Starting phenix.real_space_refine on Mon Jan 20 10:11:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ynk_39425/01_2025/8ynk_39425.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ynk_39425/01_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_39425/01_2025/8ynk_39425.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ynk_39425/01_2025/8ynk_39425.map" model { file = "/net/cci-nas-00/data/ceres_data/8ynk_39425/01_2025/8ynk_39425.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ynk_39425/01_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-5571/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: 7.52, per 1000 atoms: 0.65 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: 2.75 Conformation dependent library (CDL) restraints added in 1.4 seconds 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2736 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 0 sheets defined 76.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 15 through 26 Processing helix chain 'A' and resid 27 through 29 No H-bonds generated for 'chain 'A' and resid 27 through 29' Processing helix chain 'A' and resid 31 through 36 Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.618A pdb=" N LEU A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 51 " --> pdb=" O ARG A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 71 through 78 removed outlier: 3.776A pdb=" N LEU A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 92 removed outlier: 3.680A pdb=" N THR A 92 " --> pdb=" O ARG A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 111 removed outlier: 3.523A pdb=" N VAL A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 130 through 134 removed outlier: 3.670A pdb=" N ASP A 134 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 149 Processing helix chain 'A' and resid 157 through 168 removed outlier: 3.907A pdb=" N GLN A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE A 167 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 182 Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 15 through 26 Processing helix chain 'B' and resid 31 through 36 Processing helix chain 'B' and resid 40 through 51 removed outlier: 3.763A pdb=" N LEU B 44 " --> pdb=" O ASP B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 removed outlier: 3.537A pdb=" N ILE B 69 " --> pdb=" O LEU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 79 removed outlier: 4.205A pdb=" N LEU B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'B' and resid 99 through 111 Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 129 through 134 removed outlier: 3.956A pdb=" N ASP B 134 " --> pdb=" O CYS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 149 Processing helix chain 'B' and resid 157 through 165 Processing helix chain 'B' and resid 169 through 182 Processing helix chain 'C' and resid 2 through 14 removed outlier: 3.669A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU C 14 " --> pdb=" O ILE C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 26 Processing helix chain 'C' and resid 31 through 36 Processing helix chain 'C' and resid 40 through 51 removed outlier: 3.717A pdb=" N LEU C 44 " --> pdb=" O ASP C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 71 through 78 removed outlier: 3.721A pdb=" N LEU C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 92 removed outlier: 3.511A pdb=" N MET C 86 " --> pdb=" O ARG C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 111 removed outlier: 3.519A pdb=" N VAL C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU C 111 " --> pdb=" O GLN C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 124 Processing helix chain 'C' and resid 130 through 134 Processing helix chain 'C' and resid 138 through 149 Processing helix chain 'C' and resid 157 through 165 Processing helix chain 'C' and resid 169 through 182 Processing helix chain 'H' and resid 3 through 12 Processing helix chain 'H' and resid 14 through 26 Processing helix chain 'H' and resid 36 through 48 Processing helix chain 'H' and resid 51 through 62 removed outlier: 3.638A pdb=" N VAL H 62 " --> pdb=" O LEU H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 71 Processing helix chain 'H' and resid 75 through 86 Processing helix chain 'H' and resid 91 through 102 Processing helix chain 'H' and resid 105 through 116 Processing helix chain 'H' and resid 121 through 126 removed outlier: 3.735A pdb=" N ILE H 125 " --> pdb=" O GLY H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 141 removed outlier: 3.563A pdb=" N LEU H 134 " --> pdb=" O SER H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 159 Processing helix chain 'H' and resid 161 through 175 removed outlier: 3.946A pdb=" N LYS H 165 " --> pdb=" O ARG H 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 13 Processing helix chain 'I' and resid 14 through 25 Processing helix chain 'I' and resid 36 through 47 Processing helix chain 'I' and resid 51 through 62 Processing helix chain 'I' and resid 64 through 71 Processing helix chain 'I' and resid 75 through 86 Processing helix chain 'I' and resid 91 through 104 removed outlier: 3.825A pdb=" N VAL I 95 " --> pdb=" O SER I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 117 Processing helix chain 'I' and resid 130 through 141 Processing helix chain 'I' and resid 149 through 159 Processing helix chain 'I' and resid 161 through 176 removed outlier: 4.005A pdb=" N LYS I 165 " --> pdb=" O ARG I 161 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 13 removed outlier: 3.827A pdb=" N ILE J 6 " --> pdb=" O SER J 2 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 27 removed outlier: 4.282A pdb=" N ASP J 27 " --> pdb=" O PHE J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 47 Processing helix chain 'J' and resid 51 through 63 Processing helix chain 'J' and resid 64 through 71 removed outlier: 3.816A pdb=" N LEU J 68 " --> pdb=" O ARG J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 86 Processing helix chain 'J' and resid 91 through 104 removed outlier: 3.594A pdb=" N ASP J 103 " --> pdb=" O GLU J 99 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU J 104 " --> pdb=" O ILE J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 105 through 117 removed outlier: 3.862A pdb=" N VAL J 109 " --> pdb=" O ASP J 105 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER J 110 " --> pdb=" O LYS J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 141 Processing helix chain 'J' and resid 149 through 159 Processing helix chain 'J' and resid 161 through 175 removed outlier: 3.902A pdb=" N LYS J 165 " --> pdb=" O ARG J 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 12 removed outlier: 3.677A pdb=" N ILE K 6 " --> pdb=" O SER K 2 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 25 removed outlier: 3.539A pdb=" N LYS K 18 " --> pdb=" O ASP K 14 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU K 19 " --> pdb=" O THR K 15 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N MET K 20 " --> pdb=" O ASP K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 48 Processing helix chain 'K' and resid 51 through 62 Processing helix chain 'K' and resid 64 through 71 removed outlier: 3.568A pdb=" N LEU K 68 " --> pdb=" O ARG K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 85 removed outlier: 3.512A pdb=" N VAL K 79 " --> pdb=" O ASP K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 103 Processing helix chain 'K' and resid 105 through 116 removed outlier: 3.897A pdb=" N VAL K 109 " --> pdb=" O ASP K 105 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER K 110 " --> pdb=" O LYS K 106 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER K 111 " --> pdb=" O SER K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 141 Processing helix chain 'K' and resid 149 through 159 Processing helix chain 'K' and resid 162 through 175 Processing helix chain 'G' and resid 2 through 12 removed outlier: 3.738A pdb=" N ILE G 6 " --> pdb=" O SER G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 25 removed outlier: 3.561A pdb=" N LYS G 18 " --> pdb=" O ASP G 14 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU G 19 " --> pdb=" O THR G 15 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N MET G 20 " --> pdb=" O ASP G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 48 Processing helix chain 'G' and resid 51 through 62 removed outlier: 3.682A pdb=" N VAL G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 71 removed outlier: 3.566A pdb=" N LEU G 68 " --> pdb=" O ARG G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 85 Processing helix chain 'G' and resid 91 through 102 removed outlier: 3.526A pdb=" N VAL G 95 " --> pdb=" O SER G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 117 removed outlier: 3.737A pdb=" N SER G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 141 Processing helix chain 'G' and resid 149 through 159 removed outlier: 3.716A pdb=" N ILE G 159 " --> pdb=" O CYS G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 175 652 hydrogen bonds defined for protein. 1941 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.92 Time building geometry restraints manager: 3.17 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: 1.880 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: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 26.900 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11684 Z= 0.159 Angle : 0.400 5.312 15652 Z= 0.220 Chirality : 0.034 0.151 1821 Planarity : 0.002 0.033 1989 Dihedral : 13.746 89.483 4686 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.24), residues: 1387 helix: 2.01 (0.17), residues: 1032 sheet: None (None), residues: 0 loop : -0.76 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 88 PHE 0.009 0.001 PHE A 61 TYR 0.006 0.001 TYR B 101 ARG 0.004 0.000 ARG I 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 1.281 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: 0.2791 time to fit residues: 124.0430 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 : 1.335 ------------------------------------------------------------------------------- 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 = 36)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.078049 restraints weight = 34341.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.080778 restraints weight = 18137.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.082557 restraints weight = 12080.920| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- 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= 0.155 Angle : 0.526 7.214 15652 Z= 0.277 Chirality : 0.036 0.165 1821 Planarity : 0.003 0.036 1989 Dihedral : 3.375 12.564 1542 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.29 % Allowed : 9.55 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.24), residues: 1387 helix: 1.73 (0.17), residues: 1089 sheet: None (None), residues: 0 loop : -0.92 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 7 PHE 0.017 0.001 PHE C 24 TYR 0.011 0.001 TYR C 178 ARG 0.007 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 204 time to evaluate : 1.416 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: 0.8312 (m110) REVERT: A 138 ASN cc_start: 0.7982 (p0) cc_final: 0.7758 (p0) REVERT: B 92 THR cc_start: 0.8780 (m) cc_final: 0.8330 (p) REVERT: C 104 MET cc_start: 0.9304 (ptm) cc_final: 0.8937 (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: 0.8586 (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: 0.7775 (m-30) cc_final: 0.7433 (t70) REVERT: K 93 TYR cc_start: 0.8062 (t80) cc_final: 0.7826 (t80) REVERT: K 116 MET cc_start: 0.8495 (mtm) cc_final: 0.8079 (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: 0.8340 (p0) REVERT: G 102 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7677 (tp30) outliers start: 17 outliers final: 7 residues processed: 216 average time/residue: 0.2106 time to fit residues: 67.1714 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 : 1.442 ------------------------------------------------------------------------------- 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: 10.0000 chunk 3 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 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: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3928 r_free = 0.3928 target = 0.105228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.084567 restraints weight = 31533.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.087280 restraints weight = 16042.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.089032 restraints weight = 10493.726| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3057 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= 0.164 Angle : 0.520 8.187 15652 Z= 0.266 Chirality : 0.036 0.149 1821 Planarity : 0.003 0.032 1989 Dihedral : 3.423 13.491 1542 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.20 % Allowed : 11.45 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.24), residues: 1387 helix: 1.81 (0.17), residues: 1068 sheet: None (None), residues: 0 loop : -0.89 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS I 88 PHE 0.013 0.001 PHE H 65 TYR 0.013 0.001 TYR A 101 ARG 0.003 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8675 (t0) cc_final: 0.8472 (m110) REVERT: A 148 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8712 (mtmm) REVERT: C 104 MET cc_start: 0.9259 (ptm) cc_final: 0.8974 (ptm) REVERT: H 36 ASN cc_start: 0.8569 (m-40) cc_final: 0.8217 (t0) REVERT: H 66 ASP cc_start: 0.7710 (p0) cc_final: 0.7441 (p0) REVERT: I 176 GLN cc_start: 0.7331 (mp10) cc_final: 0.7047 (mp10) REVERT: K 116 MET cc_start: 0.8310 (mtm) cc_final: 0.8105 (mmm) REVERT: G 60 TYR cc_start: 0.9028 (t80) cc_final: 0.8563 (t80) REVERT: G 66 ASP cc_start: 0.8521 (p0) cc_final: 0.8288 (p0) REVERT: G 102 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7747 (tp30) outliers start: 29 outliers final: 19 residues processed: 192 average time/residue: 0.1924 time to fit residues: 56.2441 Evaluate side-chains 168 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 1.521 ------------------------------------------------------------------------------- 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 20 MET Chi-restraints excluded: chain I residue 91 SER Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 125 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 92 optimal weight: 0.6980 chunk 108 optimal weight: 10.0000 chunk 106 optimal weight: 0.4980 chunk 137 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN B 46 GLN C 176 ASN H 8 GLN H 173 GLN K 86 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.096905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.074925 restraints weight = 34887.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.077568 restraints weight = 18597.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.079255 restraints weight = 12545.106| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3385 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= 0.157 Angle : 0.507 11.647 15652 Z= 0.259 Chirality : 0.036 0.146 1821 Planarity : 0.003 0.032 1989 Dihedral : 3.499 14.330 1542 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.58 % Allowed : 12.74 % Favored : 84.69 % 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: 1.70 (0.24), residues: 1387 helix: 1.74 (0.17), residues: 1077 sheet: None (None), residues: 0 loop : -1.02 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS I 88 PHE 0.022 0.001 PHE B 181 TYR 0.016 0.001 TYR A 101 ARG 0.002 0.000 ARG A 114 *********************** 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 198 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 1.306 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: 0.8726 (t0) cc_final: 0.8461 (m110) REVERT: A 148 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8584 (mtmm) REVERT: C 104 MET cc_start: 0.9336 (ptm) cc_final: 0.9003 (ptm) REVERT: C 176 ASN cc_start: 0.9020 (m110) cc_final: 0.8745 (p0) REVERT: H 36 ASN cc_start: 0.8664 (m-40) cc_final: 0.8243 (t0) REVERT: H 66 ASP cc_start: 0.7703 (p0) cc_final: 0.7402 (p0) REVERT: H 97 MET cc_start: 0.8473 (mmm) cc_final: 0.7816 (mmm) REVERT: K 116 MET cc_start: 0.8512 (mtm) cc_final: 0.8306 (mmm) REVERT: G 60 TYR cc_start: 0.9065 (t80) cc_final: 0.8632 (t80) REVERT: G 66 ASP cc_start: 0.8558 (p0) cc_final: 0.8324 (p0) REVERT: G 102 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7725 (tp30) outliers start: 34 outliers final: 21 residues processed: 186 average time/residue: 0.1993 time to fit residues: 56.0826 Evaluate side-chains 175 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 1.320 ------------------------------------------------------------------------------- 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 46 GLN 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 159 ILE Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 173 GLN Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain I residue 91 SER Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 112 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 101 optimal weight: 0.1980 chunk 117 optimal weight: 0.0040 chunk 50 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.101249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.080337 restraints weight = 31579.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.082926 restraints weight = 16637.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.084641 restraints weight = 11101.795| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11684 Z= 0.189 Angle : 0.529 10.457 15652 Z= 0.269 Chirality : 0.037 0.145 1821 Planarity : 0.003 0.051 1989 Dihedral : 3.580 17.416 1542 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.43 % Allowed : 13.72 % Favored : 83.85 % 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: 1.72 (0.24), residues: 1387 helix: 1.74 (0.17), residues: 1085 sheet: None (None), residues: 0 loop : -1.02 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS I 160 PHE 0.019 0.001 PHE K 131 TYR 0.022 0.001 TYR A 101 ARG 0.002 0.000 ARG B 47 *********************** 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 189 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 1.558 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: 0.8711 (t0) cc_final: 0.8499 (m110) REVERT: B 92 THR cc_start: 0.8819 (m) cc_final: 0.8398 (p) REVERT: C 104 MET cc_start: 0.9257 (ptm) cc_final: 0.9006 (ptm) REVERT: C 110 GLU cc_start: 0.8452 (tp30) cc_final: 0.7945 (tp30) REVERT: C 176 ASN cc_start: 0.8906 (m110) cc_final: 0.8683 (p0) REVERT: H 36 ASN cc_start: 0.8590 (m-40) cc_final: 0.8233 (t0) REVERT: H 66 ASP cc_start: 0.7768 (p0) cc_final: 0.7479 (p0) REVERT: K 116 MET cc_start: 0.8232 (mtm) cc_final: 0.7935 (mmt) REVERT: G 60 TYR cc_start: 0.9101 (t80) cc_final: 0.8867 (t80) REVERT: G 66 ASP cc_start: 0.8494 (p0) cc_final: 0.8275 (p0) REVERT: G 102 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7763 (tp30) outliers start: 32 outliers final: 26 residues processed: 181 average time/residue: 0.1970 time to fit residues: 54.5384 Evaluate side-chains 176 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 1.446 ------------------------------------------------------------------------------- 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 66 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 42 LEU 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 91 SER Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 134 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 106 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 131 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 173 GLN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 169 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 = 0.3727 r_free = 0.3727 target = 0.096106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.074444 restraints weight = 33614.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.076875 restraints weight = 18324.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.078497 restraints weight = 12557.472| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11684 Z= 0.335 Angle : 0.630 10.124 15652 Z= 0.319 Chirality : 0.040 0.152 1821 Planarity : 0.003 0.033 1989 Dihedral : 3.982 18.008 1542 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.96 % Allowed : 15.01 % Favored : 82.03 % 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: 1.42 (0.23), residues: 1387 helix: 1.55 (0.17), residues: 1080 sheet: None (None), residues: 0 loop : -1.17 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 160 PHE 0.023 0.002 PHE B 181 TYR 0.014 0.002 TYR A 106 ARG 0.004 0.000 ARG H 161 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 1.484 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: B 92 THR cc_start: 0.8851 (m) cc_final: 0.8433 (p) REVERT: C 78 TYR cc_start: 0.8974 (m-80) cc_final: 0.8657 (m-10) REVERT: C 104 MET cc_start: 0.9321 (ptm) cc_final: 0.9076 (ptm) REVERT: C 110 GLU cc_start: 0.8556 (tp30) cc_final: 0.7979 (tp30) REVERT: H 66 ASP cc_start: 0.7888 (p0) cc_final: 0.7541 (p0) REVERT: H 97 MET cc_start: 0.8474 (mmm) cc_final: 0.7892 (mmm) REVERT: G 66 ASP cc_start: 0.8598 (p0) cc_final: 0.8339 (p0) REVERT: G 120 MET cc_start: 0.8287 (ppp) cc_final: 0.8017 (ppp) outliers start: 39 outliers final: 28 residues processed: 176 average time/residue: 0.1923 time to fit residues: 51.9153 Evaluate side-chains 170 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 1.382 ------------------------------------------------------------------------------- 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 42 LEU Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain H residue 19 GLU 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 164 LEU Chi-restraints excluded: chain I residue 91 SER Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 52 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: 0.8980 chunk 116 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 chunk 122 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 0 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 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 = 0.3731 r_free = 0.3731 target = 0.097203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.075056 restraints weight = 35180.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.077710 restraints weight = 18565.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.079456 restraints weight = 12507.197| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3835 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= 0.145 Angle : 0.528 11.207 15652 Z= 0.268 Chirality : 0.036 0.151 1821 Planarity : 0.003 0.030 1989 Dihedral : 3.715 17.268 1542 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.05 % Allowed : 16.60 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.24), residues: 1387 helix: 1.67 (0.17), residues: 1082 sheet: None (None), residues: 0 loop : -1.01 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 88 PHE 0.020 0.001 PHE B 181 TYR 0.017 0.001 TYR G 60 ARG 0.002 0.000 ARG G 64 *********************** 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 188 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 1.359 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: B 92 THR cc_start: 0.8847 (m) cc_final: 0.8425 (p) REVERT: C 78 TYR cc_start: 0.8979 (m-80) cc_final: 0.8673 (m-10) REVERT: C 104 MET cc_start: 0.9296 (ptm) cc_final: 0.9076 (ptm) REVERT: C 110 GLU cc_start: 0.8661 (tp30) cc_final: 0.8129 (tp30) REVERT: C 176 ASN cc_start: 0.9021 (m110) cc_final: 0.8801 (p0) REVERT: H 66 ASP cc_start: 0.7837 (p0) cc_final: 0.7488 (p0) REVERT: H 97 MET cc_start: 0.8361 (mmm) cc_final: 0.7792 (mmm) REVERT: K 88 HIS cc_start: 0.8409 (m-70) cc_final: 0.8015 (m-70) REVERT: G 66 ASP cc_start: 0.8525 (p0) cc_final: 0.8233 (p0) REVERT: G 102 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7787 (tp30) REVERT: G 120 MET cc_start: 0.8264 (ppp) cc_final: 0.7924 (ppp) REVERT: G 173 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7924 (pm20) outliers start: 27 outliers final: 19 residues processed: 183 average time/residue: 0.1991 time to fit residues: 55.0120 Evaluate side-chains 168 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 1.475 ------------------------------------------------------------------------------- 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 B residue 109 SER Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 97 GLN 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 164 LEU 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 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: 7.9990 chunk 100 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 74 optimal weight: 0.0570 chunk 49 optimal weight: 2.9990 chunk 131 optimal weight: 0.2980 chunk 121 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 overall best weight: 1.0102 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.096821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.074380 restraints weight = 35172.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.077110 restraints weight = 18175.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.078904 restraints weight = 12099.571| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3950 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= 0.165 Angle : 0.548 16.187 15652 Z= 0.273 Chirality : 0.037 0.146 1821 Planarity : 0.003 0.029 1989 Dihedral : 3.635 16.159 1542 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.20 % Allowed : 17.06 % Favored : 80.74 % 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: 1.64 (0.24), residues: 1387 helix: 1.70 (0.17), residues: 1079 sheet: None (None), residues: 0 loop : -1.05 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 88 PHE 0.029 0.001 PHE I 114 TYR 0.019 0.001 TYR H 93 ARG 0.002 0.000 ARG H 161 *********************** 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 180 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.8542 (mtt) cc_final: 0.8324 (mtt) REVERT: B 92 THR cc_start: 0.8861 (m) cc_final: 0.8412 (p) REVERT: C 78 TYR cc_start: 0.8943 (m-80) cc_final: 0.8632 (m-10) REVERT: C 104 MET cc_start: 0.9343 (ptm) cc_final: 0.9135 (ptm) REVERT: C 110 GLU cc_start: 0.8803 (tp30) cc_final: 0.8228 (tp30) REVERT: C 146 MET cc_start: 0.8686 (mmm) cc_final: 0.8189 (tpp) REVERT: C 147 GLU cc_start: 0.8427 (tt0) cc_final: 0.8011 (tp30) REVERT: C 176 ASN cc_start: 0.9082 (m110) cc_final: 0.8830 (p0) REVERT: H 66 ASP cc_start: 0.7814 (p0) cc_final: 0.7456 (p0) REVERT: K 88 HIS cc_start: 0.8408 (m-70) cc_final: 0.7852 (m-70) REVERT: G 66 ASP cc_start: 0.8602 (p0) cc_final: 0.8233 (p0) REVERT: G 102 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7742 (tp30) REVERT: G 120 MET cc_start: 0.8267 (ppp) cc_final: 0.7902 (ppp) REVERT: G 173 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7931 (pm20) outliers start: 29 outliers final: 22 residues processed: 173 average time/residue: 0.2019 time to fit residues: 52.8492 Evaluate side-chains 169 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 1.433 ------------------------------------------------------------------------------- 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 66 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 43 MET Chi-restraints excluded: chain C residue 97 GLN 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 164 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 15 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 58 optimal weight: 0.0170 chunk 114 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.096679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.074240 restraints weight = 35248.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.076950 restraints weight = 18369.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.078706 restraints weight = 12292.164| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4014 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= 0.181 Angle : 0.579 16.913 15652 Z= 0.285 Chirality : 0.037 0.158 1821 Planarity : 0.003 0.029 1989 Dihedral : 3.619 18.693 1542 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.20 % Allowed : 17.29 % Favored : 80.52 % 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: 1.77 (0.17), residues: 1074 sheet: None (None), residues: 0 loop : -1.18 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 88 PHE 0.022 0.001 PHE I 114 TYR 0.042 0.001 TYR K 93 ARG 0.005 0.000 ARG H 61 *********************** 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 178 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 THR cc_start: 0.8853 (m) cc_final: 0.8398 (p) REVERT: C 78 TYR cc_start: 0.8952 (m-80) cc_final: 0.8621 (m-10) REVERT: C 104 MET cc_start: 0.9346 (ptm) cc_final: 0.9137 (ptm) REVERT: C 110 GLU cc_start: 0.8799 (tp30) cc_final: 0.8214 (tp30) REVERT: C 146 MET cc_start: 0.8704 (mmm) cc_final: 0.8256 (tpp) REVERT: C 176 ASN cc_start: 0.9090 (m110) cc_final: 0.8830 (p0) REVERT: H 66 ASP cc_start: 0.7822 (p0) cc_final: 0.7472 (p0) REVERT: K 88 HIS cc_start: 0.8404 (m-70) cc_final: 0.7979 (m-70) REVERT: G 66 ASP cc_start: 0.8594 (p0) cc_final: 0.8234 (p0) REVERT: G 102 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7770 (tp30) REVERT: G 120 MET cc_start: 0.8260 (ppp) cc_final: 0.7900 (ppp) REVERT: G 173 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7936 (pm20) outliers start: 29 outliers final: 23 residues processed: 171 average time/residue: 0.1850 time to fit residues: 48.6451 Evaluate side-chains 170 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 1.492 ------------------------------------------------------------------------------- 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 66 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 43 MET Chi-restraints excluded: chain C residue 97 GLN 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 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 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 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: 20.0000 chunk 52 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 36 optimal weight: 8.9990 chunk 127 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.096651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.074110 restraints weight = 35477.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.076789 restraints weight = 18618.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.078556 restraints weight = 12483.192| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4113 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= 0.198 Angle : 0.595 16.922 15652 Z= 0.293 Chirality : 0.038 0.183 1821 Planarity : 0.003 0.027 1989 Dihedral : 3.650 18.805 1542 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.27 % Allowed : 17.21 % Favored : 80.52 % 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: 1.72 (0.24), residues: 1387 helix: 1.80 (0.17), residues: 1062 sheet: None (None), residues: 0 loop : -1.03 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS I 160 PHE 0.023 0.001 PHE I 114 TYR 0.052 0.001 TYR K 93 ARG 0.003 0.000 ARG H 61 ********************** 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 177 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 THR cc_start: 0.8882 (m) cc_final: 0.8423 (p) REVERT: C 78 TYR cc_start: 0.8963 (m-80) cc_final: 0.8646 (m-10) REVERT: C 104 MET cc_start: 0.9347 (ptm) cc_final: 0.9087 (ptm) REVERT: C 110 GLU cc_start: 0.8775 (tp30) cc_final: 0.8195 (tp30) REVERT: C 146 MET cc_start: 0.8738 (mmm) cc_final: 0.8306 (tpp) REVERT: C 176 ASN cc_start: 0.9088 (m110) cc_final: 0.8834 (p0) REVERT: H 66 ASP cc_start: 0.7847 (p0) cc_final: 0.7499 (p0) REVERT: H 116 MET cc_start: 0.9003 (mmm) cc_final: 0.8676 (mmt) REVERT: I 116 MET cc_start: 0.8342 (mmp) cc_final: 0.8115 (mmt) REVERT: K 88 HIS cc_start: 0.8381 (m-70) cc_final: 0.7953 (m-70) REVERT: G 66 ASP cc_start: 0.8582 (p0) cc_final: 0.8236 (p0) REVERT: G 102 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7780 (tp30) REVERT: G 120 MET cc_start: 0.8292 (ppp) cc_final: 0.7919 (ppp) REVERT: G 173 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7915 (pm20) outliers start: 30 outliers final: 26 residues processed: 167 average time/residue: 0.1899 time to fit residues: 48.8954 Evaluate side-chains 172 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 1.346 ------------------------------------------------------------------------------- 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 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 44 LEU 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 79 VAL Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 134 LEU 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: 0.4980 chunk 52 optimal weight: 9.9990 chunk 27 optimal weight: 0.0970 chunk 70 optimal weight: 4.9990 chunk 58 optimal weight: 0.0010 chunk 128 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.096393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.074504 restraints weight = 35140.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.077117 restraints weight = 18940.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.078828 restraints weight = 12851.515| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4208 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= 0.151 Angle : 0.577 17.218 15652 Z= 0.282 Chirality : 0.036 0.154 1821 Planarity : 0.003 0.028 1989 Dihedral : 3.538 18.906 1542 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.82 % Allowed : 18.04 % Favored : 80.14 % 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: 1.80 (0.24), residues: 1387 helix: 1.83 (0.17), residues: 1065 sheet: None (None), residues: 0 loop : -0.94 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 88 PHE 0.021 0.001 PHE C 24 TYR 0.051 0.001 TYR K 93 ARG 0.004 0.000 ARG H 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3339.48 seconds wall clock time: 60 minutes 43.27 seconds (3643.27 seconds total)