Starting phenix.real_space_refine on Fri Jun 13 14:21:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ynk_39425/06_2025/8ynk_39425.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ynk_39425/06_2025/8ynk_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_39425/06_2025/8ynk_39425.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ynk_39425/06_2025/8ynk_39425.map" model { file = "/net/cci-nas-00/data/ceres_data/8ynk_39425/06_2025/8ynk_39425.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ynk_39425/06_2025/8ynk_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 7.18, per 1000 atoms: 0.62 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: 2.50 Conformation dependent library (CDL) restraints added in 1.5 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: 1.05 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: 2.84 Time building geometry restraints manager: 2.91 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: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 25.930 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 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:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.740 ------------------------------------------------------------------------------- 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= 0.108 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 Details of bonding type rmsd hydrogen bonds : bond 0.15926 ( 652) hydrogen bonds : angle 4.34976 ( 1941) covalent geometry : bond 0.00246 (11684) covalent geometry : angle 0.40034 (15652) *********************** 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 : 1.356 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: 0.2690 time to fit residues: 120.0066 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 : 1.329 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.099755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.078048 restraints weight = 34341.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.080775 restraints weight = 18138.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.082562 restraints weight = 12097.332| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 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= 0.113 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 Details of bonding type rmsd hydrogen bonds : bond 0.03353 ( 652) hydrogen bonds : angle 3.70548 ( 1941) covalent geometry : bond 0.00241 (11684) covalent geometry : angle 0.52648 (15652) *********************** 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 : 1.440 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: 0.8584 (t0) cc_final: 0.8311 (m110) REVERT: A 138 ASN cc_start: 0.7982 (p0) cc_final: 0.7760 (p0) REVERT: B 92 THR cc_start: 0.8780 (m) cc_final: 0.8330 (p) REVERT: C 104 MET cc_start: 0.9306 (ptm) cc_final: 0.8940 (ptm) REVERT: C 176 ASN cc_start: 0.9007 (m110) cc_final: 0.8776 (p0) REVERT: C 178 TYR cc_start: 0.8817 (t80) cc_final: 0.8587 (t80) REVERT: H 8 GLN cc_start: 0.8940 (mt0) cc_final: 0.8662 (mt0) REVERT: H 36 ASN cc_start: 0.8680 (m-40) cc_final: 0.8269 (t0) REVERT: H 66 ASP cc_start: 0.7671 (p0) cc_final: 0.7447 (p0) REVERT: I 14 ASP cc_start: 0.7772 (m-30) cc_final: 0.7430 (t70) REVERT: K 93 TYR cc_start: 0.8064 (t80) cc_final: 0.7827 (t80) REVERT: K 116 MET cc_start: 0.8493 (mtm) cc_final: 0.8077 (mmm) REVERT: G 60 TYR cc_start: 0.8983 (t80) cc_final: 0.8601 (t80) REVERT: G 66 ASP cc_start: 0.8583 (p0) cc_final: 0.8341 (p0) REVERT: G 102 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7676 (tp30) outliers start: 17 outliers final: 7 residues processed: 216 average time/residue: 0.2067 time to fit residues: 66.0146 Evaluate side-chains 159 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 152 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 THR 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 37 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 7 optimal weight: 0.2980 chunk 5 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 88 HIS J 86 ASN K 8 GLN G 158 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.106698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.086359 restraints weight = 31414.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.089101 restraints weight = 15791.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.090878 restraints weight = 10190.980| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11684 Z= 0.104 Angle : 0.516 8.389 15652 Z= 0.263 Chirality : 0.036 0.148 1821 Planarity : 0.003 0.032 1989 Dihedral : 3.392 13.211 1542 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.20 % Allowed : 11.07 % Favored : 86.73 % 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: 1.71 (0.24), residues: 1387 helix: 1.73 (0.17), residues: 1086 sheet: None (None), residues: 0 loop : -1.03 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS I 88 PHE 0.013 0.001 PHE H 65 TYR 0.013 0.001 TYR A 101 ARG 0.003 0.000 ARG A 114 Details of bonding type rmsd hydrogen bonds : bond 0.02960 ( 652) hydrogen bonds : angle 3.60618 ( 1941) covalent geometry : bond 0.00232 (11684) covalent geometry : angle 0.51560 (15652) *********************** 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 203 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 174 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8631 (t0) cc_final: 0.8420 (m110) REVERT: A 138 ASN cc_start: 0.8039 (p0) cc_final: 0.7826 (p0) REVERT: A 148 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8698 (mtmm) REVERT: C 104 MET cc_start: 0.9253 (ptm) cc_final: 0.8970 (ptm) REVERT: H 36 ASN cc_start: 0.8597 (m-40) cc_final: 0.8248 (t0) REVERT: H 66 ASP cc_start: 0.7683 (p0) cc_final: 0.7413 (p0) REVERT: I 176 GLN cc_start: 0.7309 (mp10) cc_final: 0.7036 (mp10) REVERT: G 60 TYR cc_start: 0.9018 (t80) cc_final: 0.8574 (t80) REVERT: G 66 ASP cc_start: 0.8504 (p0) cc_final: 0.8265 (p0) REVERT: G 102 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7725 (tp30) outliers start: 29 outliers final: 18 residues processed: 196 average time/residue: 0.1865 time to fit residues: 55.6479 Evaluate side-chains 170 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 109 SER 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 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 92 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 106 optimal weight: 0.0030 chunk 137 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- 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 8 GLN H 173 GLN K 86 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.094724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.072350 restraints weight = 34987.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.074927 restraints weight = 18594.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.076624 restraints weight = 12565.715| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11684 Z= 0.161 Angle : 0.558 10.840 15652 Z= 0.285 Chirality : 0.038 0.144 1821 Planarity : 0.003 0.031 1989 Dihedral : 3.657 14.849 1542 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.73 % Allowed : 12.96 % Favored : 84.31 % 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: 1.65 (0.24), residues: 1387 helix: 1.69 (0.17), residues: 1081 sheet: None (None), residues: 0 loop : -1.04 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 88 PHE 0.021 0.002 PHE B 181 TYR 0.017 0.001 TYR A 101 ARG 0.004 0.000 ARG I 61 Details of bonding type rmsd hydrogen bonds : bond 0.03475 ( 652) hydrogen bonds : angle 3.83531 ( 1941) covalent geometry : bond 0.00379 (11684) covalent geometry : angle 0.55842 (15652) *********************** 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 193 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8762 (t0) cc_final: 0.8419 (m110) REVERT: A 101 TYR cc_start: 0.8965 (t80) cc_final: 0.8516 (t80) REVERT: A 148 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8578 (mtmm) REVERT: C 104 MET cc_start: 0.9382 (ptm) cc_final: 0.9045 (ptm) REVERT: C 176 ASN cc_start: 0.9058 (m110) cc_final: 0.8784 (p0) REVERT: H 36 ASN cc_start: 0.8659 (m-40) cc_final: 0.8227 (t0) REVERT: H 66 ASP cc_start: 0.7789 (p0) cc_final: 0.7481 (p0) REVERT: H 97 MET cc_start: 0.8540 (mmm) cc_final: 0.7855 (mmm) REVERT: J 173 GLN cc_start: 0.8200 (mt0) cc_final: 0.7803 (tm-30) REVERT: G 60 TYR cc_start: 0.9138 (t80) cc_final: 0.8890 (t80) REVERT: G 66 ASP cc_start: 0.8645 (p0) cc_final: 0.8255 (p0) outliers start: 36 outliers final: 21 residues processed: 182 average time/residue: 0.1955 time to fit residues: 53.8861 Evaluate side-chains 169 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 76 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 81 THR 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 112 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 101 optimal weight: 0.0060 chunk 117 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.095119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.072795 restraints weight = 34632.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.075394 restraints weight = 18404.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.077122 restraints weight = 12439.201| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3540 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= 0.114 Angle : 0.524 10.571 15652 Z= 0.267 Chirality : 0.037 0.148 1821 Planarity : 0.003 0.031 1989 Dihedral : 3.644 17.173 1542 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.12 % Allowed : 14.86 % Favored : 83.02 % 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: 1.66 (0.24), residues: 1387 helix: 1.71 (0.17), residues: 1081 sheet: None (None), residues: 0 loop : -1.08 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS I 88 PHE 0.021 0.001 PHE K 114 TYR 0.011 0.001 TYR K 93 ARG 0.002 0.000 ARG H 161 Details of bonding type rmsd hydrogen bonds : bond 0.02955 ( 652) hydrogen bonds : angle 3.61492 ( 1941) covalent geometry : bond 0.00264 (11684) covalent geometry : angle 0.52422 (15652) *********************** 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 188 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 1.421 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: 0.8736 (t0) cc_final: 0.8456 (m110) REVERT: A 148 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8635 (mtmm) REVERT: C 78 TYR cc_start: 0.8934 (m-80) cc_final: 0.8586 (m-10) REVERT: C 104 MET cc_start: 0.9333 (ptm) cc_final: 0.9094 (ptm) REVERT: C 110 GLU cc_start: 0.8632 (tp30) cc_final: 0.8049 (tp30) REVERT: C 146 MET cc_start: 0.8808 (tpp) cc_final: 0.8593 (mmm) REVERT: C 176 ASN cc_start: 0.9034 (m110) cc_final: 0.8771 (p0) REVERT: H 36 ASN cc_start: 0.8652 (m-40) cc_final: 0.8224 (t0) REVERT: H 66 ASP cc_start: 0.7788 (p0) cc_final: 0.7482 (p0) REVERT: H 97 MET cc_start: 0.8488 (mmm) cc_final: 0.7827 (mmm) REVERT: I 83 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8553 (mt) REVERT: J 173 GLN cc_start: 0.8081 (mt0) cc_final: 0.7802 (tm-30) REVERT: G 60 TYR cc_start: 0.9119 (t80) cc_final: 0.8854 (t80) REVERT: G 66 ASP cc_start: 0.8580 (p0) cc_final: 0.8351 (p0) REVERT: G 102 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7771 (tp30) outliers start: 28 outliers final: 23 residues processed: 179 average time/residue: 0.1878 time to fit residues: 51.4448 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 : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 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 66 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 159 ILE 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 K residue 15 THR Chi-restraints excluded: chain K residue 71 ILE 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 106 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 173 GLN G 7 HIS ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.092068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.069565 restraints weight = 36468.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.072029 restraints weight = 19893.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.073606 restraints weight = 13656.287| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 11684 Z= 0.327 Angle : 0.762 9.837 15652 Z= 0.379 Chirality : 0.043 0.162 1821 Planarity : 0.004 0.048 1989 Dihedral : 4.325 17.692 1542 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.34 % Allowed : 15.62 % Favored : 81.05 % 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: 0.95 (0.23), residues: 1387 helix: 1.19 (0.16), residues: 1076 sheet: None (None), residues: 0 loop : -1.22 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 160 PHE 0.023 0.003 PHE K 131 TYR 0.038 0.002 TYR A 101 ARG 0.005 0.001 ARG I 61 Details of bonding type rmsd hydrogen bonds : bond 0.04667 ( 652) hydrogen bonds : angle 4.61917 ( 1941) covalent geometry : bond 0.00767 (11684) covalent geometry : angle 0.76237 (15652) *********************** 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 191 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 147 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 78 TYR cc_start: 0.8981 (m-80) cc_final: 0.8681 (m-10) REVERT: C 104 MET cc_start: 0.9416 (ptm) cc_final: 0.9135 (ptm) REVERT: H 66 ASP cc_start: 0.7915 (p0) cc_final: 0.7550 (p0) REVERT: H 97 MET cc_start: 0.8648 (mmm) cc_final: 0.7926 (mmm) REVERT: K 69 LYS cc_start: 0.9334 (tttt) cc_final: 0.9049 (mmmt) REVERT: K 88 HIS cc_start: 0.8246 (m-70) cc_final: 0.7956 (m-70) REVERT: G 66 ASP cc_start: 0.8701 (p0) cc_final: 0.8386 (p0) REVERT: G 120 MET cc_start: 0.8315 (ppp) cc_final: 0.8047 (ppp) outliers start: 44 outliers final: 28 residues processed: 178 average time/residue: 0.1846 time to fit residues: 50.3691 Evaluate side-chains 164 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 43 MET Chi-restraints excluded: chain C residue 124 LEU 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 J residue 30 ILE Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain J residue 83 LEU 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 71 ILE 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 114 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 chunk 0 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.095904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.073518 restraints weight = 35551.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.076245 restraints weight = 18448.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.078009 restraints weight = 12286.352| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11684 Z= 0.107 Angle : 0.550 11.239 15652 Z= 0.278 Chirality : 0.037 0.148 1821 Planarity : 0.003 0.066 1989 Dihedral : 3.896 17.898 1542 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.05 % Allowed : 17.36 % Favored : 80.59 % 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: 1.37 (0.24), residues: 1387 helix: 1.54 (0.17), residues: 1077 sheet: None (None), residues: 0 loop : -1.31 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 88 PHE 0.021 0.002 PHE I 114 TYR 0.030 0.001 TYR A 101 ARG 0.003 0.000 ARG I 85 Details of bonding type rmsd hydrogen bonds : bond 0.03010 ( 652) hydrogen bonds : angle 3.70644 ( 1941) covalent geometry : bond 0.00239 (11684) covalent geometry : angle 0.54970 (15652) *********************** 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: 27 poor density : 163 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 THR cc_start: 0.8894 (m) cc_final: 0.8468 (p) REVERT: C 78 TYR cc_start: 0.8953 (m-80) cc_final: 0.8651 (m-10) REVERT: C 104 MET cc_start: 0.9322 (ptm) cc_final: 0.9099 (ptm) REVERT: C 107 GLN cc_start: 0.8851 (mt0) cc_final: 0.8493 (mt0) REVERT: C 146 MET cc_start: 0.8703 (tpp) cc_final: 0.8471 (tmm) REVERT: C 176 ASN cc_start: 0.9095 (m110) cc_final: 0.8865 (p0) REVERT: H 66 ASP cc_start: 0.7821 (p0) cc_final: 0.7491 (p0) REVERT: H 97 MET cc_start: 0.8530 (mmm) cc_final: 0.7867 (mmm) REVERT: K 88 HIS cc_start: 0.8327 (m-70) cc_final: 0.8003 (m-70) REVERT: G 66 ASP cc_start: 0.8618 (p0) cc_final: 0.8272 (p0) REVERT: G 102 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7774 (tp30) REVERT: G 120 MET cc_start: 0.8288 (ppp) cc_final: 0.7937 (ppp) REVERT: G 173 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7991 (pm20) outliers start: 27 outliers final: 22 residues processed: 184 average time/residue: 0.1891 time to fit residues: 53.3100 Evaluate side-chains 171 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 43 MET 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 91 SER Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 71 ILE 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 173 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 133 optimal weight: 7.9990 chunk 109 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 49 optimal weight: 0.2980 chunk 131 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 88 HIS ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.095673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.073189 restraints weight = 35585.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.075889 restraints weight = 18549.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.077655 restraints weight = 12409.301| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4048 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= 0.124 Angle : 0.573 17.360 15652 Z= 0.286 Chirality : 0.037 0.151 1821 Planarity : 0.003 0.055 1989 Dihedral : 3.791 17.502 1542 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.50 % Allowed : 18.20 % Favored : 79.30 % 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: 1.49 (0.24), residues: 1387 helix: 1.63 (0.17), residues: 1073 sheet: None (None), residues: 0 loop : -1.26 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 88 PHE 0.016 0.001 PHE I 114 TYR 0.036 0.001 TYR A 101 ARG 0.002 0.000 ARG B 149 Details of bonding type rmsd hydrogen bonds : bond 0.03083 ( 652) hydrogen bonds : angle 3.68582 ( 1941) covalent geometry : bond 0.00290 (11684) covalent geometry : angle 0.57315 (15652) *********************** 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 177 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 THR cc_start: 0.8895 (m) cc_final: 0.8519 (p) REVERT: C 78 TYR cc_start: 0.8961 (m-80) cc_final: 0.8636 (m-10) REVERT: C 104 MET cc_start: 0.9324 (ptm) cc_final: 0.9106 (ptm) REVERT: C 107 GLN cc_start: 0.8818 (mt0) cc_final: 0.8490 (mt0) REVERT: C 176 ASN cc_start: 0.9100 (m110) cc_final: 0.8860 (p0) REVERT: H 66 ASP cc_start: 0.7853 (p0) cc_final: 0.7504 (p0) REVERT: K 88 HIS cc_start: 0.8295 (m-70) cc_final: 0.7962 (m-70) REVERT: G 66 ASP cc_start: 0.8606 (p0) cc_final: 0.8251 (p0) REVERT: G 102 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7767 (tp30) REVERT: G 120 MET cc_start: 0.8301 (ppp) cc_final: 0.7937 (ppp) REVERT: G 173 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7956 (pm20) outliers start: 33 outliers final: 27 residues processed: 168 average time/residue: 0.1784 time to fit residues: 46.8019 Evaluate side-chains 168 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 43 MET Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain H residue 19 GLU 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 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 44 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 83 LEU 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 173 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 15 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 58 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 chunk 133 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.096841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.074680 restraints weight = 35257.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.077323 restraints weight = 18858.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.079013 restraints weight = 12786.287| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4128 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= 0.108 Angle : 0.569 16.766 15652 Z= 0.280 Chirality : 0.036 0.153 1821 Planarity : 0.003 0.051 1989 Dihedral : 3.635 17.413 1542 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.27 % Allowed : 18.57 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.60 (0.24), residues: 1387 helix: 1.75 (0.17), residues: 1061 sheet: None (None), residues: 0 loop : -1.25 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 88 PHE 0.020 0.001 PHE C 24 TYR 0.030 0.001 TYR A 101 ARG 0.002 0.000 ARG C 149 Details of bonding type rmsd hydrogen bonds : bond 0.02758 ( 652) hydrogen bonds : angle 3.51802 ( 1941) covalent geometry : bond 0.00248 (11684) covalent geometry : angle 0.56931 (15652) *********************** 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 181 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LEU cc_start: 0.9212 (tp) cc_final: 0.8933 (tt) REVERT: B 92 THR cc_start: 0.8872 (m) cc_final: 0.8459 (p) REVERT: C 78 TYR cc_start: 0.8996 (m-80) cc_final: 0.8659 (m-10) REVERT: C 104 MET cc_start: 0.9258 (ptm) cc_final: 0.9033 (ptm) REVERT: C 107 GLN cc_start: 0.8856 (mt0) cc_final: 0.8518 (mt0) REVERT: C 176 ASN cc_start: 0.9047 (m110) cc_final: 0.8826 (p0) REVERT: H 66 ASP cc_start: 0.7835 (p0) cc_final: 0.7512 (p0) REVERT: H 74 MET cc_start: 0.7815 (ttt) cc_final: 0.7422 (ttt) REVERT: K 88 HIS cc_start: 0.8218 (m-70) cc_final: 0.7891 (m-70) REVERT: G 66 ASP cc_start: 0.8497 (p0) cc_final: 0.8220 (p0) REVERT: G 102 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7773 (tp30) REVERT: G 120 MET cc_start: 0.8259 (ppp) cc_final: 0.7895 (ppp) REVERT: G 173 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7874 (pm20) outliers start: 30 outliers final: 26 residues processed: 173 average time/residue: 0.1784 time to fit residues: 48.0842 Evaluate side-chains 173 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 43 MET 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 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 44 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 83 LEU 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 173 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 79 optimal weight: 0.7980 chunk 52 optimal weight: 0.0040 chunk 3 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 127 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 GLN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.097231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.075059 restraints weight = 35160.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.077684 restraints weight = 18793.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.079390 restraints weight = 12767.366| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4249 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= 0.107 Angle : 0.575 16.537 15652 Z= 0.286 Chirality : 0.037 0.244 1821 Planarity : 0.003 0.050 1989 Dihedral : 3.557 17.514 1542 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.97 % Allowed : 19.18 % Favored : 78.85 % 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: 1.65 (0.24), residues: 1387 helix: 1.75 (0.17), residues: 1067 sheet: None (None), residues: 0 loop : -1.15 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 88 PHE 0.021 0.001 PHE C 181 TYR 0.043 0.001 TYR K 93 ARG 0.003 0.000 ARG B 162 Details of bonding type rmsd hydrogen bonds : bond 0.02727 ( 652) hydrogen bonds : angle 3.45331 ( 1941) covalent geometry : bond 0.00243 (11684) covalent geometry : angle 0.57513 (15652) ********************** 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 175 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LEU cc_start: 0.9220 (tp) cc_final: 0.8948 (tt) REVERT: C 78 TYR cc_start: 0.9014 (m-80) cc_final: 0.8687 (m-10) REVERT: C 104 MET cc_start: 0.9258 (ptm) cc_final: 0.9010 (ptm) REVERT: C 107 GLN cc_start: 0.8882 (mt0) cc_final: 0.8574 (mt0) REVERT: C 146 MET cc_start: 0.8911 (tpp) cc_final: 0.8349 (tpp) REVERT: C 176 ASN cc_start: 0.9032 (m110) cc_final: 0.8813 (p0) REVERT: K 88 HIS cc_start: 0.8205 (m-70) cc_final: 0.7875 (m-70) REVERT: G 66 ASP cc_start: 0.8485 (p0) cc_final: 0.8191 (p0) REVERT: G 102 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7756 (tp30) REVERT: G 120 MET cc_start: 0.8261 (ppp) cc_final: 0.7896 (ppp) REVERT: G 173 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7877 (pm20) outliers start: 26 outliers final: 23 residues processed: 169 average time/residue: 0.1834 time to fit residues: 48.2164 Evaluate side-chains 168 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 43 MET 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 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 44 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 83 LEU 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 173 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 36 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 27 optimal weight: 0.0770 chunk 70 optimal weight: 4.9990 chunk 58 optimal weight: 0.0070 chunk 128 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 GLN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.099313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.077413 restraints weight = 35784.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.080218 restraints weight = 18403.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.082022 restraints weight = 12232.186| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4324 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= 0.105 Angle : 0.576 16.538 15652 Z= 0.286 Chirality : 0.037 0.208 1821 Planarity : 0.003 0.050 1989 Dihedral : 3.485 18.923 1542 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.05 % Allowed : 19.26 % Favored : 78.70 % 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: 1.69 (0.24), residues: 1387 helix: 1.76 (0.17), residues: 1072 sheet: None (None), residues: 0 loop : -1.07 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 88 PHE 0.026 0.001 PHE I 114 TYR 0.051 0.001 TYR K 93 ARG 0.003 0.000 ARG C 149 Details of bonding type rmsd hydrogen bonds : bond 0.02633 ( 652) hydrogen bonds : angle 3.38765 ( 1941) covalent geometry : bond 0.00237 (11684) covalent geometry : angle 0.57602 (15652) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3583.42 seconds wall clock time: 62 minutes 51.44 seconds (3771.44 seconds total)