Starting phenix.real_space_refine on Fri Dec 27 11:03:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pkg_17738/12_2024/8pkg_17738.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pkg_17738/12_2024/8pkg_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_17738/12_2024/8pkg_17738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pkg_17738/12_2024/8pkg_17738.map" model { file = "/net/cci-nas-00/data/ceres_data/8pkg_17738/12_2024/8pkg_17738.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pkg_17738/12_2024/8pkg_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 2.19, per 1000 atoms: 0.51 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: 0.98 Conformation dependent library (CDL) restraints added in 514.7 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: 1.44 Time building geometry restraints manager: 1.16 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: 0.00 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: 0.010 Normalize map: mean=0, sd=1: 1.310 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.150 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.970 ------------------------------------------------------------------------------- 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 : 0.510 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: 1.0183 time to fit residues: 220.0863 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 : 0.446 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 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 : 0.541 Fit side-chains REVERT: A 13 MET cc_start: 0.6364 (ttm) cc_final: 0.6068 (ttt) REVERT: A 27 ASN cc_start: 0.8015 (m-40) cc_final: 0.7723 (m-40) REVERT: A 34 ARG cc_start: 0.7566 (ttt-90) cc_final: 0.6984 (pmt170) REVERT: A 72 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7283 (pm20) REVERT: A 76 LYS cc_start: 0.8555 (mptt) cc_final: 0.7202 (mmpt) REVERT: A 89 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7011 (pm20) REVERT: B 13 MET cc_start: 0.6503 (OUTLIER) cc_final: 0.6263 (tmm) REVERT: B 26 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8252 (mt) REVERT: B 27 ASN cc_start: 0.8536 (m110) cc_final: 0.8327 (m110) REVERT: B 89 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7059 (mt-10) REVERT: C 13 MET cc_start: 0.6702 (ttm) cc_final: 0.6415 (tmm) REVERT: C 21 ARG cc_start: 0.6651 (tpp80) cc_final: 0.6122 (tpp-160) REVERT: C 89 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6870 (mt-10) REVERT: D 95 PHE cc_start: 0.8385 (t80) cc_final: 0.8136 (t80) REVERT: D 117 SER cc_start: 0.8863 (m) cc_final: 0.8509 (m) REVERT: E 13 MET cc_start: 0.6731 (ttp) cc_final: 0.6359 (ttp) REVERT: F 35 LYS cc_start: 0.7451 (tttt) cc_final: 0.7052 (pmtt) REVERT: F 82 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8251 (mt) outliers start: 19 outliers final: 7 residues processed: 139 average time/residue: 0.9985 time to fit residues: 144.6963 Evaluate side-chains 113 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 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 27 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 48 optimal weight: 0.0770 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4416 Z= 0.246 Angle : 0.617 4.956 6006 Z= 0.327 Chirality : 0.051 0.147 708 Planarity : 0.004 0.027 738 Dihedral : 5.116 18.079 594 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 4.27 % Allowed : 20.51 % Favored : 75.21 % 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: -2.65 (0.31), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.23), 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 0.010 0.002 PHE C 64 TYR 0.015 0.002 TYR B 69 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 138 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.479 Fit side-chains REVERT: A 13 MET cc_start: 0.6398 (ttm) cc_final: 0.6069 (ttm) REVERT: A 34 ARG cc_start: 0.7575 (ttt-90) cc_final: 0.7175 (pmt170) REVERT: A 63 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7079 (tp30) REVERT: A 76 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.7219 (mmpt) REVERT: A 89 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7111 (pm20) REVERT: B 27 ASN cc_start: 0.8581 (m110) cc_final: 0.8371 (m110) REVERT: B 89 GLU cc_start: 0.7445 (mt-10) cc_final: 0.7102 (mt-10) REVERT: C 13 MET cc_start: 0.6617 (ttm) cc_final: 0.6372 (ttt) REVERT: C 21 ARG cc_start: 0.6786 (tpp80) cc_final: 0.6174 (tpp-160) REVERT: C 89 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6817 (mt-10) REVERT: D 117 SER cc_start: 0.8767 (m) cc_final: 0.8538 (m) REVERT: E 12 LEU cc_start: 0.8162 (tp) cc_final: 0.7942 (tm) REVERT: E 21 ARG cc_start: 0.6815 (tpp80) cc_final: 0.6525 (tpp80) REVERT: F 35 LYS cc_start: 0.7659 (tttt) cc_final: 0.6974 (pmtt) REVERT: F 76 LYS cc_start: 0.8344 (mppt) cc_final: 0.6979 (pmtt) REVERT: F 112 SER cc_start: 0.6746 (OUTLIER) cc_final: 0.6528 (m) outliers start: 20 outliers final: 9 residues processed: 128 average time/residue: 1.1317 time to fit residues: 150.2691 Evaluate side-chains 115 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 A residue 76 LYS Chi-restraints excluded: chain A residue 104 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 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 48 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.0370 chunk 23 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 52 optimal weight: 0.2980 chunk 46 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4416 Z= 0.205 Angle : 0.589 7.254 6006 Z= 0.307 Chirality : 0.050 0.130 708 Planarity : 0.004 0.038 738 Dihedral : 5.027 16.664 594 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 4.06 % Allowed : 22.44 % Favored : 73.50 % 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: -2.61 (0.31), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 79 HIS 0.002 0.000 HIS E 31 PHE 0.008 0.001 PHE D 64 TYR 0.022 0.002 TYR E 114 ARG 0.010 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 131 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.503 Fit side-chains REVERT: A 13 MET cc_start: 0.6284 (ttm) cc_final: 0.6014 (ttm) REVERT: A 34 ARG cc_start: 0.7765 (ttt-90) cc_final: 0.7227 (pmt170) REVERT: A 63 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7106 (tp30) REVERT: A 76 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.7159 (mmpt) REVERT: B 89 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7255 (mt-10) REVERT: C 13 MET cc_start: 0.6645 (ttm) cc_final: 0.6384 (tmm) REVERT: C 18 ASP cc_start: 0.6712 (p0) cc_final: 0.6369 (p0) REVERT: C 21 ARG cc_start: 0.6947 (tpp80) cc_final: 0.6408 (tpp-160) REVERT: C 89 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6918 (mt-10) REVERT: C 99 ASP cc_start: 0.6482 (OUTLIER) cc_final: 0.6230 (t0) REVERT: E 12 LEU cc_start: 0.8238 (tp) cc_final: 0.7995 (tm) REVERT: E 13 MET cc_start: 0.6915 (ttp) cc_final: 0.6571 (ttp) REVERT: F 18 ASP cc_start: 0.6905 (p0) cc_final: 0.6524 (p0) REVERT: F 26 ILE cc_start: 0.7787 (OUTLIER) cc_final: 0.6996 (tp) REVERT: F 35 LYS cc_start: 0.7625 (tttt) cc_final: 0.6987 (pmtt) REVERT: F 76 LYS cc_start: 0.8342 (mppt) cc_final: 0.6866 (pmtt) outliers start: 19 outliers final: 6 residues processed: 122 average time/residue: 1.1899 time to fit residues: 150.1880 Evaluate side-chains 112 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 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 29 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 46 optimal weight: 0.0670 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 overall best weight: 2.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN B 31 HIS B 88 HIS ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS C 88 HIS ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.5153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 4416 Z= 0.447 Angle : 0.734 6.839 6006 Z= 0.393 Chirality : 0.053 0.155 708 Planarity : 0.005 0.038 738 Dihedral : 5.729 18.067 594 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.06 % Allowed : 23.72 % 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: -2.48 (0.32), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 79 HIS 0.007 0.001 HIS F 31 PHE 0.019 0.003 PHE A 87 TYR 0.019 0.003 TYR E 114 ARG 0.007 0.001 ARG E 104 *********************** 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: 19 poor density : 99 time to evaluate : 0.498 Fit side-chains REVERT: A 13 MET cc_start: 0.6518 (ttm) cc_final: 0.6143 (ttm) REVERT: A 34 ARG cc_start: 0.7652 (ttt-90) cc_final: 0.7088 (pmt170) REVERT: A 63 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7243 (tp30) REVERT: A 76 LYS cc_start: 0.8572 (mptt) cc_final: 0.6949 (mmpt) REVERT: B 13 MET cc_start: 0.6757 (OUTLIER) cc_final: 0.6173 (ttm) REVERT: B 89 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7396 (mt-10) REVERT: C 18 ASP cc_start: 0.6805 (p0) cc_final: 0.6481 (p0) REVERT: C 21 ARG cc_start: 0.7032 (tpp80) cc_final: 0.6463 (tpp-160) REVERT: C 34 ARG cc_start: 0.7678 (ttt-90) cc_final: 0.7454 (ttt-90) REVERT: F 18 ASP cc_start: 0.6591 (p0) cc_final: 0.6140 (p0) REVERT: F 26 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7586 (tp) REVERT: F 35 LYS cc_start: 0.8063 (tttt) cc_final: 0.7177 (pmtt) outliers start: 19 outliers final: 5 residues processed: 110 average time/residue: 1.4149 time to fit residues: 160.3432 Evaluate side-chains 97 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 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 E residue 82 LEU Chi-restraints excluded: chain F residue 26 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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** E 88 HIS F 88 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.5384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 4416 Z= 0.319 Angle : 0.645 7.114 6006 Z= 0.339 Chirality : 0.051 0.138 708 Planarity : 0.004 0.037 738 Dihedral : 5.470 17.083 594 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.99 % Allowed : 24.57 % Favored : 72.44 % 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: -2.53 (0.32), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 79 HIS 0.003 0.001 HIS E 31 PHE 0.012 0.002 PHE A 87 TYR 0.014 0.002 TYR E 114 ARG 0.005 0.001 ARG F 21 *********************** 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 106 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.519 Fit side-chains REVERT: A 13 MET cc_start: 0.6505 (ttm) cc_final: 0.6107 (ttm) REVERT: A 34 ARG cc_start: 0.7585 (ttt-90) cc_final: 0.7055 (pmt170) REVERT: A 76 LYS cc_start: 0.8525 (mptt) cc_final: 0.6943 (mmpt) REVERT: B 13 MET cc_start: 0.6766 (OUTLIER) cc_final: 0.6238 (ttm) REVERT: B 89 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7463 (mt-10) REVERT: C 18 ASP cc_start: 0.6638 (p0) cc_final: 0.6339 (p0) REVERT: C 21 ARG cc_start: 0.6814 (tpp80) cc_final: 0.6352 (tpp-160) REVERT: C 23 SER cc_start: 0.7981 (m) cc_final: 0.7668 (m) REVERT: D 21 ARG cc_start: 0.6856 (OUTLIER) cc_final: 0.6495 (tpp80) REVERT: E 26 ILE cc_start: 0.8742 (pt) cc_final: 0.8421 (mt) REVERT: F 18 ASP cc_start: 0.6594 (p0) cc_final: 0.6164 (p0) REVERT: F 26 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7486 (tp) REVERT: F 35 LYS cc_start: 0.7925 (tttt) cc_final: 0.6964 (pmtt) outliers start: 14 outliers final: 6 residues processed: 99 average time/residue: 1.4202 time to fit residues: 144.9358 Evaluate side-chains 95 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 B residue 104 ARG Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 26 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.5496 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= 0.280 Angle : 0.638 7.290 6006 Z= 0.330 Chirality : 0.051 0.137 708 Planarity : 0.005 0.044 738 Dihedral : 5.345 16.197 594 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.35 % Allowed : 25.64 % 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: -2.53 (0.32), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 79 HIS 0.003 0.001 HIS E 31 PHE 0.011 0.002 PHE A 87 TYR 0.015 0.002 TYR E 114 ARG 0.010 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 106 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.507 Fit side-chains REVERT: A 13 MET cc_start: 0.6452 (ttm) cc_final: 0.6244 (ttm) REVERT: A 34 ARG cc_start: 0.7605 (ttt-90) cc_final: 0.7052 (pmt170) REVERT: B 13 MET cc_start: 0.6802 (OUTLIER) cc_final: 0.6301 (ttm) REVERT: B 89 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7508 (mt-10) REVERT: C 21 ARG cc_start: 0.6874 (tpp80) cc_final: 0.6348 (tpp-160) REVERT: C 23 SER cc_start: 0.8021 (m) cc_final: 0.7685 (m) REVERT: C 34 ARG cc_start: 0.7634 (ttt-90) cc_final: 0.7285 (ttt-90) REVERT: C 99 ASP cc_start: 0.6488 (OUTLIER) cc_final: 0.6135 (t0) REVERT: E 34 ARG cc_start: 0.7493 (ttt-90) cc_final: 0.7232 (ttt-90) REVERT: F 18 ASP cc_start: 0.6607 (p0) cc_final: 0.6156 (p0) REVERT: F 26 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7098 (tp) REVERT: F 35 LYS cc_start: 0.7976 (tttt) cc_final: 0.6971 (pmtt) REVERT: F 76 LYS cc_start: 0.8234 (mppt) cc_final: 0.6852 (pmtt) outliers start: 11 outliers final: 6 residues processed: 101 average time/residue: 1.3606 time to fit residues: 142.0563 Evaluate side-chains 96 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 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 26 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.5715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 4416 Z= 0.434 Angle : 0.717 10.657 6006 Z= 0.377 Chirality : 0.052 0.146 708 Planarity : 0.005 0.038 738 Dihedral : 5.645 17.621 594 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.78 % Allowed : 26.50 % Favored : 70.73 % 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: -2.57 (0.32), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 79 HIS 0.005 0.001 HIS F 31 PHE 0.012 0.002 PHE A 87 TYR 0.015 0.003 TYR E 69 ARG 0.009 0.001 ARG E 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 104 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.606 Fit side-chains REVERT: A 34 ARG cc_start: 0.7628 (ttt-90) cc_final: 0.7027 (pmt170) REVERT: A 76 LYS cc_start: 0.8553 (mptt) cc_final: 0.6952 (mmpt) REVERT: B 13 MET cc_start: 0.6880 (OUTLIER) cc_final: 0.6430 (ttm) REVERT: B 89 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7571 (mt-10) REVERT: C 21 ARG cc_start: 0.6999 (tpp80) cc_final: 0.6549 (tpp-160) REVERT: C 23 SER cc_start: 0.7994 (m) cc_final: 0.7677 (m) REVERT: C 34 ARG cc_start: 0.7690 (ttt-90) cc_final: 0.7428 (ttt-90) REVERT: D 21 ARG cc_start: 0.6968 (OUTLIER) cc_final: 0.6473 (tpp80) REVERT: E 13 MET cc_start: 0.7028 (tmm) cc_final: 0.6786 (tmm) REVERT: E 15 LYS cc_start: 0.8166 (mtpt) cc_final: 0.7887 (mtmm) REVERT: F 26 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7475 (tp) REVERT: F 35 LYS cc_start: 0.8109 (tttt) cc_final: 0.7081 (pmtt) outliers start: 13 outliers final: 7 residues processed: 97 average time/residue: 1.5085 time to fit residues: 150.8644 Evaluate side-chains 100 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 B residue 104 ARG Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 26 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 45 optimal weight: 6.9990 chunk 48 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.5780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4416 Z= 0.275 Angle : 0.657 10.589 6006 Z= 0.336 Chirality : 0.051 0.138 708 Planarity : 0.005 0.043 738 Dihedral : 5.381 16.649 594 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.35 % Allowed : 26.28 % Favored : 71.37 % 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: -2.54 (0.32), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 79 HIS 0.003 0.001 HIS E 31 PHE 0.011 0.001 PHE A 87 TYR 0.014 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 111 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.486 Fit side-chains REVERT: A 34 ARG cc_start: 0.7615 (ttt-90) cc_final: 0.7058 (pmt170) REVERT: A 76 LYS cc_start: 0.8509 (mptt) cc_final: 0.6947 (mmpt) REVERT: B 13 MET cc_start: 0.6831 (OUTLIER) cc_final: 0.6363 (ttm) REVERT: B 89 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7583 (mt-10) REVERT: B 110 LEU cc_start: 0.8796 (tt) cc_final: 0.8480 (tt) REVERT: C 21 ARG cc_start: 0.6954 (tpp80) cc_final: 0.6516 (tpp-160) REVERT: C 23 SER cc_start: 0.7994 (m) cc_final: 0.7647 (m) REVERT: C 34 ARG cc_start: 0.7730 (ttt-90) cc_final: 0.7487 (ttt-90) REVERT: C 99 ASP cc_start: 0.6509 (OUTLIER) cc_final: 0.6128 (t0) REVERT: D 13 MET cc_start: 0.6955 (OUTLIER) cc_final: 0.6715 (ttp) REVERT: D 21 ARG cc_start: 0.6957 (tpp80) cc_final: 0.6621 (ttp80) REVERT: E 13 MET cc_start: 0.7060 (tmm) cc_final: 0.5815 (tmm) REVERT: E 34 ARG cc_start: 0.7462 (ttt-90) cc_final: 0.7186 (ttt-90) REVERT: F 26 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7099 (tp) REVERT: F 35 LYS cc_start: 0.8055 (tttt) cc_final: 0.7197 (pmtt) REVERT: F 76 LYS cc_start: 0.8260 (mppt) cc_final: 0.6855 (pmtt) outliers start: 11 outliers final: 6 residues processed: 105 average time/residue: 1.4542 time to fit residues: 157.3458 Evaluate side-chains 102 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 B residue 104 ARG Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain D residue 13 MET Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 26 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 0.0570 chunk 13 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.9904 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.5862 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= 0.246 Angle : 0.639 11.037 6006 Z= 0.327 Chirality : 0.050 0.146 708 Planarity : 0.005 0.041 738 Dihedral : 5.203 16.334 594 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.56 % Allowed : 26.92 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.33), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (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 0.009 0.001 PHE A 87 TYR 0.014 0.002 TYR E 114 ARG 0.010 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 110 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7612 (ttt-90) cc_final: 0.7057 (pmt170) REVERT: A 76 LYS cc_start: 0.8520 (mptt) cc_final: 0.6965 (mmpt) REVERT: B 13 MET cc_start: 0.6838 (OUTLIER) cc_final: 0.6344 (ttm) REVERT: B 89 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7625 (mt-10) REVERT: B 110 LEU cc_start: 0.8723 (tt) cc_final: 0.8461 (tt) REVERT: C 21 ARG cc_start: 0.6897 (tpp80) cc_final: 0.6429 (tpp-160) REVERT: C 23 SER cc_start: 0.8006 (m) cc_final: 0.7656 (m) REVERT: C 34 ARG cc_start: 0.7736 (ttt-90) cc_final: 0.7521 (ttt-90) REVERT: C 99 ASP cc_start: 0.6562 (OUTLIER) cc_final: 0.6121 (t0) REVERT: D 21 ARG cc_start: 0.6980 (tpp80) cc_final: 0.6658 (ttp80) REVERT: E 13 MET cc_start: 0.7080 (tmm) cc_final: 0.5879 (tmm) REVERT: E 15 LYS cc_start: 0.8073 (mtpt) cc_final: 0.7666 (mtpm) REVERT: E 34 ARG cc_start: 0.7450 (ttt-90) cc_final: 0.7156 (ttt-90) REVERT: F 26 ILE cc_start: 0.7670 (OUTLIER) cc_final: 0.7016 (tp) REVERT: F 35 LYS cc_start: 0.8058 (tttt) cc_final: 0.7025 (pmtt) REVERT: F 76 LYS cc_start: 0.8204 (mppt) cc_final: 0.6810 (pmtt) outliers start: 12 outliers final: 6 residues processed: 102 average time/residue: 1.5830 time to fit residues: 166.2596 Evaluate side-chains 102 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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 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 26 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 4.9990 chunk 5 optimal weight: 0.0070 chunk 7 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 2 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 49 optimal weight: 0.0020 chunk 28 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 1 optimal weight: 0.0770 chunk 34 optimal weight: 0.7980 overall best weight: 0.2964 ------------------------------------------------------------------------------- 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 = 0.4198 r_free = 0.4198 target = 0.128935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.112103 restraints weight = 6361.249| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 2.59 r_work: 0.3919 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3809 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.5983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4416 Z= 0.192 Angle : 0.614 12.188 6006 Z= 0.308 Chirality : 0.050 0.136 708 Planarity : 0.004 0.041 738 Dihedral : 4.905 16.207 594 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.71 % Allowed : 27.56 % Favored : 70.73 % 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: -2.44 (0.33), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 79 HIS 0.003 0.000 HIS D 31 PHE 0.007 0.001 PHE D 64 TYR 0.015 0.001 TYR E 114 ARG 0.010 0.001 ARG E 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2789.42 seconds wall clock time: 50 minutes 32.01 seconds (3032.01 seconds total)