10) cc_final: 0.6903 (tp30) REVERT: A 76 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.6586 (mmpt) REVERT: B 13 MET cc_start: 0.7021 (OUTLIER) cc_final: 0.6625 (tmm) REVERT: B 89 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7630 (mt-10) REVERT: C 13 MET cc_start: 0.6899 (ttm) cc_final: 0.6017 (tmm) REVERT: C 21 ARG cc_start: 0.7197 (tpp80) cc_final: 0.6257 (tpp-160) REVERT: C 34 ARG cc_start: 0.8008 (ttt-90) cc_final: 0.7807 (ttt-90) REVERT: C 99 ASP cc_start: 0.6991 (OUTLIER) cc_final: 0.6362 (t0) REVERT: D 13 MET cc_start: 0.7079 (ttp) cc_final: 0.6582 (tmm) REVERT: D 15 LYS cc_start: 0.7776 (mtpt) cc_final: 0.7421 (mtpp) REVERT: D 21 ARG cc_start: 0.6759 (tpp80) cc_final: 0.6481 (ttp80) REVERT: D 89 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7222 (mt-10) REVERT: E 89 GLU cc_start: 0.8093 (tt0) cc_final: 0.7831 (mt-10) REVERT: F 12 LEU cc_start: 0.8415 (mt) cc_final: 0.8021 (tm) REVERT: F 18 ASP cc_start: 0.6882 (p0) cc_final: 0.6561 (p0) REVERT: F 21 ARG cc_start: 0.6664 (ttt180) cc_final: 0.5420 (ppt90) REVERT: F 26 ILE cc_start: 0.7591 (OUTLIER) cc_final: 0.6727 (tp) REVERT: F 35 LYS cc_start: 0.8229 (tttt) cc_final: 0.6987 (pmtt) REVERT: F 76 LYS cc_start: 0.8613 (mppt) cc_final: 0.6752 (pmtt) outliers start: 9 outliers final: 4 residues processed: 101 average time/residue: 0.6074 time to fit residues: 63.0960 Evaluate side-chains 99 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 76 LYS 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 E residue 82 LEU Chi-restraints excluded: chain F residue 26 ILE 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 47 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 49 optimal weight: 0.0370 chunk 36 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 overall best weight: 1.5262 ------------------------------------------------------------------------------- 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 = 0.4148 r_free = 0.4148 target = 0.126106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.109385 restraints weight = 6619.969| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 2.62 r_work: 0.3861 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3751 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.5476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4416 Z= 0.179 Angle : 0.641 9.614 6006 Z= 0.329 Chirality : 0.050 0.142 708 Planarity : 0.004 0.036 738 Dihedral : 5.137 17.623 594 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.71 % Allowed : 25.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.46 (0.33), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 34 TYR 0.020 0.002 TYR C 114 PHE 0.012 0.002 PHE A 87 TRP 0.008 0.001 TRP C 79 HIS 0.003 0.001 HIS F 31 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 4416) covalent geometry : angle 0.64138 ( 6006) hydrogen bonds : bond 0.03477 ( 90) hydrogen bonds : angle 5.45359 ( 270) *********************** 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 105 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.115 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.6948 (ttm) cc_final: 0.6322 (ttm) REVERT: A 34 ARG cc_start: 0.8217 (ttt-90) cc_final: 0.6710 (pmt170) REVERT: B 13 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.6949 (tmm) REVERT: B 89 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7773 (mt-10) REVERT: C 13 MET cc_start: 0.7132 (ttm) cc_final: 0.6218 (tmm) REVERT: C 21 ARG cc_start: 0.7344 (tpp80) cc_final: 0.6381 (tpp-160) REVERT: C 34 ARG cc_start: 0.8108 (ttt-90) cc_final: 0.7852 (ttt-90) REVERT: C 99 ASP cc_start: 0.7073 (OUTLIER) cc_final: 0.6377 (t0) REVERT: D 15 LYS cc_start: 0.7877 (mtpt) cc_final: 0.7414 (ttpp) REVERT: D 21 ARG cc_start: 0.6784 (tpp80) cc_final: 0.6510 (ttp80) REVERT: D 89 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7329 (mt-10) REVERT: E 89 GLU cc_start: 0.8230 (tt0) cc_final: 0.7947 (mt-10) REVERT: F 12 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8152 (tm) REVERT: F 18 ASP cc_start: 0.6997 (p0) cc_final: 0.6713 (p0) REVERT: F 21 ARG cc_start: 0.7008 (ttt180) cc_final: 0.5829 (ppt90) REVERT: F 26 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.6926 (tp) REVERT: F 35 LYS cc_start: 0.8274 (tttt) cc_final: 0.6913 (pmtt) REVERT: F 76 LYS cc_start: 0.8569 (mppt) cc_final: 0.6781 (pmtt) outliers start: 8 outliers final: 4 residues processed: 101 average time/residue: 0.5950 time to fit residues: 61.8637 Evaluate side-chains 100 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL 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 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 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 3 optimal weight: 0.4980 chunk 32 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.4155 r_free = 0.4155 target = 0.126719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.110075 restraints weight = 6541.614| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 2.61 r_work: 0.3874 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3764 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4416 Z= 0.155 Angle : 0.633 11.931 6006 Z= 0.322 Chirality : 0.050 0.142 708 Planarity : 0.005 0.047 738 Dihedral : 5.132 17.045 594 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.14 % Allowed : 25.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.46 (0.33), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 34 TYR 0.018 0.002 TYR C 114 PHE 0.010 0.001 PHE A 87 TRP 0.006 0.001 TRP C 79 HIS 0.003 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 4416) covalent geometry : angle 0.63280 ( 6006) hydrogen bonds : bond 0.03418 ( 90) hydrogen bonds : angle 5.42282 ( 270) ********************** 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 105 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.6919 (ttm) cc_final: 0.6298 (ttm) REVERT: A 34 ARG cc_start: 0.8215 (ttt-90) cc_final: 0.6707 (pmt170) REVERT: A 63 GLU cc_start: 0.8143 (mt-10) cc_final: 0.6959 (tp30) REVERT: B 13 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.6918 (tmm) REVERT: B 89 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7850 (mt-10) REVERT: B 110 LEU cc_start: 0.8726 (tt) cc_final: 0.8277 (tt) REVERT: C 13 MET cc_start: 0.7141 (ttm) cc_final: 0.6225 (tmm) REVERT: C 21 ARG cc_start: 0.7344 (tpp80) cc_final: 0.6386 (tpp-160) REVERT: C 34 ARG cc_start: 0.8118 (ttt-90) cc_final: 0.7820 (ttt-90) REVERT: C 99 ASP cc_start: 0.7090 (OUTLIER) cc_final: 0.6369 (t0) REVERT: D 15 LYS cc_start: 0.7949 (mtpt) cc_final: 0.7434 (ttpp) REVERT: D 21 ARG cc_start: 0.6797 (tpp80) cc_final: 0.6527 (ttp80) REVERT: D 89 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7336 (mt-10) REVERT: E 15 LYS cc_start: 0.8177 (mtpt) cc_final: 0.7727 (mtpm) REVERT: E 34 ARG cc_start: 0.8021 (ttt-90) cc_final: 0.7707 (ttt-90) REVERT: E 89 GLU cc_start: 0.8220 (tt0) cc_final: 0.7950 (mt-10) REVERT: F 12 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8165 (tm) REVERT: F 18 ASP cc_start: 0.7094 (p0) cc_final: 0.6826 (p0) REVERT: F 21 ARG cc_start: 0.7261 (ttt180) cc_final: 0.5894 (ppt90) REVERT: F 26 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.6910 (tp) REVERT: F 35 LYS cc_start: 0.8236 (tttt) cc_final: 0.6920 (pmtt) REVERT: F 76 LYS cc_start: 0.8606 (mppt) cc_final: 0.6793 (pmtt) outliers start: 10 outliers final: 5 residues processed: 101 average time/residue: 0.6540 time to fit residues: 67.8787 Evaluate side-chains 101 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 104 ARG Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 99 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 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 22 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 1 optimal weight: 0.0370 chunk 24 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 5 optimal weight: 0.0020 chunk 32 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.4666 ------------------------------------------------------------------------------- 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 = 0.4191 r_free = 0.4191 target = 0.137265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.114939 restraints weight = 6642.572| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 2.76 r_work: 0.3924 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.5673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4416 Z= 0.108 Angle : 0.608 12.107 6006 Z= 0.304 Chirality : 0.050 0.132 708 Planarity : 0.004 0.041 738 Dihedral : 4.926 15.861 594 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.71 % Allowed : 26.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.010 0.001 ARG C 34 TYR 0.019 0.001 TYR C 114 PHE 0.006 0.001 PHE D 64 TRP 0.004 0.001 TRP F 79 HIS 0.002 0.000 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 4416) covalent geometry : angle 0.60783 ( 6006) hydrogen bonds : bond 0.03062 ( 90) hydrogen bonds : angle 5.38732 ( 270) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1642.54 seconds wall clock time: 28 minutes 36.36 seconds (1716.36 seconds total)