Starting phenix.real_space_refine on Sat Jun 14 18:25:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ynl_39426/06_2025/8ynl_39426.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ynl_39426/06_2025/8ynl_39426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ynl_39426/06_2025/8ynl_39426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ynl_39426/06_2025/8ynl_39426.map" model { file = "/net/cci-nas-00/data/ceres_data/8ynl_39426/06_2025/8ynl_39426.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ynl_39426/06_2025/8ynl_39426.cif" } resolution = 3.55 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= 0.045 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 74 5.16 5 C 8243 2.51 5 N 2226 2.21 5 O 2434 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12977 Number of models: 1 Model: "" Number of chains: 9 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: 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: "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} Chain: "F" 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: 8.79, per 1000 atoms: 0.68 Number of scatterers: 12977 At special positions: 0 Unit cell: (104.16, 101.64, 146.16, 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 74 16.00 O 2434 8.00 N 2226 7.00 C 8243 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: 3.03 Conformation dependent library (CDL) restraints added in 1.8 seconds 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3074 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 0 sheets defined 76.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 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 31 through 36 Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.606A pdb=" N LEU A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 71 through 78 removed outlier: 4.106A pdb=" N LEU A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 92 removed outlier: 3.585A pdb=" N MET A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR A 92 " --> pdb=" O ARG A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 111 removed outlier: 3.552A pdb=" N VAL A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU A 111 " --> pdb=" O GLN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 129 through 134 removed outlier: 3.848A 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: 4.124A pdb=" N GLN A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 4.023A 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: 3.767A pdb=" N LEU B 44 " --> pdb=" O ASP B 40 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 removed outlier: 3.617A pdb=" N ILE B 69 " --> pdb=" O LEU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 79 removed outlier: 4.003A 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 110 Processing helix chain 'B' and resid 113 through 124 Processing helix chain 'B' and resid 129 through 134 removed outlier: 3.828A pdb=" N ASP B 134 " --> pdb=" O CYS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 149 removed outlier: 3.578A pdb=" N ILE B 142 " --> pdb=" O ASN B 138 " (cutoff:3.500A) 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: 3.837A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) removed outlier: 4.088A 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: 3.502A pdb=" N LEU C 44 " --> pdb=" O ASP C 40 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS C 51 " --> pdb=" O ARG C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 71 through 79 removed outlier: 3.736A pdb=" N LEU C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 79 " --> pdb=" O LEU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 92 Processing helix chain 'C' and resid 99 through 111 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 removed outlier: 3.880A pdb=" N HIS H 7 " --> pdb=" O ALA H 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 26 Processing helix chain 'H' and resid 36 through 47 Processing helix chain 'H' and resid 51 through 61 Processing helix chain 'H' and resid 64 through 71 Processing helix chain 'H' and resid 75 through 86 removed outlier: 3.551A pdb=" N VAL H 79 " --> pdb=" O ASP H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 102 Processing helix chain 'H' and resid 105 through 117 Processing helix chain 'H' and resid 121 through 126 Processing helix chain 'H' and resid 130 through 142 Processing helix chain 'H' and resid 149 through 159 Processing helix chain 'H' and resid 162 through 174 Processing helix chain 'I' and resid 2 through 13 removed outlier: 3.654A pdb=" N ILE I 6 " --> pdb=" O SER I 2 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 25 Processing helix chain 'I' and resid 26 through 30 removed outlier: 3.867A pdb=" N ILE I 30 " --> pdb=" O ASP I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 47 Processing helix chain 'I' and resid 51 through 61 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 102 removed outlier: 3.609A 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: 3.859A pdb=" N LYS I 165 " --> pdb=" O ARG I 161 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN I 176 " --> pdb=" O LYS I 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 13 removed outlier: 3.641A pdb=" N ILE J 6 " --> pdb=" O SER J 2 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 26 Processing helix chain 'J' and resid 36 through 47 Processing helix chain 'J' and resid 51 through 62 Processing helix chain 'J' and resid 64 through 71 removed outlier: 3.743A 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 103 removed outlier: 3.531A pdb=" N VAL J 95 " --> pdb=" O SER J 91 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP J 103 " --> pdb=" O GLU J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 117 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: 3.957A pdb=" N LYS J 165 " --> pdb=" O ARG J 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 12 removed outlier: 3.724A pdb=" N ILE K 6 " --> pdb=" O SER K 2 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 25 removed outlier: 3.619A pdb=" N LYS K 18 " --> pdb=" O ASP K 14 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLU K 19 " --> pdb=" O THR K 15 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N MET K 20 " --> pdb=" O ASP K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 47 Processing helix chain 'K' and resid 51 through 62 Processing helix chain 'K' and resid 64 through 71 Processing helix chain 'K' and resid 75 through 86 removed outlier: 3.631A pdb=" N VAL K 79 " --> pdb=" O ASP K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 102 removed outlier: 3.530A pdb=" N VAL K 95 " --> pdb=" O SER K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 116 removed outlier: 3.560A pdb=" N VAL K 109 " --> pdb=" O ASP K 105 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER K 110 " --> pdb=" O LYS K 106 " (cutoff:3.500A) removed outlier: 4.401A 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: 3.728A pdb=" N ILE G 6 " --> pdb=" O SER G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 25 removed outlier: 3.663A pdb=" N GLU G 19 " --> pdb=" O THR G 15 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET G 20 " --> pdb=" O ASP G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 47 Processing helix chain 'G' and resid 51 through 62 Processing helix chain 'G' and resid 64 through 71 Processing helix chain 'G' and resid 75 through 85 Processing helix chain 'G' and resid 91 through 103 Processing helix chain 'G' and resid 105 through 116 removed outlier: 4.121A 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: 3.516A pdb=" N ILE G 159 " --> pdb=" O CYS G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 175 removed outlier: 3.644A pdb=" N VAL G 175 " --> pdb=" O TYR G 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 13 removed outlier: 3.550A pdb=" N LEU F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 25 removed outlier: 3.591A pdb=" N LYS F 18 " --> pdb=" O ASP F 14 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU F 19 " --> pdb=" O THR F 15 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET F 20 " --> pdb=" O ASP F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 47 Processing helix chain 'F' and resid 51 through 62 removed outlier: 3.523A pdb=" N VAL F 62 " --> pdb=" O LEU F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 71 Processing helix chain 'F' and resid 75 through 86 removed outlier: 3.524A pdb=" N VAL F 79 " --> pdb=" O ASP F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 104 Processing helix chain 'F' and resid 105 through 117 removed outlier: 3.617A pdb=" N SER F 111 " --> pdb=" O SER F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 141 Processing helix chain 'F' and resid 149 through 158 Processing helix chain 'F' and resid 161 through 175 removed outlier: 4.027A pdb=" N LYS F 165 " --> pdb=" O ARG F 161 " (cutoff:3.500A) 724 hydrogen bonds defined for protein. 2151 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: 3.03 Time building geometry restraints manager: 3.61 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: 4343 1.34 - 1.46: 2271 1.46 - 1.58: 6368 1.58 - 1.69: 0 1.69 - 1.81: 130 Bond restraints: 13112 Sorted by residual: bond pdb=" CA THR H 166 " pdb=" C THR H 166 " ideal model delta sigma weight residual 1.524 1.499 0.025 1.26e-02 6.30e+03 4.00e+00 bond pdb=" C THR H 166 " pdb=" N LYS H 167 " ideal model delta sigma weight residual 1.335 1.323 0.011 1.25e-02 6.40e+03 8.11e-01 bond pdb=" CA PRO H 34 " pdb=" C PRO H 34 " ideal model delta sigma weight residual 1.517 1.511 0.006 6.70e-03 2.23e+04 6.76e-01 bond pdb=" C ILE B 151 " pdb=" N LEU B 152 " ideal model delta sigma weight residual 1.330 1.341 -0.011 1.36e-02 5.41e+03 6.26e-01 bond pdb=" CB PRO H 87 " pdb=" CG PRO H 87 " ideal model delta sigma weight residual 1.492 1.529 -0.037 5.00e-02 4.00e+02 5.41e-01 ... (remaining 13107 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 17121 1.00 - 1.99: 352 1.99 - 2.99: 61 2.99 - 3.98: 24 3.98 - 4.98: 11 Bond angle restraints: 17569 Sorted by residual: angle pdb=" N THR H 166 " pdb=" CA THR H 166 " pdb=" C THR H 166 " ideal model delta sigma weight residual 111.14 106.35 4.79 1.08e+00 8.57e-01 1.97e+01 angle pdb=" N ILE A 69 " pdb=" CA ILE A 69 " pdb=" C ILE A 69 " ideal model delta sigma weight residual 112.29 108.98 3.31 9.40e-01 1.13e+00 1.24e+01 angle pdb=" N VAL J 62 " pdb=" CA VAL J 62 " pdb=" C VAL J 62 " ideal model delta sigma weight residual 112.98 108.68 4.30 1.25e+00 6.40e-01 1.18e+01 angle pdb=" CA THR H 166 " pdb=" CB THR H 166 " pdb=" OG1 THR H 166 " ideal model delta sigma weight residual 109.60 104.62 4.98 1.50e+00 4.44e-01 1.10e+01 angle pdb=" C LYS H 165 " pdb=" N THR H 166 " pdb=" CA THR H 166 " ideal model delta sigma weight residual 120.44 116.90 3.54 1.36e+00 5.41e-01 6.78e+00 ... (remaining 17564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 7451 17.54 - 35.08: 738 35.08 - 52.62: 107 52.62 - 70.16: 18 70.16 - 87.69: 15 Dihedral angle restraints: 8329 sinusoidal: 3642 harmonic: 4687 Sorted by residual: dihedral pdb=" CA ASP A 73 " pdb=" CB ASP A 73 " pdb=" CG ASP A 73 " pdb=" OD1 ASP A 73 " ideal model delta sinusoidal sigma weight residual -30.00 -86.67 56.67 1 2.00e+01 2.50e-03 1.08e+01 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 -85.29 85.29 1 3.00e+01 1.11e-03 9.79e+00 dihedral pdb=" CB MET G 97 " pdb=" CG MET G 97 " pdb=" SD MET G 97 " pdb=" CE MET G 97 " ideal model delta sinusoidal sigma weight residual 180.00 120.91 59.09 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 8326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1432 0.028 - 0.056: 414 0.056 - 0.084: 149 0.084 - 0.113: 45 0.113 - 0.141: 10 Chirality restraints: 2050 Sorted by residual: chirality pdb=" CB VAL F 62 " pdb=" CA VAL F 62 " pdb=" CG1 VAL F 62 " pdb=" CG2 VAL F 62 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.95e-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 4.47e-01 chirality pdb=" CB VAL C 150 " pdb=" CA VAL C 150 " pdb=" CG1 VAL C 150 " pdb=" CG2 VAL C 150 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 2047 not shown) Planarity restraints: 2230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS H 165 " -0.007 2.00e-02 2.50e+03 1.33e-02 1.77e+00 pdb=" C LYS H 165 " 0.023 2.00e-02 2.50e+03 pdb=" O LYS H 165 " -0.009 2.00e-02 2.50e+03 pdb=" N THR H 166 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA F 145 " 0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO F 146 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO F 146 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO F 146 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA I 145 " 0.018 5.00e-02 4.00e+02 2.71e-02 1.17e+00 pdb=" N PRO I 146 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO I 146 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO I 146 " 0.015 5.00e-02 4.00e+02 ... (remaining 2227 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3144 2.80 - 3.33: 12718 3.33 - 3.85: 19691 3.85 - 4.38: 21996 4.38 - 4.90: 38279 Nonbonded interactions: 95828 Sorted by model distance: nonbonded pdb=" OE1 GLU F 17 " pdb=" NH2 ARG F 64 " model vdw 2.280 3.120 nonbonded pdb=" O ASP K 163 " pdb=" OG1 THR K 166 " model vdw 2.282 3.040 nonbonded pdb=" OE1 GLU G 17 " pdb=" NH2 ARG G 64 " model vdw 2.296 3.120 nonbonded pdb=" OD1 ASP B 28 " pdb=" NH2 ARG B 102 " model vdw 2.308 3.120 nonbonded pdb=" O ASP G 163 " pdb=" OG1 THR G 166 " model vdw 2.320 3.040 ... (remaining 95823 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 'F' and (resid 2 through 28 or resid 31 through 121 or resid 128 through \ 175)) selection = (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: 2.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 30.660 Find NCS groups from input model: 0.560 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 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 0.037 13112 Z= 0.083 Angle : 0.390 4.980 17569 Z= 0.221 Chirality : 0.033 0.141 2050 Planarity : 0.002 0.028 2230 Dihedral : 13.834 87.694 5255 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: 1.87 (0.22), residues: 1559 helix: 1.94 (0.16), residues: 1171 sheet: None (None), residues: 0 loop : -0.96 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 160 PHE 0.011 0.001 PHE B 3 TYR 0.010 0.001 TYR C 101 ARG 0.001 0.000 ARG K 64 Details of bonding type rmsd hydrogen bonds : bond 0.15677 ( 724) hydrogen bonds : angle 4.35926 ( 2151) covalent geometry : bond 0.00170 (13112) covalent geometry : angle 0.38982 (17569) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 1.538 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 101 TYR cc_start: 0.8322 (t80) cc_final: 0.8037 (t80) REVERT: B 172 LEU cc_start: 0.9114 (mp) cc_final: 0.8893 (mm) REVERT: C 1 MET cc_start: 0.6163 (ptt) cc_final: 0.5920 (ttt) REVERT: C 29 TYR cc_start: 0.8558 (m-80) cc_final: 0.8303 (m-80) REVERT: C 34 LYS cc_start: 0.8550 (mmtm) cc_final: 0.8289 (mttt) REVERT: C 46 GLN cc_start: 0.8480 (mt0) cc_final: 0.8268 (mt0) REVERT: C 95 ARG cc_start: 0.7532 (mmt90) cc_final: 0.6868 (tpp80) REVERT: C 101 TYR cc_start: 0.7802 (t80) cc_final: 0.7542 (t80) REVERT: C 124 LEU cc_start: 0.8208 (mt) cc_final: 0.7681 (pp) REVERT: C 163 VAL cc_start: 0.9215 (t) cc_final: 0.8761 (p) REVERT: C 181 PHE cc_start: 0.7862 (m-10) cc_final: 0.7308 (m-80) REVERT: H 41 LEU cc_start: 0.9397 (mm) cc_final: 0.9107 (mt) REVERT: I 6 ILE cc_start: 0.8891 (pt) cc_final: 0.8560 (mt) REVERT: I 86 ASN cc_start: 0.8545 (m-40) cc_final: 0.8070 (m110) REVERT: J 93 TYR cc_start: 0.8598 (t80) cc_final: 0.8297 (t80) REVERT: J 97 MET cc_start: 0.8806 (mmt) cc_final: 0.8468 (mmt) REVERT: K 74 MET cc_start: 0.7815 (mtp) cc_final: 0.7515 (ttm) REVERT: G 1 MET cc_start: 0.6529 (ttp) cc_final: 0.5969 (mpp) REVERT: G 133 ASP cc_start: 0.8192 (t0) cc_final: 0.7946 (t0) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.2451 time to fit residues: 128.2458 Evaluate side-chains 200 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 122 optimal weight: 0.0980 chunk 47 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 GLN B 176 ASN H 88 HIS I 86 ASN I 148 GLN G 8 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.123458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.101096 restraints weight = 29072.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.104072 restraints weight = 14317.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.106072 restraints weight = 8944.921| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13112 Z= 0.127 Angle : 0.538 11.525 17569 Z= 0.279 Chirality : 0.037 0.140 2050 Planarity : 0.003 0.042 2230 Dihedral : 3.350 12.310 1731 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.76 % Allowed : 9.59 % Favored : 88.66 % 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 (0.22), residues: 1559 helix: 1.69 (0.16), residues: 1199 sheet: None (None), residues: 0 loop : -0.77 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 160 PHE 0.017 0.001 PHE A 120 TYR 0.008 0.001 TYR H 119 ARG 0.007 0.000 ARG B 114 Details of bonding type rmsd hydrogen bonds : bond 0.03620 ( 724) hydrogen bonds : angle 3.85743 ( 2151) covalent geometry : bond 0.00289 (13112) covalent geometry : angle 0.53781 (17569) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 211 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.8618 (tt0) cc_final: 0.8298 (mm-40) REVERT: B 137 MET cc_start: 0.8131 (mtp) cc_final: 0.7923 (mtp) REVERT: C 29 TYR cc_start: 0.8496 (m-80) cc_final: 0.8238 (m-80) REVERT: C 95 ARG cc_start: 0.7351 (mmt90) cc_final: 0.7023 (mmt90) REVERT: C 101 TYR cc_start: 0.7920 (t80) cc_final: 0.7671 (t80) REVERT: C 124 LEU cc_start: 0.8161 (mt) cc_final: 0.7786 (pp) REVERT: C 163 VAL cc_start: 0.9263 (t) cc_final: 0.8996 (p) REVERT: H 44 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8694 (mm) REVERT: H 82 HIS cc_start: 0.8350 (OUTLIER) cc_final: 0.8086 (m-70) REVERT: I 85 ARG cc_start: 0.7759 (ttp-110) cc_final: 0.7522 (ttp-110) REVERT: I 86 ASN cc_start: 0.8566 (m110) cc_final: 0.8280 (m-40) REVERT: J 1 MET cc_start: 0.7024 (ttm) cc_final: 0.6707 (ttp) REVERT: J 11 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7220 (mp0) REVERT: J 93 TYR cc_start: 0.8622 (t80) cc_final: 0.8242 (t80) REVERT: G 75 ASP cc_start: 0.7512 (p0) cc_final: 0.7167 (p0) REVERT: G 116 MET cc_start: 0.8630 (mmm) cc_final: 0.8172 (mmm) REVERT: G 133 ASP cc_start: 0.8214 (t0) cc_final: 0.7899 (t0) REVERT: F 17 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8007 (mt-10) outliers start: 26 outliers final: 15 residues processed: 224 average time/residue: 0.2312 time to fit residues: 77.1807 Evaluate side-chains 203 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 4 GLU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain J residue 11 GLU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 118 ASP Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain F residue 166 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 122 optimal weight: 0.9980 chunk 125 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 88 HIS ** K 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 GLN G 86 ASN F 36 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.120929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.098416 restraints weight = 29781.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.101328 restraints weight = 14583.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.103270 restraints weight = 9116.889| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13112 Z= 0.163 Angle : 0.545 6.929 17569 Z= 0.281 Chirality : 0.038 0.143 2050 Planarity : 0.003 0.031 2230 Dihedral : 3.459 13.815 1731 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.09 % Allowed : 11.68 % Favored : 86.23 % 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 (0.22), residues: 1559 helix: 1.62 (0.16), residues: 1197 sheet: None (None), residues: 0 loop : -0.74 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 160 PHE 0.010 0.001 PHE B 120 TYR 0.010 0.001 TYR B 106 ARG 0.009 0.000 ARG J 85 Details of bonding type rmsd hydrogen bonds : bond 0.03794 ( 724) hydrogen bonds : angle 3.98243 ( 2151) covalent geometry : bond 0.00388 (13112) covalent geometry : angle 0.54452 (17569) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 2.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8309 (tm-30) cc_final: 0.8105 (tm-30) REVERT: A 46 GLN cc_start: 0.8681 (tt0) cc_final: 0.8355 (mm-40) REVERT: B 137 MET cc_start: 0.8218 (mtp) cc_final: 0.7963 (mtp) REVERT: C 95 ARG cc_start: 0.7491 (mmt90) cc_final: 0.7113 (mmt90) REVERT: C 101 TYR cc_start: 0.8090 (t80) cc_final: 0.7742 (t80) REVERT: C 124 LEU cc_start: 0.8058 (mt) cc_final: 0.7817 (pp) REVERT: H 82 HIS cc_start: 0.8369 (OUTLIER) cc_final: 0.8093 (m-70) REVERT: I 86 ASN cc_start: 0.8519 (m110) cc_final: 0.8099 (m110) REVERT: I 120 MET cc_start: 0.7534 (ptm) cc_final: 0.7179 (ptm) REVERT: J 1 MET cc_start: 0.7059 (ttm) cc_final: 0.6819 (ttp) REVERT: J 93 TYR cc_start: 0.8735 (t80) cc_final: 0.8271 (t80) REVERT: K 31 ASP cc_start: 0.7074 (p0) cc_final: 0.6823 (t0) REVERT: G 1 MET cc_start: 0.7066 (mpp) cc_final: 0.6503 (mmt) REVERT: G 116 MET cc_start: 0.8746 (mmm) cc_final: 0.7602 (mmt) REVERT: F 17 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8024 (mt-10) REVERT: F 116 MET cc_start: 0.8126 (mmm) cc_final: 0.7908 (mmt) outliers start: 31 outliers final: 21 residues processed: 217 average time/residue: 0.2185 time to fit residues: 71.8892 Evaluate side-chains 203 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 4 GLU Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain J residue 118 ASP Chi-restraints excluded: chain J residue 169 GLN Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 125 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 71 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 151 optimal weight: 9.9990 chunk 96 optimal weight: 0.9980 chunk 105 optimal weight: 0.0770 chunk 113 optimal weight: 9.9990 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 88 HIS J 82 HIS G 8 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.121911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.099764 restraints weight = 29449.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.102614 restraints weight = 14508.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.104555 restraints weight = 9113.238| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13112 Z= 0.127 Angle : 0.516 11.346 17569 Z= 0.264 Chirality : 0.036 0.150 2050 Planarity : 0.003 0.055 2230 Dihedral : 3.478 13.503 1731 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.09 % Allowed : 14.18 % Favored : 83.73 % 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: 1.63 (0.22), residues: 1559 helix: 1.64 (0.16), residues: 1198 sheet: None (None), residues: 0 loop : -0.75 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS G 7 PHE 0.006 0.001 PHE A 61 TYR 0.008 0.001 TYR B 106 ARG 0.013 0.000 ARG B 114 Details of bonding type rmsd hydrogen bonds : bond 0.03213 ( 724) hydrogen bonds : angle 3.82359 ( 2151) covalent geometry : bond 0.00301 (13112) covalent geometry : angle 0.51642 (17569) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LEU cc_start: 0.8974 (tp) cc_final: 0.8750 (tt) REVERT: B 137 MET cc_start: 0.8172 (mtp) cc_final: 0.7944 (mtp) REVERT: C 95 ARG cc_start: 0.7525 (mmt90) cc_final: 0.7113 (mmt90) REVERT: C 101 TYR cc_start: 0.8072 (t80) cc_final: 0.7721 (t80) REVERT: C 124 LEU cc_start: 0.8107 (mt) cc_final: 0.7772 (pp) REVERT: H 82 HIS cc_start: 0.8357 (OUTLIER) cc_final: 0.8077 (m-70) REVERT: J 1 MET cc_start: 0.7041 (ttm) cc_final: 0.6799 (ttp) REVERT: J 83 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8188 (mt) REVERT: J 93 TYR cc_start: 0.8680 (t80) cc_final: 0.8096 (t80) REVERT: G 1 MET cc_start: 0.6954 (mpp) cc_final: 0.6389 (mmp) REVERT: G 8 GLN cc_start: 0.8458 (mm110) cc_final: 0.8243 (mm-40) REVERT: G 116 MET cc_start: 0.8711 (mmm) cc_final: 0.8403 (mmp) REVERT: F 116 MET cc_start: 0.8139 (mmm) cc_final: 0.7915 (mmt) outliers start: 31 outliers final: 21 residues processed: 212 average time/residue: 0.2226 time to fit residues: 70.5552 Evaluate side-chains 197 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 4 GLU Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 118 ASP Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 166 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 45 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 103 optimal weight: 0.0980 chunk 58 optimal weight: 0.4980 chunk 97 optimal weight: 4.9990 chunk 146 optimal weight: 9.9990 chunk 133 optimal weight: 0.8980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 88 HIS F 173 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.099995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.076632 restraints weight = 33397.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.079536 restraints weight = 17899.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.081484 restraints weight = 11978.027| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13112 Z= 0.096 Angle : 0.478 8.836 17569 Z= 0.251 Chirality : 0.035 0.139 2050 Planarity : 0.003 0.030 2230 Dihedral : 3.415 14.739 1731 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.55 % Allowed : 15.80 % Favored : 82.65 % 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 (0.22), residues: 1559 helix: 1.65 (0.16), residues: 1198 sheet: None (None), residues: 0 loop : -0.68 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS G 160 PHE 0.019 0.001 PHE A 181 TYR 0.009 0.001 TYR K 93 ARG 0.007 0.000 ARG I 85 Details of bonding type rmsd hydrogen bonds : bond 0.02781 ( 724) hydrogen bonds : angle 3.58312 ( 2151) covalent geometry : bond 0.00215 (13112) covalent geometry : angle 0.47816 (17569) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 ARG cc_start: 0.7545 (mmt90) cc_final: 0.7092 (mmt90) REVERT: C 101 TYR cc_start: 0.7963 (t80) cc_final: 0.7618 (t80) REVERT: C 124 LEU cc_start: 0.8217 (mt) cc_final: 0.7927 (pp) REVERT: H 82 HIS cc_start: 0.8343 (OUTLIER) cc_final: 0.8071 (m-70) REVERT: J 1 MET cc_start: 0.6967 (ttm) cc_final: 0.6744 (ttp) REVERT: J 83 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8169 (mt) REVERT: K 116 MET cc_start: 0.8093 (mtm) cc_final: 0.7626 (mtm) REVERT: G 1 MET cc_start: 0.7062 (mpp) cc_final: 0.6507 (mmp) REVERT: G 8 GLN cc_start: 0.8633 (mm110) cc_final: 0.8384 (mm-40) REVERT: F 97 MET cc_start: 0.8389 (mmm) cc_final: 0.8005 (mmm) REVERT: F 116 MET cc_start: 0.7979 (mmm) cc_final: 0.7754 (mmt) outliers start: 23 outliers final: 15 residues processed: 210 average time/residue: 0.2180 time to fit residues: 70.2034 Evaluate side-chains 198 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 181 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain I residue 4 GLU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 125 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 34 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 98 optimal weight: 0.4980 chunk 147 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 GLN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 88 HIS F 173 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.098864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.075512 restraints weight = 33514.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.078387 restraints weight = 18144.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.080302 restraints weight = 12195.983| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13112 Z= 0.099 Angle : 0.502 11.981 17569 Z= 0.256 Chirality : 0.035 0.152 2050 Planarity : 0.003 0.061 2230 Dihedral : 3.399 13.585 1731 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.55 % Allowed : 16.81 % Favored : 81.63 % 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: 1.68 (0.22), residues: 1559 helix: 1.65 (0.16), residues: 1199 sheet: None (None), residues: 0 loop : -0.61 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS H 7 PHE 0.008 0.001 PHE B 120 TYR 0.010 0.001 TYR K 93 ARG 0.016 0.000 ARG B 114 Details of bonding type rmsd hydrogen bonds : bond 0.02697 ( 724) hydrogen bonds : angle 3.55280 ( 2151) covalent geometry : bond 0.00223 (13112) covalent geometry : angle 0.50165 (17569) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 86 MET cc_start: 0.9026 (mmm) cc_final: 0.8724 (mpp) REVERT: C 95 ARG cc_start: 0.7488 (mmt90) cc_final: 0.7014 (mmt90) REVERT: C 101 TYR cc_start: 0.8022 (t80) cc_final: 0.7717 (t80) REVERT: C 124 LEU cc_start: 0.8004 (mt) cc_final: 0.7709 (pp) REVERT: H 82 HIS cc_start: 0.8361 (OUTLIER) cc_final: 0.8095 (m-70) REVERT: I 120 MET cc_start: 0.7576 (ptm) cc_final: 0.7166 (ptm) REVERT: J 83 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8207 (pp) REVERT: J 93 TYR cc_start: 0.8457 (t80) cc_final: 0.8056 (t80) REVERT: J 132 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8358 (mm) REVERT: K 116 MET cc_start: 0.7915 (mtm) cc_final: 0.7483 (mtm) REVERT: G 1 MET cc_start: 0.7166 (mpp) cc_final: 0.6572 (mmp) REVERT: G 8 GLN cc_start: 0.8683 (mm110) cc_final: 0.8449 (mm-40) REVERT: F 74 MET cc_start: 0.8006 (mtt) cc_final: 0.7761 (mtt) REVERT: F 97 MET cc_start: 0.8408 (mmm) cc_final: 0.8038 (mmm) outliers start: 23 outliers final: 16 residues processed: 201 average time/residue: 0.2090 time to fit residues: 64.2670 Evaluate side-chains 197 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain I residue 4 GLU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain F residue 15 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 143 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 155 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 GLN H 88 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.099486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.076373 restraints weight = 33635.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.079278 restraints weight = 18000.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.081234 restraints weight = 12033.133| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13112 Z= 0.107 Angle : 0.501 8.670 17569 Z= 0.259 Chirality : 0.036 0.146 2050 Planarity : 0.003 0.030 2230 Dihedral : 3.406 18.683 1731 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.76 % Allowed : 16.54 % Favored : 81.70 % 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: 1.68 (0.22), residues: 1559 helix: 1.64 (0.16), residues: 1200 sheet: None (None), residues: 0 loop : -0.59 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 7 PHE 0.020 0.001 PHE A 181 TYR 0.013 0.001 TYR K 93 ARG 0.005 0.000 ARG K 122 Details of bonding type rmsd hydrogen bonds : bond 0.02769 ( 724) hydrogen bonds : angle 3.58032 ( 2151) covalent geometry : bond 0.00251 (13112) covalent geometry : angle 0.50105 (17569) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 ARG cc_start: 0.7517 (mmt90) cc_final: 0.7008 (mmt90) REVERT: C 101 TYR cc_start: 0.8070 (t80) cc_final: 0.7687 (t80) REVERT: C 124 LEU cc_start: 0.7991 (mt) cc_final: 0.7781 (pp) REVERT: H 82 HIS cc_start: 0.8378 (OUTLIER) cc_final: 0.8108 (m-70) REVERT: I 120 MET cc_start: 0.7642 (ptm) cc_final: 0.7266 (ptm) REVERT: J 83 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8210 (pp) REVERT: J 93 TYR cc_start: 0.8492 (t80) cc_final: 0.8049 (t80) REVERT: J 132 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8368 (mm) REVERT: K 116 MET cc_start: 0.8015 (mtm) cc_final: 0.7623 (mtm) REVERT: G 1 MET cc_start: 0.7000 (mpp) cc_final: 0.6468 (mmp) REVERT: G 8 GLN cc_start: 0.8763 (mm110) cc_final: 0.8532 (mm-40) REVERT: F 74 MET cc_start: 0.8029 (mtt) cc_final: 0.7777 (mtt) REVERT: F 97 MET cc_start: 0.8441 (mmm) cc_final: 0.8067 (mmm) outliers start: 26 outliers final: 18 residues processed: 194 average time/residue: 0.2200 time to fit residues: 64.7429 Evaluate side-chains 196 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain I residue 4 GLU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain F residue 15 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 14 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 122 optimal weight: 0.7980 chunk 5 optimal weight: 0.0670 chunk 68 optimal weight: 0.0370 chunk 2 optimal weight: 0.7980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 GLN H 88 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.100398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.077299 restraints weight = 33655.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.080248 restraints weight = 17997.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.082202 restraints weight = 11987.029| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13112 Z= 0.095 Angle : 0.507 8.415 17569 Z= 0.263 Chirality : 0.035 0.161 2050 Planarity : 0.002 0.032 2230 Dihedral : 3.366 19.385 1731 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.55 % Allowed : 17.42 % Favored : 81.03 % 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: 1.70 (0.22), residues: 1559 helix: 1.64 (0.16), residues: 1203 sheet: None (None), residues: 0 loop : -0.53 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS G 7 PHE 0.007 0.001 PHE B 120 TYR 0.011 0.001 TYR K 93 ARG 0.005 0.000 ARG I 85 Details of bonding type rmsd hydrogen bonds : bond 0.02495 ( 724) hydrogen bonds : angle 3.50465 ( 2151) covalent geometry : bond 0.00210 (13112) covalent geometry : angle 0.50700 (17569) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 ARG cc_start: 0.7526 (mmt90) cc_final: 0.7010 (mmt90) REVERT: C 101 TYR cc_start: 0.7962 (t80) cc_final: 0.7598 (t80) REVERT: H 82 HIS cc_start: 0.8396 (OUTLIER) cc_final: 0.8132 (m-70) REVERT: I 120 MET cc_start: 0.7592 (ptm) cc_final: 0.7251 (ptm) REVERT: J 83 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8206 (pp) REVERT: K 116 MET cc_start: 0.7930 (mtm) cc_final: 0.7572 (mtm) REVERT: G 1 MET cc_start: 0.7049 (mpp) cc_final: 0.6551 (mmp) REVERT: G 8 GLN cc_start: 0.8796 (mm110) cc_final: 0.8553 (mm-40) REVERT: F 97 MET cc_start: 0.8414 (mmm) cc_final: 0.8071 (mmm) outliers start: 23 outliers final: 15 residues processed: 201 average time/residue: 0.2211 time to fit residues: 68.1473 Evaluate side-chains 191 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain I residue 4 GLU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 125 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 48 optimal weight: 0.0970 chunk 74 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 GLN H 88 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.100165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.077198 restraints weight = 33692.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.080136 restraints weight = 17992.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.082124 restraints weight = 11996.663| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13112 Z= 0.101 Angle : 0.517 8.348 17569 Z= 0.268 Chirality : 0.036 0.154 2050 Planarity : 0.002 0.031 2230 Dihedral : 3.340 18.977 1731 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.49 % Allowed : 17.69 % Favored : 80.82 % 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 (0.22), residues: 1559 helix: 1.62 (0.16), residues: 1207 sheet: None (None), residues: 0 loop : -0.52 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS G 7 PHE 0.021 0.001 PHE A 181 TYR 0.012 0.001 TYR C 101 ARG 0.005 0.000 ARG I 85 Details of bonding type rmsd hydrogen bonds : bond 0.02524 ( 724) hydrogen bonds : angle 3.51497 ( 2151) covalent geometry : bond 0.00231 (13112) covalent geometry : angle 0.51741 (17569) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 ARG cc_start: 0.7590 (mmt90) cc_final: 0.7042 (mmt90) REVERT: C 101 TYR cc_start: 0.7765 (t80) cc_final: 0.7539 (t80) REVERT: H 82 HIS cc_start: 0.8391 (OUTLIER) cc_final: 0.8142 (m-70) REVERT: J 83 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8239 (pp) REVERT: K 116 MET cc_start: 0.7971 (mtm) cc_final: 0.7606 (mtm) REVERT: G 8 GLN cc_start: 0.8795 (mm110) cc_final: 0.8520 (mm-40) REVERT: G 120 MET cc_start: 0.8361 (mpp) cc_final: 0.7928 (ptp) outliers start: 22 outliers final: 16 residues processed: 199 average time/residue: 0.2970 time to fit residues: 92.4408 Evaluate side-chains 193 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain I residue 4 GLU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 125 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 39 optimal weight: 0.0000 chunk 72 optimal weight: 0.9990 chunk 127 optimal weight: 0.6980 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 GLN H 88 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.099113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.076060 restraints weight = 33269.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.078945 restraints weight = 17987.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.080863 restraints weight = 12057.710| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13112 Z= 0.108 Angle : 0.537 11.025 17569 Z= 0.273 Chirality : 0.036 0.152 2050 Planarity : 0.003 0.033 2230 Dihedral : 3.378 19.981 1731 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.49 % Allowed : 18.03 % Favored : 80.49 % 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: 1.68 (0.22), residues: 1559 helix: 1.62 (0.16), residues: 1207 sheet: None (None), residues: 0 loop : -0.53 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS G 7 PHE 0.016 0.001 PHE C 143 TYR 0.011 0.001 TYR K 93 ARG 0.006 0.000 ARG I 85 Details of bonding type rmsd hydrogen bonds : bond 0.02627 ( 724) hydrogen bonds : angle 3.53853 ( 2151) covalent geometry : bond 0.00251 (13112) covalent geometry : angle 0.53703 (17569) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 2.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8285 (tm-30) cc_final: 0.8020 (tm-30) REVERT: B 137 MET cc_start: 0.8041 (ptm) cc_final: 0.7747 (ptp) REVERT: C 95 ARG cc_start: 0.7612 (mmt90) cc_final: 0.7063 (mmt90) REVERT: C 101 TYR cc_start: 0.7830 (t80) cc_final: 0.7554 (t80) REVERT: H 82 HIS cc_start: 0.8392 (OUTLIER) cc_final: 0.8155 (m-70) REVERT: J 83 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8242 (pp) REVERT: K 116 MET cc_start: 0.7913 (mtm) cc_final: 0.7577 (mtm) REVERT: G 8 GLN cc_start: 0.8768 (mm110) cc_final: 0.8496 (mm-40) REVERT: G 120 MET cc_start: 0.8341 (mpp) cc_final: 0.7813 (ptp) outliers start: 22 outliers final: 19 residues processed: 191 average time/residue: 0.3083 time to fit residues: 91.6324 Evaluate side-chains 193 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain I residue 4 GLU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain F residue 15 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 75 optimal weight: 0.2980 chunk 93 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 108 optimal weight: 0.8980 chunk 153 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN C 35 GLN ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 88 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.099184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.076105 restraints weight = 33539.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.078969 restraints weight = 18199.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.080894 restraints weight = 12216.468| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13112 Z= 0.105 Angle : 0.524 8.687 17569 Z= 0.270 Chirality : 0.036 0.151 2050 Planarity : 0.003 0.034 2230 Dihedral : 3.378 19.667 1731 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.42 % Allowed : 18.10 % Favored : 80.49 % 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: 1.68 (0.22), residues: 1559 helix: 1.62 (0.16), residues: 1203 sheet: None (None), residues: 0 loop : -0.55 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS G 7 PHE 0.020 0.001 PHE A 181 TYR 0.011 0.001 TYR C 101 ARG 0.006 0.000 ARG I 85 Details of bonding type rmsd hydrogen bonds : bond 0.02559 ( 724) hydrogen bonds : angle 3.52887 ( 2151) covalent geometry : bond 0.00242 (13112) covalent geometry : angle 0.52377 (17569) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4495.19 seconds wall clock time: 80 minutes 40.95 seconds (4840.95 seconds total)