Starting phenix.real_space_refine on Tue Dec 31 07:03:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ynk_39425/12_2024/8ynk_39425.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ynk_39425/12_2024/8ynk_39425.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ynk_39425/12_2024/8ynk_39425.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ynk_39425/12_2024/8ynk_39425.map" model { file = "/net/cci-nas-00/data/ceres_data/8ynk_39425/12_2024/8ynk_39425.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ynk_39425/12_2024/8ynk_39425.cif" } resolution = 3.62 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= 0.001 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4446 atoms to isotropic. 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 66 5.16 5 C 7343 2.51 5 N 1983 2.21 5 O 2172 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11564 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1510 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 3, 'TRANS': 178} Chain: "B" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1510 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 3, 'TRANS': 178} Chain: "C" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1510 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 3, 'TRANS': 178} Chain: "H" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1403 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain breaks: 1 Chain: "I" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1386 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 4, 'TRANS': 165} Chain breaks: 1 Chain: "J" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1397 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 4, 'TRANS': 166} Chain breaks: 1 Chain: "K" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1424 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 4, 'TRANS': 170} Chain: "G" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1424 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 4, 'TRANS': 170} Time building chain proxies: 7.39, per 1000 atoms: 0.64 Number of scatterers: 11564 At special positions: 0 Unit cell: (102.48, 101.64, 141.96, 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 66 16.00 O 2172 8.00 N 1983 7.00 C 7343 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.4 seconds 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2736 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 0 sheets defined 76.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 15 through 26 Processing helix chain 'A' and resid 27 through 29 No H-bonds generated for 'chain 'A' and resid 27 through 29' Processing helix chain 'A' and resid 31 through 36 Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.618A pdb=" N LEU A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 51 " --> pdb=" O ARG A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 71 through 78 removed outlier: 3.776A pdb=" N LEU A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 92 removed outlier: 3.680A pdb=" N THR A 92 " --> pdb=" O ARG A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 111 removed outlier: 3.523A pdb=" N VAL A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 130 through 134 removed outlier: 3.670A pdb=" N ASP A 134 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 149 Processing helix chain 'A' and resid 157 through 168 removed outlier: 3.907A pdb=" N GLN A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE A 167 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 182 Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 15 through 26 Processing helix chain 'B' and resid 31 through 36 Processing helix chain 'B' and resid 40 through 51 removed outlier: 3.763A pdb=" N LEU B 44 " --> pdb=" O ASP B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 removed outlier: 3.537A pdb=" N ILE B 69 " --> pdb=" O LEU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 79 removed outlier: 4.205A pdb=" N LEU B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'B' and resid 99 through 111 Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 129 through 134 removed outlier: 3.956A pdb=" N ASP B 134 " --> pdb=" O CYS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 149 Processing helix chain 'B' and resid 157 through 165 Processing helix chain 'B' and resid 169 through 182 Processing helix chain 'C' and resid 2 through 14 removed outlier: 3.669A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU C 14 " --> pdb=" O ILE C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 26 Processing helix chain 'C' and resid 31 through 36 Processing helix chain 'C' and resid 40 through 51 removed outlier: 3.717A pdb=" N LEU C 44 " --> pdb=" O ASP C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 71 through 78 removed outlier: 3.721A pdb=" N LEU C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 92 removed outlier: 3.511A pdb=" N MET C 86 " --> pdb=" O ARG C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 111 removed outlier: 3.519A pdb=" N VAL C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU C 111 " --> pdb=" O GLN C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 124 Processing helix chain 'C' and resid 130 through 134 Processing helix chain 'C' and resid 138 through 149 Processing helix chain 'C' and resid 157 through 165 Processing helix chain 'C' and resid 169 through 182 Processing helix chain 'H' and resid 3 through 12 Processing helix chain 'H' and resid 14 through 26 Processing helix chain 'H' and resid 36 through 48 Processing helix chain 'H' and resid 51 through 62 removed outlier: 3.638A pdb=" N VAL H 62 " --> pdb=" O LEU H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 71 Processing helix chain 'H' and resid 75 through 86 Processing helix chain 'H' and resid 91 through 102 Processing helix chain 'H' and resid 105 through 116 Processing helix chain 'H' and resid 121 through 126 removed outlier: 3.735A pdb=" N ILE H 125 " --> pdb=" O GLY H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 141 removed outlier: 3.563A pdb=" N LEU H 134 " --> pdb=" O SER H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 159 Processing helix chain 'H' and resid 161 through 175 removed outlier: 3.946A pdb=" N LYS H 165 " --> pdb=" O ARG H 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 13 Processing helix chain 'I' and resid 14 through 25 Processing helix chain 'I' and resid 36 through 47 Processing helix chain 'I' and resid 51 through 62 Processing helix chain 'I' and resid 64 through 71 Processing helix chain 'I' and resid 75 through 86 Processing helix chain 'I' and resid 91 through 104 removed outlier: 3.825A pdb=" N VAL I 95 " --> pdb=" O SER I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 117 Processing helix chain 'I' and resid 130 through 141 Processing helix chain 'I' and resid 149 through 159 Processing helix chain 'I' and resid 161 through 176 removed outlier: 4.005A pdb=" N LYS I 165 " --> pdb=" O ARG I 161 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 13 removed outlier: 3.827A pdb=" N ILE J 6 " --> pdb=" O SER J 2 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 27 removed outlier: 4.282A pdb=" N ASP J 27 " --> pdb=" O PHE J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 47 Processing helix chain 'J' and resid 51 through 63 Processing helix chain 'J' and resid 64 through 71 removed outlier: 3.816A pdb=" N LEU J 68 " --> pdb=" O ARG J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 86 Processing helix chain 'J' and resid 91 through 104 removed outlier: 3.594A pdb=" N ASP J 103 " --> pdb=" O GLU J 99 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU J 104 " --> pdb=" O ILE J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 105 through 117 removed outlier: 3.862A pdb=" N VAL J 109 " --> pdb=" O ASP J 105 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER J 110 " --> pdb=" O LYS J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 141 Processing helix chain 'J' and resid 149 through 159 Processing helix chain 'J' and resid 161 through 175 removed outlier: 3.902A pdb=" N LYS J 165 " --> pdb=" O ARG J 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 12 removed outlier: 3.677A pdb=" N ILE K 6 " --> pdb=" O SER K 2 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 25 removed outlier: 3.539A pdb=" N LYS K 18 " --> pdb=" O ASP K 14 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU K 19 " --> pdb=" O THR K 15 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N MET K 20 " --> pdb=" O ASP K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 48 Processing helix chain 'K' and resid 51 through 62 Processing helix chain 'K' and resid 64 through 71 removed outlier: 3.568A pdb=" N LEU K 68 " --> pdb=" O ARG K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 85 removed outlier: 3.512A pdb=" N VAL K 79 " --> pdb=" O ASP K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 103 Processing helix chain 'K' and resid 105 through 116 removed outlier: 3.897A pdb=" N VAL K 109 " --> pdb=" O ASP K 105 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER K 110 " --> pdb=" O LYS K 106 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER K 111 " --> pdb=" O SER K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 141 Processing helix chain 'K' and resid 149 through 159 Processing helix chain 'K' and resid 162 through 175 Processing helix chain 'G' and resid 2 through 12 removed outlier: 3.738A pdb=" N ILE G 6 " --> pdb=" O SER G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 25 removed outlier: 3.561A pdb=" N LYS G 18 " --> pdb=" O ASP G 14 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU G 19 " --> pdb=" O THR G 15 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N MET G 20 " --> pdb=" O ASP G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 48 Processing helix chain 'G' and resid 51 through 62 removed outlier: 3.682A pdb=" N VAL G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 71 removed outlier: 3.566A pdb=" N LEU G 68 " --> pdb=" O ARG G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 85 Processing helix chain 'G' and resid 91 through 102 removed outlier: 3.526A pdb=" N VAL G 95 " --> pdb=" O SER G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 117 removed outlier: 3.737A pdb=" N SER G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 141 Processing helix chain 'G' and resid 149 through 159 removed outlier: 3.716A pdb=" N ILE G 159 " --> pdb=" O CYS G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 175 652 hydrogen bonds defined for protein. 1941 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.78 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3872 1.34 - 1.46: 2053 1.46 - 1.58: 5643 1.58 - 1.69: 0 1.69 - 1.81: 116 Bond restraints: 11684 Sorted by residual: bond pdb=" CB PRO H 87 " pdb=" CG PRO H 87 " ideal model delta sigma weight residual 1.492 1.531 -0.039 5.00e-02 4.00e+02 6.14e-01 bond pdb=" CA ILE B 69 " pdb=" C ILE B 69 " ideal model delta sigma weight residual 1.530 1.522 0.008 1.12e-02 7.97e+03 5.53e-01 bond pdb=" CA ILE K 159 " pdb=" C ILE K 159 " ideal model delta sigma weight residual 1.523 1.531 -0.008 1.27e-02 6.20e+03 4.11e-01 bond pdb=" CA ILE G 159 " pdb=" C ILE G 159 " ideal model delta sigma weight residual 1.530 1.523 0.007 1.12e-02 7.97e+03 4.11e-01 bond pdb=" N GLU H 128 " pdb=" CA GLU H 128 " ideal model delta sigma weight residual 1.462 1.472 -0.010 1.54e-02 4.22e+03 3.85e-01 ... (remaining 11679 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 15275 1.06 - 2.12: 306 2.12 - 3.19: 55 3.19 - 4.25: 13 4.25 - 5.31: 3 Bond angle restraints: 15652 Sorted by residual: angle pdb=" N ILE A 151 " pdb=" CA ILE A 151 " pdb=" C ILE A 151 " ideal model delta sigma weight residual 113.16 108.45 4.71 1.49e+00 4.50e-01 9.99e+00 angle pdb=" C ARG B 149 " pdb=" N VAL B 150 " pdb=" CA VAL B 150 " ideal model delta sigma weight residual 121.97 126.15 -4.18 1.80e+00 3.09e-01 5.40e+00 angle pdb=" N ILE B 69 " pdb=" CA ILE B 69 " pdb=" C ILE B 69 " ideal model delta sigma weight residual 111.91 109.91 2.00 8.90e-01 1.26e+00 5.05e+00 angle pdb=" C ARG A 149 " pdb=" N VAL A 150 " pdb=" CA VAL A 150 " ideal model delta sigma weight residual 121.97 125.96 -3.99 1.80e+00 3.09e-01 4.91e+00 angle pdb=" N ILE G 159 " pdb=" CA ILE G 159 " pdb=" C ILE G 159 " ideal model delta sigma weight residual 111.91 109.97 1.94 8.90e-01 1.26e+00 4.76e+00 ... (remaining 15647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 6662 17.90 - 35.79: 652 35.79 - 53.69: 82 53.69 - 71.59: 16 71.59 - 89.48: 10 Dihedral angle restraints: 7422 sinusoidal: 3250 harmonic: 4172 Sorted by residual: dihedral pdb=" CB GLU B 12 " pdb=" CG GLU B 12 " pdb=" CD GLU B 12 " pdb=" OE1 GLU B 12 " ideal model delta sinusoidal sigma weight residual 0.00 -88.41 88.41 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB MET K 97 " pdb=" CG MET K 97 " pdb=" SD MET K 97 " pdb=" CE MET K 97 " ideal model delta sinusoidal sigma weight residual 60.00 117.05 -57.05 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CG ARG K 38 " pdb=" CD ARG K 38 " pdb=" NE ARG K 38 " pdb=" CZ ARG K 38 " ideal model delta sinusoidal sigma weight residual -90.00 -131.52 41.52 2 1.50e+01 4.44e-03 9.38e+00 ... (remaining 7419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1251 0.030 - 0.061: 439 0.061 - 0.091: 94 0.091 - 0.121: 34 0.121 - 0.151: 3 Chirality restraints: 1821 Sorted by residual: chirality pdb=" CB VAL H 62 " pdb=" CA VAL H 62 " pdb=" CG1 VAL H 62 " pdb=" CG2 VAL H 62 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.72e-01 chirality pdb=" CB VAL A 150 " pdb=" CA VAL A 150 " pdb=" CG1 VAL A 150 " pdb=" CG2 VAL A 150 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE A 128 " pdb=" N ILE A 128 " pdb=" C ILE A 128 " pdb=" CB ILE A 128 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 1818 not shown) Planarity restraints: 1989 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA H 145 " 0.022 5.00e-02 4.00e+02 3.33e-02 1.78e+00 pdb=" N PRO H 146 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO H 146 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO H 146 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 150 " -0.006 2.00e-02 2.50e+03 1.15e-02 1.32e+00 pdb=" C VAL C 150 " 0.020 2.00e-02 2.50e+03 pdb=" O VAL C 150 " -0.008 2.00e-02 2.50e+03 pdb=" N ILE C 151 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA G 145 " -0.018 5.00e-02 4.00e+02 2.74e-02 1.20e+00 pdb=" N PRO G 146 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO G 146 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO G 146 " -0.015 5.00e-02 4.00e+02 ... (remaining 1986 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2223 2.77 - 3.30: 11199 3.30 - 3.84: 17845 3.84 - 4.37: 19893 4.37 - 4.90: 34337 Nonbonded interactions: 85497 Sorted by model distance: nonbonded pdb=" OH TYR A 29 " pdb=" O GLN A 97 " model vdw 2.242 3.040 nonbonded pdb=" O TYR B 106 " pdb=" OG SER B 109 " model vdw 2.246 3.040 nonbonded pdb=" OH TYR A 106 " pdb=" OE2 GLU A 110 " model vdw 2.251 3.040 nonbonded pdb=" O ASP K 163 " pdb=" OG1 THR K 166 " model vdw 2.270 3.040 nonbonded pdb=" OD1 ASP B 28 " pdb=" NH2 ARG B 102 " model vdw 2.312 3.120 ... (remaining 85492 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' } ncs_group { reference = (chain 'G' and (resid 2 through 28 or resid 31 through 121 or resid 128 through \ 175)) selection = (chain 'H' and (resid 2 through 121 or resid 128 through 175)) selection = (chain 'I' and (resid 2 through 28 or resid 31 through 175)) selection = (chain 'J' and (resid 2 through 28 or resid 31 through 121 or resid 128 through \ 175)) selection = (chain 'K' and (resid 2 through 28 or resid 31 through 121 or resid 128 through \ 175)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 26.190 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 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 : 0.002 0.039 11684 Z= 0.159 Angle : 0.400 5.312 15652 Z= 0.220 Chirality : 0.034 0.151 1821 Planarity : 0.002 0.033 1989 Dihedral : 13.746 89.483 4686 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.24), residues: 1387 helix: 2.01 (0.17), residues: 1032 sheet: None (None), residues: 0 loop : -0.76 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 88 PHE 0.009 0.001 PHE A 61 TYR 0.006 0.001 TYR B 101 ARG 0.004 0.000 ARG I 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8512 (t0) cc_final: 0.8039 (m110) REVERT: A 101 TYR cc_start: 0.8909 (t80) cc_final: 0.8494 (t80) REVERT: A 124 LEU cc_start: 0.9147 (mt) cc_final: 0.8754 (tt) REVERT: C 104 MET cc_start: 0.9507 (ptm) cc_final: 0.9004 (ptm) REVERT: H 8 GLN cc_start: 0.8910 (mt0) cc_final: 0.8640 (mp10) REVERT: H 36 ASN cc_start: 0.8654 (m-40) cc_final: 0.8290 (t0) REVERT: H 71 ILE cc_start: 0.8843 (mm) cc_final: 0.8587 (mm) REVERT: H 116 MET cc_start: 0.9138 (mmm) cc_final: 0.8873 (mmm) REVERT: I 82 HIS cc_start: 0.8883 (t70) cc_final: 0.8620 (t70) REVERT: J 57 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7912 (tm-30) REVERT: J 86 ASN cc_start: 0.8878 (t0) cc_final: 0.8576 (m-40) REVERT: K 39 ASP cc_start: 0.8812 (m-30) cc_final: 0.8605 (m-30) REVERT: K 86 ASN cc_start: 0.7231 (m110) cc_final: 0.6824 (t0) REVERT: K 166 THR cc_start: 0.9230 (p) cc_final: 0.8888 (p) REVERT: G 6 ILE cc_start: 0.9203 (mt) cc_final: 0.8825 (mt) REVERT: G 43 ILE cc_start: 0.9597 (mm) cc_final: 0.9386 (mt) REVERT: G 60 TYR cc_start: 0.8835 (t80) cc_final: 0.8559 (t80) REVERT: G 66 ASP cc_start: 0.8700 (p0) cc_final: 0.8405 (p0) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.2828 time to fit residues: 125.7683 Evaluate side-chains 173 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 0.0270 chunk 105 optimal weight: 0.2980 chunk 58 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 56 optimal weight: 0.0670 chunk 108 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 173 GLN K 8 GLN K 169 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11684 Z= 0.155 Angle : 0.526 7.214 15652 Z= 0.277 Chirality : 0.036 0.165 1821 Planarity : 0.003 0.036 1989 Dihedral : 3.375 12.564 1542 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.29 % Allowed : 9.55 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.24), residues: 1387 helix: 1.73 (0.17), residues: 1089 sheet: None (None), residues: 0 loop : -0.92 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 7 PHE 0.017 0.001 PHE C 24 TYR 0.011 0.001 TYR C 178 ARG 0.007 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 204 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.8506 (tt0) cc_final: 0.8252 (tt0) REVERT: A 76 ILE cc_start: 0.8932 (tp) cc_final: 0.8694 (pt) REVERT: A 80 ASN cc_start: 0.8373 (t0) cc_final: 0.7904 (m110) REVERT: A 138 ASN cc_start: 0.7864 (p0) cc_final: 0.7664 (p0) REVERT: B 43 MET cc_start: 0.7107 (mtt) cc_final: 0.6874 (mtt) REVERT: B 92 THR cc_start: 0.8769 (m) cc_final: 0.8294 (p) REVERT: B 110 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7539 (pp20) REVERT: C 104 MET cc_start: 0.9340 (ptm) cc_final: 0.8996 (ptm) REVERT: C 176 ASN cc_start: 0.9038 (m110) cc_final: 0.8798 (p0) REVERT: C 178 TYR cc_start: 0.8815 (t80) cc_final: 0.8606 (t80) REVERT: H 8 GLN cc_start: 0.8963 (mt0) cc_final: 0.8688 (mt0) REVERT: H 36 ASN cc_start: 0.8719 (m-40) cc_final: 0.8261 (t0) REVERT: H 66 ASP cc_start: 0.7622 (p0) cc_final: 0.7345 (p0) REVERT: H 133 ASP cc_start: 0.8200 (m-30) cc_final: 0.7978 (m-30) REVERT: I 14 ASP cc_start: 0.7757 (m-30) cc_final: 0.7359 (t70) REVERT: J 57 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7788 (tm-30) REVERT: J 86 ASN cc_start: 0.8930 (t0) cc_final: 0.8702 (m110) REVERT: K 93 TYR cc_start: 0.8063 (t80) cc_final: 0.7812 (t80) REVERT: K 116 MET cc_start: 0.8596 (mtm) cc_final: 0.8128 (mmm) REVERT: K 131 PHE cc_start: 0.8896 (t80) cc_final: 0.8692 (t80) REVERT: G 60 TYR cc_start: 0.8942 (t80) cc_final: 0.8581 (t80) REVERT: G 66 ASP cc_start: 0.8645 (p0) cc_final: 0.8391 (p0) REVERT: G 102 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7669 (tp30) outliers start: 17 outliers final: 7 residues processed: 216 average time/residue: 0.2072 time to fit residues: 66.3445 Evaluate side-chains 164 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 156 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 125 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 105 optimal weight: 0.2980 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 101 optimal weight: 0.0970 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 88 HIS K 8 GLN G 158 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11684 Z= 0.172 Angle : 0.524 8.403 15652 Z= 0.267 Chirality : 0.037 0.150 1821 Planarity : 0.003 0.032 1989 Dihedral : 3.440 13.635 1542 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.12 % Allowed : 11.68 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.24), residues: 1387 helix: 1.82 (0.17), residues: 1068 sheet: None (None), residues: 0 loop : -0.89 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS I 88 PHE 0.014 0.001 PHE H 65 TYR 0.013 0.001 TYR A 101 ARG 0.003 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 174 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.8514 (tt0) cc_final: 0.8272 (tt0) REVERT: A 80 ASN cc_start: 0.8535 (t0) cc_final: 0.8060 (m110) REVERT: A 148 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8592 (mtmm) REVERT: B 110 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7275 (pp20) REVERT: C 42 LEU cc_start: 0.8476 (mt) cc_final: 0.8269 (mt) REVERT: C 104 MET cc_start: 0.9372 (ptm) cc_final: 0.9117 (ptm) REVERT: C 146 MET cc_start: 0.8644 (mmp) cc_final: 0.8442 (mmp) REVERT: H 36 ASN cc_start: 0.8677 (m-40) cc_final: 0.8212 (t0) REVERT: H 66 ASP cc_start: 0.7662 (p0) cc_final: 0.7330 (p0) REVERT: H 133 ASP cc_start: 0.8229 (m-30) cc_final: 0.7963 (m-30) REVERT: I 176 GLN cc_start: 0.7384 (mp10) cc_final: 0.7067 (mp10) REVERT: J 57 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7803 (tm-30) REVERT: J 86 ASN cc_start: 0.8992 (t0) cc_final: 0.8775 (m110) REVERT: K 116 MET cc_start: 0.8596 (mtm) cc_final: 0.8229 (mmm) REVERT: G 60 TYR cc_start: 0.8997 (t80) cc_final: 0.8551 (t80) REVERT: G 66 ASP cc_start: 0.8664 (p0) cc_final: 0.8408 (p0) REVERT: G 102 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7735 (tp30) outliers start: 28 outliers final: 16 residues processed: 194 average time/residue: 0.2011 time to fit residues: 58.4801 Evaluate side-chains 174 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain I residue 91 SER Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 125 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 126 optimal weight: 0.0030 chunk 134 optimal weight: 0.0060 chunk 66 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 36 optimal weight: 8.9990 overall best weight: 1.2010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN C 176 ASN H 173 GLN K 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11684 Z= 0.174 Angle : 0.515 11.107 15652 Z= 0.263 Chirality : 0.037 0.144 1821 Planarity : 0.003 0.031 1989 Dihedral : 3.517 14.059 1542 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.12 % Allowed : 13.27 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.24), residues: 1387 helix: 1.72 (0.17), residues: 1088 sheet: None (None), residues: 0 loop : -1.01 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS I 88 PHE 0.022 0.001 PHE B 181 TYR 0.016 0.001 TYR A 101 ARG 0.002 0.000 ARG H 161 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8560 (t0) cc_final: 0.8065 (m110) REVERT: A 101 TYR cc_start: 0.8963 (t80) cc_final: 0.8716 (t80) REVERT: A 148 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8658 (mtmm) REVERT: B 110 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7419 (pp20) REVERT: C 42 LEU cc_start: 0.8457 (mt) cc_final: 0.8224 (mt) REVERT: C 104 MET cc_start: 0.9373 (ptm) cc_final: 0.9065 (ptm) REVERT: C 176 ASN cc_start: 0.9043 (m110) cc_final: 0.8763 (p0) REVERT: H 36 ASN cc_start: 0.8684 (m-40) cc_final: 0.8225 (t0) REVERT: H 66 ASP cc_start: 0.7681 (p0) cc_final: 0.7333 (p0) REVERT: H 97 MET cc_start: 0.8511 (mmm) cc_final: 0.7876 (mmm) REVERT: H 133 ASP cc_start: 0.8245 (m-30) cc_final: 0.7992 (m-30) REVERT: J 57 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7803 (tm-30) REVERT: K 116 MET cc_start: 0.8596 (mtm) cc_final: 0.8250 (mmm) REVERT: G 60 TYR cc_start: 0.9038 (t80) cc_final: 0.8627 (t80) REVERT: G 66 ASP cc_start: 0.8656 (p0) cc_final: 0.8395 (p0) REVERT: G 102 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7736 (tp30) outliers start: 28 outliers final: 18 residues processed: 186 average time/residue: 0.2042 time to fit residues: 57.4924 Evaluate side-chains 173 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 173 GLN Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain I residue 91 SER Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 52 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 86 ASN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11684 Z= 0.205 Angle : 0.529 9.927 15652 Z= 0.269 Chirality : 0.037 0.145 1821 Planarity : 0.003 0.052 1989 Dihedral : 3.604 17.423 1542 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.43 % Allowed : 14.18 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.24), residues: 1387 helix: 1.77 (0.17), residues: 1079 sheet: None (None), residues: 0 loop : -1.00 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS I 160 PHE 0.011 0.001 PHE A 61 TYR 0.012 0.001 TYR A 101 ARG 0.002 0.000 ARG H 161 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8583 (t0) cc_final: 0.8064 (m110) REVERT: A 101 TYR cc_start: 0.8985 (t80) cc_final: 0.8729 (t80) REVERT: A 148 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8529 (mtmm) REVERT: B 92 THR cc_start: 0.8836 (m) cc_final: 0.8372 (p) REVERT: B 110 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7475 (pp20) REVERT: C 42 LEU cc_start: 0.8415 (mt) cc_final: 0.8116 (mt) REVERT: C 78 TYR cc_start: 0.8894 (m-80) cc_final: 0.8557 (m-10) REVERT: C 104 MET cc_start: 0.9377 (ptm) cc_final: 0.9162 (ptm) REVERT: C 110 GLU cc_start: 0.8754 (tp30) cc_final: 0.8118 (tp30) REVERT: C 124 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8567 (tt) REVERT: H 36 ASN cc_start: 0.8658 (m-40) cc_final: 0.8202 (t0) REVERT: H 66 ASP cc_start: 0.7746 (p0) cc_final: 0.7391 (p0) REVERT: H 97 MET cc_start: 0.8549 (mmm) cc_final: 0.7847 (mmm) REVERT: H 133 ASP cc_start: 0.8249 (m-30) cc_final: 0.7998 (m-30) REVERT: J 57 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7823 (tm-30) REVERT: J 173 GLN cc_start: 0.8223 (mt0) cc_final: 0.7815 (tm-30) REVERT: K 116 MET cc_start: 0.8584 (mtm) cc_final: 0.8274 (mmm) REVERT: G 60 TYR cc_start: 0.9079 (t80) cc_final: 0.8827 (t80) REVERT: G 66 ASP cc_start: 0.8659 (p0) cc_final: 0.8411 (p0) REVERT: G 102 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7768 (tp30) outliers start: 32 outliers final: 22 residues processed: 181 average time/residue: 0.2032 time to fit residues: 56.0007 Evaluate side-chains 178 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain I residue 91 SER Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 134 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 11 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 173 GLN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 11684 Z= 0.400 Angle : 0.690 9.637 15652 Z= 0.346 Chirality : 0.041 0.159 1821 Planarity : 0.004 0.035 1989 Dihedral : 4.139 19.386 1542 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.96 % Allowed : 15.31 % Favored : 81.73 % 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: 1.22 (0.23), residues: 1387 helix: 1.39 (0.16), residues: 1079 sheet: None (None), residues: 0 loop : -1.18 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 160 PHE 0.023 0.002 PHE B 181 TYR 0.013 0.002 TYR A 106 ARG 0.004 0.001 ARG H 161 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 TYR cc_start: 0.9170 (t80) cc_final: 0.8685 (t80) REVERT: A 148 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8453 (mtmm) REVERT: B 110 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7472 (pp20) REVERT: C 78 TYR cc_start: 0.8931 (m-80) cc_final: 0.8625 (m-10) REVERT: C 104 MET cc_start: 0.9434 (ptm) cc_final: 0.9171 (ptm) REVERT: C 124 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8627 (tt) REVERT: C 176 ASN cc_start: 0.9121 (m110) cc_final: 0.8851 (p0) REVERT: H 66 ASP cc_start: 0.7837 (p0) cc_final: 0.7420 (p0) REVERT: H 97 MET cc_start: 0.8630 (mmm) cc_final: 0.7943 (mmm) REVERT: J 57 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7929 (tm-30) REVERT: J 99 GLU cc_start: 0.9082 (tp30) cc_final: 0.8874 (tp30) REVERT: K 69 LYS cc_start: 0.9329 (tttt) cc_final: 0.9046 (mmmt) REVERT: K 88 HIS cc_start: 0.8452 (m-70) cc_final: 0.7860 (m-70) REVERT: G 66 ASP cc_start: 0.8728 (p0) cc_final: 0.8377 (p0) REVERT: G 120 MET cc_start: 0.8291 (ppp) cc_final: 0.8028 (ppp) outliers start: 39 outliers final: 27 residues processed: 180 average time/residue: 0.2140 time to fit residues: 57.1977 Evaluate side-chains 171 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain I residue 91 SER Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 134 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 133 optimal weight: 2.9990 chunk 83 optimal weight: 0.0870 chunk 81 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN H 8 GLN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11684 Z= 0.208 Angle : 0.550 10.744 15652 Z= 0.281 Chirality : 0.038 0.163 1821 Planarity : 0.003 0.070 1989 Dihedral : 3.891 18.284 1542 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.43 % Allowed : 16.30 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.24), residues: 1387 helix: 1.57 (0.17), residues: 1080 sheet: None (None), residues: 0 loop : -1.20 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS I 160 PHE 0.020 0.001 PHE B 181 TYR 0.018 0.001 TYR G 60 ARG 0.007 0.000 ARG C 149 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 TYR cc_start: 0.8953 (t80) cc_final: 0.8727 (t80) REVERT: A 148 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8540 (mtmm) REVERT: B 92 THR cc_start: 0.8890 (m) cc_final: 0.8443 (p) REVERT: B 110 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7724 (pp20) REVERT: C 78 TYR cc_start: 0.8959 (m-80) cc_final: 0.8647 (m-10) REVERT: C 104 MET cc_start: 0.9353 (ptm) cc_final: 0.9145 (ptm) REVERT: C 107 GLN cc_start: 0.8866 (mt0) cc_final: 0.8511 (mt0) REVERT: C 176 ASN cc_start: 0.9081 (m110) cc_final: 0.8829 (p0) REVERT: H 66 ASP cc_start: 0.7815 (p0) cc_final: 0.7426 (p0) REVERT: H 97 MET cc_start: 0.8555 (mmm) cc_final: 0.7881 (mmm) REVERT: I 57 GLU cc_start: 0.8744 (tp30) cc_final: 0.8195 (tt0) REVERT: J 57 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7899 (tm-30) REVERT: J 99 GLU cc_start: 0.9022 (tp30) cc_final: 0.8736 (tp30) REVERT: K 88 HIS cc_start: 0.8442 (m-70) cc_final: 0.8034 (m-70) REVERT: K 116 MET cc_start: 0.8465 (mtm) cc_final: 0.8070 (mmm) REVERT: G 66 ASP cc_start: 0.8640 (p0) cc_final: 0.8281 (p0) REVERT: G 102 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7804 (tp30) REVERT: G 120 MET cc_start: 0.8291 (ppp) cc_final: 0.7950 (ppp) outliers start: 32 outliers final: 21 residues processed: 182 average time/residue: 0.1993 time to fit residues: 55.1107 Evaluate side-chains 173 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 91 SER Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 134 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 8 GLN H 88 HIS ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 169 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11684 Z= 0.199 Angle : 0.563 10.353 15652 Z= 0.287 Chirality : 0.038 0.153 1821 Planarity : 0.003 0.057 1989 Dihedral : 3.814 19.023 1542 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.35 % Allowed : 17.21 % Favored : 80.44 % 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: 1.54 (0.24), residues: 1387 helix: 1.68 (0.17), residues: 1068 sheet: None (None), residues: 0 loop : -1.22 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 88 PHE 0.021 0.001 PHE C 120 TYR 0.041 0.001 TYR K 93 ARG 0.007 0.000 ARG C 149 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 TYR cc_start: 0.8934 (t80) cc_final: 0.8726 (t80) REVERT: A 148 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8542 (mtmm) REVERT: B 110 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7788 (pp20) REVERT: C 78 TYR cc_start: 0.8966 (m-80) cc_final: 0.8643 (m-10) REVERT: C 104 MET cc_start: 0.9336 (ptm) cc_final: 0.9132 (ptm) REVERT: C 107 GLN cc_start: 0.8828 (mt0) cc_final: 0.8491 (mt0) REVERT: C 176 ASN cc_start: 0.9094 (m110) cc_final: 0.8847 (p0) REVERT: H 66 ASP cc_start: 0.7828 (p0) cc_final: 0.7431 (p0) REVERT: H 133 ASP cc_start: 0.8253 (m-30) cc_final: 0.8011 (m-30) REVERT: I 57 GLU cc_start: 0.8759 (tp30) cc_final: 0.8229 (tt0) REVERT: I 116 MET cc_start: 0.8593 (mmt) cc_final: 0.8325 (mmt) REVERT: J 57 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7890 (tm-30) REVERT: J 99 GLU cc_start: 0.9020 (tp30) cc_final: 0.8717 (tp30) REVERT: K 88 HIS cc_start: 0.8458 (m-70) cc_final: 0.8034 (m-70) REVERT: K 116 MET cc_start: 0.8465 (mtm) cc_final: 0.7970 (mmt) REVERT: G 66 ASP cc_start: 0.8614 (p0) cc_final: 0.8254 (p0) REVERT: G 102 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7787 (tp30) REVERT: G 120 MET cc_start: 0.8276 (ppp) cc_final: 0.7934 (ppp) outliers start: 31 outliers final: 24 residues processed: 176 average time/residue: 0.1997 time to fit residues: 54.0204 Evaluate side-chains 173 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 91 SER Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 134 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 132 optimal weight: 5.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11684 Z= 0.207 Angle : 0.575 10.320 15652 Z= 0.290 Chirality : 0.038 0.204 1821 Planarity : 0.003 0.048 1989 Dihedral : 3.778 19.069 1542 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.20 % Allowed : 17.44 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.24), residues: 1387 helix: 1.68 (0.17), residues: 1067 sheet: None (None), residues: 0 loop : -1.15 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 88 PHE 0.032 0.002 PHE I 114 TYR 0.025 0.001 TYR K 93 ARG 0.007 0.000 ARG C 149 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 TYR cc_start: 0.8932 (t80) cc_final: 0.8724 (t80) REVERT: A 148 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8535 (mtmm) REVERT: B 92 THR cc_start: 0.8888 (m) cc_final: 0.8485 (p) REVERT: B 110 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7814 (pp20) REVERT: C 78 TYR cc_start: 0.8986 (m-80) cc_final: 0.8668 (m-10) REVERT: C 104 MET cc_start: 0.9344 (ptm) cc_final: 0.9140 (ptm) REVERT: C 107 GLN cc_start: 0.8879 (mt0) cc_final: 0.8554 (mt0) REVERT: C 146 MET cc_start: 0.8890 (tpp) cc_final: 0.8526 (mmm) REVERT: C 176 ASN cc_start: 0.9078 (m110) cc_final: 0.8826 (p0) REVERT: H 66 ASP cc_start: 0.7834 (p0) cc_final: 0.7442 (p0) REVERT: H 116 MET cc_start: 0.9043 (mmm) cc_final: 0.8742 (mmt) REVERT: H 133 ASP cc_start: 0.8222 (m-30) cc_final: 0.7986 (m-30) REVERT: I 57 GLU cc_start: 0.8759 (tp30) cc_final: 0.8233 (tt0) REVERT: J 57 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7890 (tm-30) REVERT: J 99 GLU cc_start: 0.9024 (tp30) cc_final: 0.8760 (tp30) REVERT: K 88 HIS cc_start: 0.8440 (m-70) cc_final: 0.7883 (m-70) REVERT: K 116 MET cc_start: 0.8476 (mtm) cc_final: 0.8015 (mmp) REVERT: G 66 ASP cc_start: 0.8609 (p0) cc_final: 0.8258 (p0) REVERT: G 102 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7785 (tp30) REVERT: G 120 MET cc_start: 0.8242 (ppp) cc_final: 0.7906 (ppp) outliers start: 29 outliers final: 24 residues processed: 170 average time/residue: 0.1980 time to fit residues: 51.1771 Evaluate side-chains 176 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 91 SER Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 134 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 110 optimal weight: 0.1980 chunk 11 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11684 Z= 0.184 Angle : 0.564 10.964 15652 Z= 0.286 Chirality : 0.038 0.206 1821 Planarity : 0.003 0.044 1989 Dihedral : 3.714 18.973 1542 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.27 % Allowed : 17.74 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.24), residues: 1387 helix: 1.74 (0.17), residues: 1065 sheet: None (None), residues: 0 loop : -1.19 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 88 PHE 0.025 0.002 PHE I 114 TYR 0.022 0.001 TYR K 93 ARG 0.007 0.000 ARG C 149 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 TYR cc_start: 0.8914 (t80) cc_final: 0.8683 (t80) REVERT: A 124 LEU cc_start: 0.9205 (tp) cc_final: 0.8927 (tt) REVERT: A 148 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8544 (mtmm) REVERT: B 92 THR cc_start: 0.8888 (m) cc_final: 0.8431 (p) REVERT: B 110 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7832 (pp20) REVERT: C 78 TYR cc_start: 0.8983 (m-80) cc_final: 0.8654 (m-10) REVERT: C 104 MET cc_start: 0.9340 (ptm) cc_final: 0.9138 (ptm) REVERT: C 107 GLN cc_start: 0.8899 (mt0) cc_final: 0.8589 (mt0) REVERT: C 146 MET cc_start: 0.8892 (tpp) cc_final: 0.8507 (mmm) REVERT: C 176 ASN cc_start: 0.9071 (m110) cc_final: 0.8820 (p0) REVERT: H 66 ASP cc_start: 0.7845 (p0) cc_final: 0.7462 (p0) REVERT: H 133 ASP cc_start: 0.8205 (m-30) cc_final: 0.7967 (m-30) REVERT: I 57 GLU cc_start: 0.8762 (tp30) cc_final: 0.8245 (tt0) REVERT: J 99 GLU cc_start: 0.8998 (tp30) cc_final: 0.8729 (tp30) REVERT: K 88 HIS cc_start: 0.8419 (m-70) cc_final: 0.7993 (m-70) REVERT: K 116 MET cc_start: 0.8442 (mtm) cc_final: 0.8045 (mmp) REVERT: G 66 ASP cc_start: 0.8585 (p0) cc_final: 0.8246 (p0) REVERT: G 102 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7752 (tp30) REVERT: G 120 MET cc_start: 0.8267 (ppp) cc_final: 0.7924 (ppp) outliers start: 30 outliers final: 24 residues processed: 179 average time/residue: 0.1983 time to fit residues: 54.1017 Evaluate side-chains 176 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 91 SER Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 134 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 113 optimal weight: 20.0000 chunk 13 optimal weight: 0.0970 chunk 20 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.097252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.075277 restraints weight = 34979.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.077916 restraints weight = 18664.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.079655 restraints weight = 12616.287| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11684 Z= 0.153 Angle : 0.564 11.231 15652 Z= 0.284 Chirality : 0.037 0.203 1821 Planarity : 0.003 0.042 1989 Dihedral : 3.585 19.388 1542 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.82 % Allowed : 18.12 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.24), residues: 1387 helix: 1.81 (0.17), residues: 1065 sheet: None (None), residues: 0 loop : -1.16 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 7 PHE 0.022 0.001 PHE I 114 TYR 0.028 0.001 TYR K 93 ARG 0.007 0.000 ARG C 149 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2240.41 seconds wall clock time: 41 minutes 53.27 seconds (2513.27 seconds total)